Starting phenix.real_space_refine on Wed Jun 25 07:53:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gxu_34362/06_2025/8gxu_34362.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gxu_34362/06_2025/8gxu_34362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gxu_34362/06_2025/8gxu_34362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gxu_34362/06_2025/8gxu_34362.map" model { file = "/net/cci-nas-00/data/ceres_data/8gxu_34362/06_2025/8gxu_34362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gxu_34362/06_2025/8gxu_34362.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 105 5.16 5 C 18715 2.51 5 N 5121 2.21 5 O 5559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29503 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.66, per 1000 atoms: 0.63 Number of scatterers: 29503 At special positions: 0 Unit cell: (147.74, 149.4, 177.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 3 15.00 O 5559 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: 7.17 Conformation dependent library (CDL) restraints added in 4.0 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 25 sheets defined 48.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.878A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.113A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.780A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.528A 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 431 through 443 Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 446 through 472 removed outlier: 4.001A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'A' and resid 535 through 541 Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.659A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 577 removed outlier: 3.671A pdb=" N GLN A 571 " --> pdb=" O MET A 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.977A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.658A 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 removed outlier: 3.516A pdb=" N GLU B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 463 Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 508 through 532 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 542 through 550 removed outlier: 4.085A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 removed outlier: 3.658A pdb=" N VAL B 554 " --> pdb=" O ALA B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 555 through 557 No H-bonds generated for 'chain 'B' and resid 555 through 557' Processing helix chain 'B' and resid 558 through 575 removed outlier: 3.813A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.881A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.009A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 3.823A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 353 through 364 removed outlier: 3.677A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.617A pdb=" N ASP C 390 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.559A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.511A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 removed outlier: 3.606A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 472 removed outlier: 3.908A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.587A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.685A pdb=" N GLN C 571 " --> pdb=" O MET C 567 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 578 " --> pdb=" O PHE C 574 " (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 212 removed outlier: 3.677A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.809A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 removed outlier: 3.559A pdb=" N ASP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 467 through 472 removed outlier: 4.182A pdb=" N GLY D 472 " --> pdb=" O GLU D 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.546A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 removed outlier: 3.796A pdb=" N SER E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 212 through 215 removed outlier: 3.854A pdb=" N SER E 215 " --> pdb=" O GLY E 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 212 through 215' Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 233 through 250 Processing helix chain 'E' and resid 259 through 275 removed outlier: 3.693A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.566A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 362 through 366 removed outlier: 3.874A pdb=" N VAL E 366 " --> pdb=" O ASN E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.776A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 404 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 445 through 446 No H-bonds generated for 'chain 'E' and resid 445 through 446' Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.829A pdb=" N LEU E 451 " --> pdb=" O GLN E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.724A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 3.791A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 347 Processing helix chain 'F' and resid 361 through 366 removed outlier: 4.065A pdb=" N VAL F 366 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.870A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 4.216A 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: 3.730A 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 470 Processing helix chain 'G' and resid 7 through 71 Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'G' and resid 122 through 167 removed outlier: 3.531A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 209 Processing helix chain 'H' and resid 6 through 16 removed outlier: 4.479A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 Processing helix chain 'H' and resid 54 through 59 Processing helix chain 'H' and resid 59 through 64 Processing helix chain 'H' and resid 76 through 81 Processing helix chain 'H' and resid 85 through 99 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.922A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 62 through 93 Processing helix chain 'J' and resid 94 through 97 Processing helix chain 'J' and resid 99 through 115 Processing helix chain 'J' and resid 127 through 138 removed outlier: 5.345A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.854A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 119 removed outlier: 3.835A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 93 Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 127 through 139 removed outlier: 3.899A pdb=" N LEU L 131 " --> pdb=" O ASP L 127 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 188 removed outlier: 3.515A pdb=" N ARG L 170 " --> pdb=" O SER L 166 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.323A 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: 6.399A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 6.468A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 6.507A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.598A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 5.803A pdb=" N GLY D 45 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE D 60 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.631A 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 60 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 6.627A pdb=" N VAL E 56 " --> pdb=" O ILE E 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 21 current: chain 'F' and resid 42 through 51 removed outlier: 6.565A pdb=" N VAL F 56 " --> pdb=" O ILE F 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 55 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 141 through 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 291 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 291 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 145 removed outlier: 5.741A 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: 6.868A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 291 current: chain 'B' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 148 removed outlier: 3.593A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.580A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 204 through 205 removed outlier: 4.730A pdb=" N VAL B 218 " --> pdb=" O PHE B 205 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.701A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.669A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.728A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 91 through 93 removed outlier: 4.032A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.587A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.621A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.953A pdb=" N ARG E 91 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 219 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET E 194 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU E 257 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLN E 338 " --> pdb=" O PRO E 356 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.513A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.512A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.805A pdb=" N ARG F 91 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.518A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 90 through 96 removed outlier: 3.778A pdb=" N GLU G 92 " --> pdb=" O ARG G 103 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 19 through 22 removed outlier: 3.674A pdb=" N ALA H 46 " --> pdb=" O ALA H 2 " (cutoff:3.500A) 1376 hydrogen bonds defined for protein. 3903 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: 10.58 Time building geometry restraints manager: 8.53 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: 9954 1.34 - 1.46: 4260 1.46 - 1.57: 15643 1.57 - 1.69: 5 1.69 - 1.81: 194 Bond restraints: 30056 Sorted by residual: bond pdb=" O4 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.448 0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" O1 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.498 1.449 0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" O2 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.498 1.449 0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" O3 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.450 0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" O3 SO4 C 600 " pdb=" S SO4 C 600 " ideal model delta sigma weight residual 1.499 1.452 0.047 2.00e-02 2.50e+03 5.47e+00 ... (remaining 30051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 39641 1.49 - 2.97: 851 2.97 - 4.46: 212 4.46 - 5.95: 15 5.95 - 7.44: 3 Bond angle restraints: 40722 Sorted by residual: angle pdb=" N VAL H 59 " pdb=" CA VAL H 59 " pdb=" C VAL H 59 " ideal model delta sigma weight residual 112.29 108.76 3.53 9.40e-01 1.13e+00 1.41e+01 angle pdb=" N ILE F 96 " pdb=" CA ILE F 96 " pdb=" C ILE F 96 " ideal model delta sigma weight residual 111.77 108.58 3.19 1.04e+00 9.25e-01 9.41e+00 angle pdb=" N PRO C 420 " pdb=" CA PRO C 420 " pdb=" C PRO C 420 " ideal model delta sigma weight residual 112.10 119.54 -7.44 2.60e+00 1.48e-01 8.18e+00 angle pdb=" N PRO A 420 " pdb=" CA PRO A 420 " pdb=" C PRO A 420 " ideal model delta sigma weight residual 112.10 118.88 -6.78 2.60e+00 1.48e-01 6.80e+00 angle pdb=" N ASP B 177 " pdb=" CA ASP B 177 " pdb=" C ASP B 177 " ideal model delta sigma weight residual 113.01 110.08 2.93 1.20e+00 6.94e-01 5.96e+00 ... (remaining 40717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 16505 17.73 - 35.45: 1412 35.45 - 53.18: 308 53.18 - 70.91: 72 70.91 - 88.64: 41 Dihedral angle restraints: 18338 sinusoidal: 7516 harmonic: 10822 Sorted by residual: 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 -154.36 -25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA TYR F 8 " pdb=" C TYR F 8 " pdb=" N THR F 9 " pdb=" CA THR F 9 " ideal model delta harmonic sigma weight residual 180.00 156.72 23.28 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ARG E 372 " pdb=" C ARG E 372 " pdb=" N GLU E 373 " pdb=" CA GLU E 373 " ideal model delta harmonic sigma weight residual -180.00 -156.89 -23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 18335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3732 0.058 - 0.117: 762 0.117 - 0.175: 66 0.175 - 0.234: 1 0.234 - 0.292: 3 Chirality restraints: 4564 Sorted by residual: chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C3' ATP B 601 " pdb=" C2' ATP B 601 " pdb=" C4' ATP B 601 " pdb=" O3' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.90 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C4' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" C5' ATP B 601 " pdb=" O4' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.76 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 4561 not shown) Planarity restraints: 5331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " 0.056 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO B 229 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 364 " -0.228 9.50e-02 1.11e+02 1.02e-01 6.88e+00 pdb=" NE ARG A 364 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 364 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 364 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 364 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 294 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A 295 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.032 5.00e-02 4.00e+02 ... (remaining 5328 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 100 2.46 - 3.07: 20381 3.07 - 3.68: 43848 3.68 - 4.29: 68089 4.29 - 4.90: 114219 Nonbonded interactions: 246637 Sorted by model distance: nonbonded pdb=" OH TYR F 8 " pdb=" OD1 ASP F 26 " model vdw 1.855 3.040 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 1.923 3.040 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 1.946 3.040 nonbonded pdb=" OD2 ASP C 410 " pdb=" OG SER C 412 " model vdw 1.947 3.040 nonbonded pdb=" NH2 ARG D 91 " pdb=" O PRO D 104 " model vdw 2.007 3.120 ... (remaining 246632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 24.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.310 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 66.810 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.140 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:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.007 0.090 30056 Z= 0.291 Angle : 0.575 7.435 40722 Z= 0.302 Chirality : 0.046 0.292 4564 Planarity : 0.005 0.102 5331 Dihedral : 14.574 88.636 11420 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3764 helix: 1.48 (0.13), residues: 1576 sheet: -0.30 (0.21), residues: 574 loop : 0.05 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 119 HIS 0.016 0.002 HIS C 283 PHE 0.018 0.002 PHE D 418 TYR 0.020 0.002 TYR C 428 ARG 0.014 0.001 ARG E 146 Details of bonding type rmsd hydrogen bonds : bond 0.13700 ( 1376) hydrogen bonds : angle 6.37125 ( 3903) covalent geometry : bond 0.00694 (30056) covalent geometry : angle 0.57480 (40722) *********************** 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 796 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 796 time to evaluate : 3.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.6981 (pt0) cc_final: 0.6676 (pt0) REVERT: A 79 MET cc_start: 0.8721 (mtm) cc_final: 0.8288 (mtp) REVERT: A 158 LYS cc_start: 0.7400 (ttpp) cc_final: 0.6336 (tttm) REVERT: A 172 VAL cc_start: 0.7681 (t) cc_final: 0.7395 (m) REVERT: A 197 ARG cc_start: 0.7702 (ptm-80) cc_final: 0.7270 (ptm160) REVERT: A 264 ASP cc_start: 0.6882 (m-30) cc_final: 0.6571 (m-30) REVERT: A 294 MET cc_start: 0.8199 (mtp) cc_final: 0.7912 (mtp) REVERT: A 340 ARG cc_start: 0.7312 (tpp-160) cc_final: 0.6720 (tpp-160) REVERT: A 410 ASP cc_start: 0.7691 (t0) cc_final: 0.7365 (t0) REVERT: A 412 SER cc_start: 0.8443 (p) cc_final: 0.8216 (p) REVERT: A 488 ARG cc_start: 0.7488 (ttp80) cc_final: 0.7270 (ttp80) REVERT: B 7 GLN cc_start: 0.7909 (tt0) cc_final: 0.7472 (tm130) REVERT: B 19 MET cc_start: 0.8083 (mmm) cc_final: 0.7815 (mmm) REVERT: B 53 GLU cc_start: 0.6890 (mp0) cc_final: 0.6157 (pm20) REVERT: B 109 HIS cc_start: 0.7460 (m170) cc_final: 0.7223 (m170) REVERT: B 122 MET cc_start: 0.7131 (mtt) cc_final: 0.5872 (tpp) REVERT: B 162 PRO cc_start: 0.7470 (Cg_endo) cc_final: 0.7156 (Cg_exo) REVERT: B 243 LYS cc_start: 0.7261 (mtpt) cc_final: 0.6667 (mtpt) REVERT: B 264 ASP cc_start: 0.6955 (m-30) cc_final: 0.6754 (m-30) REVERT: B 325 ASP cc_start: 0.7556 (t0) cc_final: 0.7337 (t0) REVERT: B 339 SER cc_start: 0.8139 (m) cc_final: 0.7711 (t) REVERT: B 374 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6733 (mm-30) REVERT: B 391 MET cc_start: 0.6999 (mmp) cc_final: 0.6714 (mmt) REVERT: B 393 GLU cc_start: 0.6936 (tt0) cc_final: 0.6375 (pt0) REVERT: B 432 THR cc_start: 0.7586 (m) cc_final: 0.7124 (p) REVERT: B 439 TYR cc_start: 0.7924 (m-80) cc_final: 0.7722 (m-80) REVERT: B 460 ARG cc_start: 0.7292 (mmm-85) cc_final: 0.6970 (mtp180) REVERT: B 467 ILE cc_start: 0.8128 (tp) cc_final: 0.7801 (tt) REVERT: B 469 GLN cc_start: 0.6662 (mt0) cc_final: 0.6357 (mm110) REVERT: B 500 TYR cc_start: 0.7079 (m-80) cc_final: 0.6815 (m-80) REVERT: B 501 HIS cc_start: 0.7633 (t-90) cc_final: 0.7415 (t70) REVERT: C 19 MET cc_start: 0.8586 (mmm) cc_final: 0.8219 (mmm) REVERT: C 103 THR cc_start: 0.7843 (m) cc_final: 0.7641 (p) REVERT: C 133 MET cc_start: 0.7992 (mtm) cc_final: 0.7768 (mtp) REVERT: C 200 ASP cc_start: 0.7792 (m-30) cc_final: 0.7580 (m-30) REVERT: C 264 ASP cc_start: 0.7423 (t0) cc_final: 0.7193 (t0) REVERT: C 342 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6955 (mm-30) REVERT: C 391 MET cc_start: 0.8293 (mmt) cc_final: 0.7961 (mmt) REVERT: C 459 GLN cc_start: 0.7024 (mt0) cc_final: 0.6764 (mt0) REVERT: D 22 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7287 (mt-10) REVERT: D 98 LYS cc_start: 0.7299 (mmmm) cc_final: 0.7037 (ttpt) REVERT: D 126 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7783 (mtmt) REVERT: D 274 ARG cc_start: 0.7050 (mtt-85) cc_final: 0.6713 (mtp85) REVERT: D 280 ARG cc_start: 0.7328 (mtp85) cc_final: 0.7064 (mtm180) REVERT: D 305 LYS cc_start: 0.7459 (mttt) cc_final: 0.7246 (mmtt) REVERT: D 331 TYR cc_start: 0.6496 (m-80) cc_final: 0.6215 (t80) REVERT: D 363 ASN cc_start: 0.8304 (m-40) cc_final: 0.8067 (m110) REVERT: D 398 ILE cc_start: 0.7909 (mt) cc_final: 0.7670 (mm) REVERT: D 456 LYS cc_start: 0.5914 (mmtt) cc_final: 0.5626 (mmtt) REVERT: E 81 ARG cc_start: 0.7357 (mtt-85) cc_final: 0.7100 (mtt90) REVERT: E 98 LYS cc_start: 0.7461 (mmmt) cc_final: 0.7227 (mptt) REVERT: E 198 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8093 (tp40) REVERT: E 209 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6972 (mt-10) REVERT: E 216 ARG cc_start: 0.7982 (ptt90) cc_final: 0.7501 (ptp90) REVERT: E 251 TYR cc_start: 0.8404 (m-80) cc_final: 0.8053 (m-80) REVERT: E 274 ARG cc_start: 0.7044 (mtp180) cc_final: 0.6631 (mmm160) REVERT: E 276 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6674 (mt-10) REVERT: E 318 ASP cc_start: 0.7141 (t0) cc_final: 0.6743 (t0) REVERT: E 404 LEU cc_start: 0.7243 (mt) cc_final: 0.6958 (mt) REVERT: E 453 ARG cc_start: 0.7912 (mmt90) cc_final: 0.7384 (mpt180) REVERT: F 36 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7678 (ttpp) REVERT: F 92 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7468 (mtt-85) REVERT: F 109 GLU cc_start: 0.6649 (mt-10) cc_final: 0.6147 (tp30) REVERT: F 126 LYS cc_start: 0.8228 (tttm) cc_final: 0.7904 (tttp) REVERT: F 129 GLN cc_start: 0.7867 (mm110) cc_final: 0.7582 (mm-40) REVERT: F 200 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7131 (mt-10) REVERT: F 248 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6740 (tt0) REVERT: F 413 GLN cc_start: 0.7466 (mt0) cc_final: 0.7167 (mt0) REVERT: F 421 PHE cc_start: 0.8127 (m-80) cc_final: 0.7917 (m-80) REVERT: G 10 ASN cc_start: 0.8055 (m-40) cc_final: 0.7659 (m-40) REVERT: G 22 GLN cc_start: 0.7986 (mt0) cc_final: 0.7705 (mt0) REVERT: G 23 LYS cc_start: 0.7744 (mttm) cc_final: 0.7438 (mtpm) REVERT: G 30 LYS cc_start: 0.8076 (mttm) cc_final: 0.7840 (mtmm) REVERT: G 38 GLU cc_start: 0.7452 (tt0) cc_final: 0.7235 (tt0) REVERT: G 97 TRP cc_start: 0.5702 (m100) cc_final: 0.5502 (m100) REVERT: G 181 GLN cc_start: 0.7168 (mm-40) cc_final: 0.6599 (tp-100) REVERT: J 81 GLU cc_start: 0.5513 (mm-30) cc_final: 0.5043 (tm-30) REVERT: J 178 LEU cc_start: 0.5529 (mt) cc_final: 0.5283 (mt) REVERT: L 86 ARG cc_start: 0.5337 (mtp180) cc_final: 0.5092 (ttp-170) REVERT: L 88 ARG cc_start: 0.5491 (ttp80) cc_final: 0.4785 (ttp-110) REVERT: L 141 GLU cc_start: 0.5088 (tm-30) cc_final: 0.4532 (mp0) REVERT: L 150 LEU cc_start: 0.6036 (mt) cc_final: 0.5764 (tp) outliers start: 0 outliers final: 1 residues processed: 796 average time/residue: 2.4174 time to fit residues: 2167.0696 Evaluate side-chains 463 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 462 time to evaluate : 4.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 277 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 292 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 338 optimal weight: 0.0020 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN A 498 ASN B 316 GLN B 397 GLN C 238 GLN C 397 GLN C 496 GLN C 571 GLN D 129 GLN D 166 GLN D 206 GLN D 338 GLN D 413 GLN E 364 ASN E 427 GLN E 428 GLN E 437 GLN E 458 HIS ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.158832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124699 restraints weight = 33173.563| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.37 r_work: 0.3247 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30056 Z= 0.131 Angle : 0.550 7.086 40722 Z= 0.287 Chirality : 0.044 0.153 4564 Planarity : 0.005 0.058 5331 Dihedral : 5.309 67.891 4216 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.37 % Allowed : 13.17 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.14), residues: 3764 helix: 1.85 (0.14), residues: 1597 sheet: -0.02 (0.22), residues: 537 loop : 0.21 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 100 HIS 0.006 0.001 HIS C 283 PHE 0.015 0.002 PHE B 559 TYR 0.015 0.001 TYR D 263 ARG 0.008 0.001 ARG E 210 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 1376) hydrogen bonds : angle 4.95887 ( 3903) covalent geometry : bond 0.00291 (30056) covalent geometry : angle 0.54951 (40722) *********************** 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 548 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 475 time to evaluate : 3.290 Fit side-chains REVERT: A 79 MET cc_start: 0.8825 (mtm) cc_final: 0.8361 (mtp) REVERT: A 83 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8383 (tp) REVERT: A 340 ARG cc_start: 0.7402 (tpp-160) cc_final: 0.7003 (tpp-160) REVERT: A 343 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6925 (mt-10) REVERT: A 488 ARG cc_start: 0.7690 (ttp80) cc_final: 0.7484 (ttp80) REVERT: A 491 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7326 (mpt90) REVERT: A 517 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7839 (ttpt) REVERT: A 527 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: A 530 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7203 (mt) REVERT: B 7 GLN cc_start: 0.8016 (tt0) cc_final: 0.7693 (tm130) REVERT: B 53 GLU cc_start: 0.7067 (mp0) cc_final: 0.6288 (pm20) REVERT: B 122 MET cc_start: 0.7043 (mtt) cc_final: 0.5937 (tpp) REVERT: B 162 PRO cc_start: 0.7510 (Cg_endo) cc_final: 0.7196 (Cg_exo) REVERT: B 197 ARG cc_start: 0.7600 (ttp-110) cc_final: 0.7303 (ttp80) REVERT: B 243 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7013 (mtpt) REVERT: B 261 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7301 (mt-10) REVERT: B 391 MET cc_start: 0.6936 (mmp) cc_final: 0.6692 (mmt) REVERT: B 393 GLU cc_start: 0.6940 (tt0) cc_final: 0.6407 (pt0) REVERT: B 417 ARG cc_start: 0.6943 (mmm160) cc_final: 0.6336 (mmt180) REVERT: B 432 THR cc_start: 0.7567 (m) cc_final: 0.7062 (p) REVERT: B 467 ILE cc_start: 0.8050 (tp) cc_final: 0.7665 (tt) REVERT: B 481 ARG cc_start: 0.6319 (ttt-90) cc_final: 0.6007 (tpp80) REVERT: B 500 TYR cc_start: 0.7239 (m-80) cc_final: 0.7031 (m-80) REVERT: B 502 GLU cc_start: 0.6230 (pm20) cc_final: 0.5571 (pm20) REVERT: C 19 MET cc_start: 0.8761 (mmm) cc_final: 0.8489 (mmm) REVERT: C 54 ASP cc_start: 0.7884 (t0) cc_final: 0.7593 (t0) REVERT: C 92 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: C 133 MET cc_start: 0.8220 (mtm) cc_final: 0.7997 (mtp) REVERT: C 342 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7461 (mm-30) REVERT: C 391 MET cc_start: 0.8420 (mmt) cc_final: 0.8143 (mmt) REVERT: C 459 GLN cc_start: 0.7341 (mt0) cc_final: 0.7081 (mt0) REVERT: C 547 ARG cc_start: 0.7180 (tpp-160) cc_final: 0.6717 (ttm-80) REVERT: D 6 LYS cc_start: 0.6564 (tttm) cc_final: 0.6007 (ttmt) REVERT: D 62 GLU cc_start: 0.6426 (pm20) cc_final: 0.6158 (mm-30) REVERT: D 274 ARG cc_start: 0.7312 (mtt-85) cc_final: 0.6999 (mtp85) REVERT: D 280 ARG cc_start: 0.7563 (mtp85) cc_final: 0.7347 (mtm180) REVERT: D 305 LYS cc_start: 0.7712 (mttt) cc_final: 0.7480 (mmtt) REVERT: D 327 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: D 363 ASN cc_start: 0.8397 (m-40) cc_final: 0.8097 (m110) REVERT: D 398 ILE cc_start: 0.7777 (mt) cc_final: 0.7565 (mm) REVERT: D 433 GLU cc_start: 0.7656 (mp0) cc_final: 0.7431 (mp0) REVERT: D 456 LYS cc_start: 0.6076 (mmtt) cc_final: 0.5782 (mmtt) REVERT: E 78 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7147 (m-30) REVERT: E 81 ARG cc_start: 0.7577 (mtt-85) cc_final: 0.7357 (mtt90) REVERT: E 198 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8266 (mm-40) REVERT: E 216 ARG cc_start: 0.8033 (ptt90) cc_final: 0.7381 (ptp90) REVERT: E 251 TYR cc_start: 0.8385 (m-80) cc_final: 0.8176 (m-80) REVERT: E 274 ARG cc_start: 0.7261 (mtp180) cc_final: 0.7035 (mmp-170) REVERT: E 276 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7222 (mt-10) REVERT: E 318 ASP cc_start: 0.7751 (t0) cc_final: 0.7313 (t0) REVERT: E 353 ASP cc_start: 0.7755 (t0) cc_final: 0.7427 (t0) REVERT: E 416 ASP cc_start: 0.7575 (t70) cc_final: 0.7286 (t0) REVERT: E 453 ARG cc_start: 0.7782 (mmt90) cc_final: 0.7100 (mpt180) REVERT: F 36 LYS cc_start: 0.8260 (ttpt) cc_final: 0.8036 (ttpp) REVERT: F 67 ASP cc_start: 0.7875 (p0) cc_final: 0.7668 (p0) REVERT: F 92 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7865 (mtt-85) REVERT: F 109 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6463 (tp30) REVERT: F 248 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7079 (tt0) REVERT: F 342 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: F 421 PHE cc_start: 0.8378 (m-80) cc_final: 0.8147 (m-80) REVERT: G 10 ASN cc_start: 0.8111 (m-40) cc_final: 0.7819 (m-40) REVERT: G 22 GLN cc_start: 0.8031 (mt0) cc_final: 0.7810 (mt0) REVERT: G 23 LYS cc_start: 0.7966 (mttm) cc_final: 0.7738 (mtpm) REVERT: G 30 LYS cc_start: 0.8077 (mttm) cc_final: 0.7849 (mtmm) REVERT: G 86 LEU cc_start: 0.1098 (OUTLIER) cc_final: 0.0869 (mm) REVERT: G 97 TRP cc_start: 0.5569 (m100) cc_final: 0.5238 (m100) REVERT: G 181 GLN cc_start: 0.7396 (mm-40) cc_final: 0.7143 (tp-100) REVERT: J 81 GLU cc_start: 0.5635 (mm-30) cc_final: 0.4981 (tm-30) REVERT: J 142 LEU cc_start: 0.3672 (OUTLIER) cc_final: 0.3365 (pp) REVERT: J 178 LEU cc_start: 0.5401 (mt) cc_final: 0.5188 (mt) REVERT: L 86 ARG cc_start: 0.5194 (mtp180) cc_final: 0.4935 (ttp-170) REVERT: L 88 ARG cc_start: 0.5044 (ttp80) cc_final: 0.4576 (ttm110) REVERT: L 141 GLU cc_start: 0.5046 (tm-30) cc_final: 0.4398 (mp0) outliers start: 73 outliers final: 14 residues processed: 522 average time/residue: 1.9027 time to fit residues: 1123.1307 Evaluate side-chains 421 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 395 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 0.2980 chunk 113 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 301 optimal weight: 0.5980 chunk 300 optimal weight: 0.6980 chunk 275 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 GLN B 496 GLN B 501 HIS D 206 GLN D 413 GLN E 58 GLN E 428 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.157681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125585 restraints weight = 33983.909| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.39 r_work: 0.3234 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30056 Z= 0.134 Angle : 0.534 7.638 40722 Z= 0.278 Chirality : 0.044 0.155 4564 Planarity : 0.005 0.055 5331 Dihedral : 5.172 66.791 4214 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.40 % Allowed : 14.08 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.14), residues: 3764 helix: 1.94 (0.13), residues: 1587 sheet: -0.12 (0.22), residues: 553 loop : 0.27 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 100 HIS 0.007 0.001 HIS C 283 PHE 0.015 0.002 PHE B 559 TYR 0.013 0.001 TYR F 203 ARG 0.008 0.001 ARG L 105 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 1376) hydrogen bonds : angle 4.79762 ( 3903) covalent geometry : bond 0.00305 (30056) covalent geometry : angle 0.53358 (40722) *********************** 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 482 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 408 time to evaluate : 3.495 Fit side-chains revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8455 (tp) REVERT: A 152 ASP cc_start: 0.6919 (p0) cc_final: 0.6597 (m-30) REVERT: A 340 ARG cc_start: 0.7449 (tpp-160) cc_final: 0.7096 (tpp-160) REVERT: A 491 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7456 (mpt90) REVERT: A 517 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7882 (ttpt) REVERT: A 527 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6631 (mt-10) REVERT: A 530 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7317 (mt) REVERT: B 53 GLU cc_start: 0.7041 (mp0) cc_final: 0.6231 (pm20) REVERT: B 243 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7063 (mtpt) REVERT: B 391 MET cc_start: 0.6977 (mmp) cc_final: 0.6768 (mmt) REVERT: B 393 GLU cc_start: 0.6861 (tt0) cc_final: 0.6219 (pt0) REVERT: B 432 THR cc_start: 0.7602 (m) cc_final: 0.7101 (p) REVERT: B 467 ILE cc_start: 0.8098 (tp) cc_final: 0.7708 (tt) REVERT: B 481 ARG cc_start: 0.6323 (ttt-90) cc_final: 0.6087 (tpt90) REVERT: B 500 TYR cc_start: 0.7376 (m-80) cc_final: 0.7076 (m-80) REVERT: B 502 GLU cc_start: 0.6002 (pm20) cc_final: 0.5517 (pm20) REVERT: C 19 MET cc_start: 0.8800 (mmm) cc_final: 0.8382 (mmm) REVERT: C 54 ASP cc_start: 0.7914 (t0) cc_final: 0.7589 (t0) REVERT: C 92 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: C 133 MET cc_start: 0.8177 (mtm) cc_final: 0.7925 (mtp) REVERT: C 177 ASP cc_start: 0.7934 (p0) cc_final: 0.7590 (p0) REVERT: C 342 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7482 (mm-30) REVERT: C 363 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7952 (tp30) REVERT: C 459 GLN cc_start: 0.7350 (mt0) cc_final: 0.7035 (mt0) REVERT: C 547 ARG cc_start: 0.7181 (tpp-160) cc_final: 0.6707 (ttm-80) REVERT: D 6 LYS cc_start: 0.6541 (tttm) cc_final: 0.6085 (tttt) REVERT: D 62 GLU cc_start: 0.6496 (pm20) cc_final: 0.6197 (mm-30) REVERT: D 162 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: D 274 ARG cc_start: 0.7244 (mtt-85) cc_final: 0.7036 (mtp85) REVERT: D 280 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7397 (mtm180) REVERT: D 305 LYS cc_start: 0.7754 (mttt) cc_final: 0.7529 (mmtt) REVERT: D 368 LYS cc_start: 0.7161 (ttpp) cc_final: 0.6892 (tmtt) REVERT: D 433 GLU cc_start: 0.7666 (mp0) cc_final: 0.7456 (mp0) REVERT: E 78 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: E 81 ARG cc_start: 0.7644 (mtt-85) cc_final: 0.7416 (mtt90) REVERT: E 198 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8278 (mm-40) REVERT: E 216 ARG cc_start: 0.8045 (ptt90) cc_final: 0.7771 (ptt90) REVERT: E 274 ARG cc_start: 0.7253 (mtp180) cc_final: 0.7035 (mmp-170) REVERT: E 318 ASP cc_start: 0.7795 (t0) cc_final: 0.7365 (t0) REVERT: E 353 ASP cc_start: 0.7742 (t0) cc_final: 0.7416 (t0) REVERT: E 364 ASN cc_start: 0.7121 (m110) cc_final: 0.6763 (m110) REVERT: E 404 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6701 (mt) REVERT: E 416 ASP cc_start: 0.7616 (t70) cc_final: 0.7337 (t0) REVERT: E 453 ARG cc_start: 0.7766 (mmt90) cc_final: 0.7018 (mpt180) REVERT: F 67 ASP cc_start: 0.7993 (p0) cc_final: 0.7776 (p0) REVERT: F 92 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7891 (mtt-85) REVERT: F 223 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7997 (mtmt) REVERT: F 230 GLU cc_start: 0.7816 (tt0) cc_final: 0.7615 (tt0) REVERT: F 248 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7035 (tt0) REVERT: F 342 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: F 421 PHE cc_start: 0.8380 (m-80) cc_final: 0.8154 (m-80) REVERT: G 10 ASN cc_start: 0.8135 (m-40) cc_final: 0.7812 (m-40) REVERT: G 22 GLN cc_start: 0.8016 (mt0) cc_final: 0.7795 (mt0) REVERT: G 23 LYS cc_start: 0.7949 (mttm) cc_final: 0.7736 (mtpm) REVERT: G 30 LYS cc_start: 0.8143 (mttm) cc_final: 0.7938 (mtmm) REVERT: G 86 LEU cc_start: 0.1172 (OUTLIER) cc_final: 0.0869 (mm) REVERT: G 97 TRP cc_start: 0.5652 (m100) cc_final: 0.5351 (m100) REVERT: G 181 GLN cc_start: 0.7436 (mm-40) cc_final: 0.7234 (tp-100) REVERT: G 187 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: J 81 GLU cc_start: 0.5654 (mm-30) cc_final: 0.5096 (tm-30) REVERT: J 141 GLU cc_start: 0.4213 (tp30) cc_final: 0.4003 (tp30) REVERT: L 88 ARG cc_start: 0.5161 (ttp80) cc_final: 0.4265 (mtp85) REVERT: L 141 GLU cc_start: 0.5072 (tm-30) cc_final: 0.4473 (mp0) REVERT: L 168 LEU cc_start: 0.5537 (mt) cc_final: 0.5179 (mm) outliers start: 74 outliers final: 31 residues processed: 459 average time/residue: 1.8931 time to fit residues: 985.4882 Evaluate side-chains 424 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 379 time to evaluate : 3.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 80 optimal weight: 0.6980 chunk 363 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 335 optimal weight: 6.9990 chunk 311 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN B 469 GLN C 283 HIS C 571 GLN D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN E 428 GLN F 252 HIS ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.153985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122030 restraints weight = 34071.332| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.39 r_work: 0.3190 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 30056 Z= 0.310 Angle : 0.778 10.059 40722 Z= 0.407 Chirality : 0.053 0.246 4564 Planarity : 0.008 0.101 5331 Dihedral : 6.035 77.667 4214 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.73 % Allowed : 14.14 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.13), residues: 3764 helix: 1.11 (0.13), residues: 1580 sheet: -0.32 (0.21), residues: 584 loop : -0.07 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP J 100 HIS 0.016 0.002 HIS C 283 PHE 0.023 0.003 PHE F 421 TYR 0.026 0.003 TYR C 25 ARG 0.012 0.001 ARG E 41 Details of bonding type rmsd hydrogen bonds : bond 0.06265 ( 1376) hydrogen bonds : angle 5.40263 ( 3903) covalent geometry : bond 0.00738 (30056) covalent geometry : angle 0.77791 (40722) *********************** 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 514 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 399 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8453 (tp) REVERT: A 156 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6412 (ttp80) REVERT: A 340 ARG cc_start: 0.7557 (tpp-160) cc_final: 0.7071 (ttp-110) REVERT: A 491 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7397 (mpt90) REVERT: A 517 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8041 (ttpp) REVERT: A 527 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6780 (mt-10) REVERT: A 530 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7347 (mt) REVERT: A 537 ASP cc_start: 0.5563 (OUTLIER) cc_final: 0.5225 (t0) REVERT: B 124 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6127 (mmmm) REVERT: B 243 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7011 (mttt) REVERT: B 261 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7375 (mt-10) REVERT: B 393 GLU cc_start: 0.6970 (tt0) cc_final: 0.6362 (pt0) REVERT: B 467 ILE cc_start: 0.8041 (tp) cc_final: 0.7630 (tt) REVERT: B 552 ARG cc_start: 0.6905 (mtp180) cc_final: 0.6569 (mtm110) REVERT: C 92 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: C 133 MET cc_start: 0.8181 (mtm) cc_final: 0.7953 (mtp) REVERT: C 154 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7332 (ttm-80) REVERT: C 161 LYS cc_start: 0.8119 (mtpp) cc_final: 0.7875 (mttp) REVERT: C 170 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6308 (tp30) REVERT: C 177 ASP cc_start: 0.7776 (p0) cc_final: 0.7438 (p0) REVERT: C 342 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7520 (mm-30) REVERT: C 363 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7987 (tp30) REVERT: C 547 ARG cc_start: 0.7159 (tpp-160) cc_final: 0.6770 (ttm-80) REVERT: C 565 GLU cc_start: 0.6565 (tm-30) cc_final: 0.6234 (tm-30) REVERT: D 67 ASP cc_start: 0.7018 (p0) cc_final: 0.6815 (p0) REVERT: D 162 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: D 177 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7124 (mp) REVERT: D 274 ARG cc_start: 0.7474 (mtm-85) cc_final: 0.7238 (mtp85) REVERT: D 280 ARG cc_start: 0.7691 (mtp85) cc_final: 0.7333 (mtm110) REVERT: D 368 LYS cc_start: 0.7224 (ttpp) cc_final: 0.6952 (tmtt) REVERT: E 78 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7201 (m-30) REVERT: E 103 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7002 (tp) REVERT: E 274 ARG cc_start: 0.7253 (mtp180) cc_final: 0.7040 (mmp-170) REVERT: E 318 ASP cc_start: 0.7840 (t0) cc_final: 0.7501 (t0) REVERT: E 393 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7680 (ttp-170) REVERT: E 404 LEU cc_start: 0.6843 (mt) cc_final: 0.6643 (mt) REVERT: E 416 ASP cc_start: 0.7610 (t70) cc_final: 0.7333 (t0) REVERT: E 453 ARG cc_start: 0.7791 (mmt90) cc_final: 0.7466 (mmt-90) REVERT: F 41 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.5724 (tpt-90) REVERT: F 92 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7941 (mtt-85) REVERT: F 110 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7821 (mttt) REVERT: F 248 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7125 (tt0) REVERT: F 342 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: F 376 LYS cc_start: 0.8121 (tptt) cc_final: 0.7791 (tptt) REVERT: F 452 LYS cc_start: 0.7780 (mttp) cc_final: 0.7561 (mttt) REVERT: G 10 ASN cc_start: 0.8235 (m-40) cc_final: 0.7810 (m-40) REVERT: G 30 LYS cc_start: 0.8273 (mttm) cc_final: 0.8044 (mtmm) REVERT: G 86 LEU cc_start: 0.1466 (OUTLIER) cc_final: 0.1047 (mt) REVERT: G 175 GLN cc_start: 0.8685 (mt0) cc_final: 0.8458 (mt0) REVERT: G 181 GLN cc_start: 0.7534 (mm-40) cc_final: 0.7320 (tp40) REVERT: H 1 MET cc_start: 0.2392 (ttp) cc_final: 0.2106 (ttt) REVERT: I 119 LEU cc_start: 0.4713 (OUTLIER) cc_final: 0.4217 (tp) REVERT: J 81 GLU cc_start: 0.5576 (mm-30) cc_final: 0.4896 (tm-30) REVERT: J 130 HIS cc_start: 0.3731 (OUTLIER) cc_final: 0.3475 (m-70) REVERT: J 141 GLU cc_start: 0.4055 (tp30) cc_final: 0.3745 (tp30) REVERT: J 160 LYS cc_start: 0.6080 (mmtm) cc_final: 0.5698 (mtmm) REVERT: L 67 LEU cc_start: 0.4418 (mt) cc_final: 0.4117 (tp) REVERT: L 88 ARG cc_start: 0.5454 (ttp80) cc_final: 0.4567 (mtp85) REVERT: L 178 LEU cc_start: 0.6247 (mt) cc_final: 0.6007 (mm) outliers start: 115 outliers final: 47 residues processed: 480 average time/residue: 1.8919 time to fit residues: 1027.4933 Evaluate side-chains 451 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 381 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 393 ARG Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 26 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 367 optimal weight: 0.9990 chunk 369 optimal weight: 0.0980 chunk 344 optimal weight: 0.0870 chunk 357 optimal weight: 6.9990 chunk 269 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 HIS B 469 GLN C 571 GLN D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN E 129 GLN E 428 GLN F 323 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124323 restraints weight = 34025.268| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.35 r_work: 0.3248 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30056 Z= 0.126 Angle : 0.539 8.765 40722 Z= 0.281 Chirality : 0.044 0.151 4564 Planarity : 0.005 0.060 5331 Dihedral : 5.439 72.800 4214 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.66 % Allowed : 15.37 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3764 helix: 1.64 (0.13), residues: 1591 sheet: -0.22 (0.22), residues: 550 loop : 0.05 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 100 HIS 0.005 0.001 HIS A 185 PHE 0.012 0.001 PHE E 418 TYR 0.014 0.001 TYR D 29 ARG 0.005 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 1376) hydrogen bonds : angle 4.80480 ( 3903) covalent geometry : bond 0.00284 (30056) covalent geometry : angle 0.53909 (40722) *********************** 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 482 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 400 time to evaluate : 3.773 Fit side-chains revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8331 (tp) REVERT: A 340 ARG cc_start: 0.7530 (tpp-160) cc_final: 0.7083 (ttp-170) REVERT: A 491 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7409 (mpt90) REVERT: A 517 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7955 (ttpt) REVERT: A 527 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6734 (mt-10) REVERT: A 530 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7324 (mt) REVERT: B 243 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7081 (mtpt) REVERT: B 393 GLU cc_start: 0.6869 (tt0) cc_final: 0.6197 (pt0) REVERT: B 432 THR cc_start: 0.7751 (m) cc_final: 0.7208 (p) REVERT: B 467 ILE cc_start: 0.8062 (tp) cc_final: 0.7655 (tt) REVERT: B 502 GLU cc_start: 0.6554 (mp0) cc_final: 0.5709 (pm20) REVERT: C 54 ASP cc_start: 0.7968 (t0) cc_final: 0.7672 (t0) REVERT: C 92 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: C 133 MET cc_start: 0.8170 (mtm) cc_final: 0.7877 (mtp) REVERT: C 154 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6980 (ttm-80) REVERT: C 161 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7962 (mttp) REVERT: C 177 ASP cc_start: 0.7819 (p0) cc_final: 0.7495 (p0) REVERT: C 342 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7601 (mm-30) REVERT: C 363 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7949 (tp30) REVERT: C 461 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: C 547 ARG cc_start: 0.7002 (tpp-160) cc_final: 0.6478 (ttm-80) REVERT: C 569 GLU cc_start: 0.6737 (tt0) cc_final: 0.5838 (tm-30) REVERT: D 6 LYS cc_start: 0.6546 (tttm) cc_final: 0.6079 (tttt) REVERT: D 52 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7661 (mt-10) REVERT: D 62 GLU cc_start: 0.6645 (pm20) cc_final: 0.6350 (mm-30) REVERT: D 162 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: D 280 ARG cc_start: 0.7600 (mtp85) cc_final: 0.7239 (mtm180) REVERT: D 358 LEU cc_start: 0.8701 (tp) cc_final: 0.8488 (tp) REVERT: D 368 LYS cc_start: 0.7202 (ttpp) cc_final: 0.6944 (tmtt) REVERT: D 393 ARG cc_start: 0.8211 (ttp-170) cc_final: 0.7987 (mtm-85) REVERT: E 216 ARG cc_start: 0.8008 (ptt90) cc_final: 0.7633 (ptt90) REVERT: E 318 ASP cc_start: 0.7850 (t0) cc_final: 0.7441 (t0) REVERT: E 342 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: E 416 ASP cc_start: 0.7636 (t70) cc_final: 0.7363 (t0) REVERT: E 453 ARG cc_start: 0.7774 (mmt90) cc_final: 0.7479 (mmt-90) REVERT: F 92 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7931 (mtt-85) REVERT: F 110 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7814 (mttt) REVERT: F 342 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: F 376 LYS cc_start: 0.8001 (tptt) cc_final: 0.7727 (tptt) REVERT: F 393 ARG cc_start: 0.8231 (mtt180) cc_final: 0.8015 (mtt180) REVERT: F 452 LYS cc_start: 0.7737 (mttp) cc_final: 0.7517 (mttt) REVERT: G 10 ASN cc_start: 0.8176 (m-40) cc_final: 0.7826 (m-40) REVERT: G 30 LYS cc_start: 0.8226 (mttm) cc_final: 0.8004 (mtmm) REVERT: J 81 GLU cc_start: 0.5553 (mm-30) cc_final: 0.4923 (tm-30) REVERT: L 88 ARG cc_start: 0.5530 (ttp80) cc_final: 0.4533 (ttp-110) REVERT: L 141 GLU cc_start: 0.5089 (tm-30) cc_final: 0.4393 (mt-10) outliers start: 82 outliers final: 28 residues processed: 452 average time/residue: 2.1155 time to fit residues: 1082.9724 Evaluate side-chains 425 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 384 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 292 optimal weight: 0.9990 chunk 323 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 316 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 305 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 287 optimal weight: 0.0870 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 442 ASN C 571 GLN D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN E 428 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124192 restraints weight = 34210.521| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.37 r_work: 0.3237 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30056 Z= 0.134 Angle : 0.544 8.913 40722 Z= 0.281 Chirality : 0.044 0.155 4564 Planarity : 0.005 0.062 5331 Dihedral : 5.323 73.504 4214 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.69 % Allowed : 16.15 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3764 helix: 1.76 (0.13), residues: 1587 sheet: -0.14 (0.22), residues: 540 loop : 0.11 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 100 HIS 0.005 0.001 HIS A 185 PHE 0.014 0.002 PHE B 559 TYR 0.013 0.001 TYR D 29 ARG 0.004 0.000 ARG D 91 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 1376) hydrogen bonds : angle 4.75572 ( 3903) covalent geometry : bond 0.00309 (30056) covalent geometry : angle 0.54424 (40722) *********************** 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 470 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 387 time to evaluate : 3.304 Fit side-chains revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8320 (tp) REVERT: A 340 ARG cc_start: 0.7528 (tpp-160) cc_final: 0.7121 (tpp-160) REVERT: A 491 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7302 (mpt90) REVERT: A 517 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7966 (ttpt) REVERT: A 527 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6662 (mt-10) REVERT: A 530 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7275 (mt) REVERT: B 243 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7073 (mtpt) REVERT: B 393 GLU cc_start: 0.6915 (tt0) cc_final: 0.6238 (pt0) REVERT: B 467 ILE cc_start: 0.8040 (tp) cc_final: 0.7623 (tt) REVERT: B 502 GLU cc_start: 0.6434 (mp0) cc_final: 0.5592 (pm20) REVERT: C 54 ASP cc_start: 0.8010 (t0) cc_final: 0.7719 (t0) REVERT: C 92 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: C 133 MET cc_start: 0.8168 (mtm) cc_final: 0.7904 (mtp) REVERT: C 154 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6986 (ttm-80) REVERT: C 161 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7962 (mttp) REVERT: C 177 ASP cc_start: 0.7874 (p0) cc_final: 0.7531 (p0) REVERT: C 342 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7596 (mm-30) REVERT: C 363 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7973 (tp30) REVERT: C 461 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: C 547 ARG cc_start: 0.6956 (tpp-160) cc_final: 0.6479 (ttm-80) REVERT: C 565 GLU cc_start: 0.6377 (tm-30) cc_final: 0.6063 (tm-30) REVERT: C 569 GLU cc_start: 0.6807 (tt0) cc_final: 0.5814 (tm-30) REVERT: D 6 LYS cc_start: 0.6516 (tttm) cc_final: 0.6066 (tttt) REVERT: D 52 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7670 (mt-10) REVERT: D 62 GLU cc_start: 0.6579 (pm20) cc_final: 0.6321 (mm-30) REVERT: D 162 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: D 248 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: D 280 ARG cc_start: 0.7672 (mtp85) cc_final: 0.7355 (mtm110) REVERT: D 368 LYS cc_start: 0.7135 (ttpp) cc_final: 0.6879 (tmtt) REVERT: E 216 ARG cc_start: 0.8012 (ptt90) cc_final: 0.7648 (ptt90) REVERT: E 237 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8353 (mtt) REVERT: E 251 TYR cc_start: 0.8340 (m-80) cc_final: 0.8132 (m-80) REVERT: E 318 ASP cc_start: 0.7843 (t0) cc_final: 0.7433 (t0) REVERT: E 342 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: E 393 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7546 (ttp-170) REVERT: E 416 ASP cc_start: 0.7612 (t70) cc_final: 0.7324 (t0) REVERT: E 453 ARG cc_start: 0.7784 (mmt90) cc_final: 0.7141 (mpt180) REVERT: E 456 LYS cc_start: 0.6748 (mmmm) cc_final: 0.6359 (mmmt) REVERT: F 67 ASP cc_start: 0.7990 (p0) cc_final: 0.7692 (p0) REVERT: F 92 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7921 (mtt-85) REVERT: F 110 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7763 (mttp) REVERT: F 342 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: F 376 LYS cc_start: 0.7977 (tptt) cc_final: 0.7704 (tptt) REVERT: F 393 ARG cc_start: 0.8252 (mtt180) cc_final: 0.8039 (mtt180) REVERT: F 452 LYS cc_start: 0.7742 (mttp) cc_final: 0.7521 (mttt) REVERT: G 10 ASN cc_start: 0.8161 (m-40) cc_final: 0.7818 (m-40) REVERT: G 30 LYS cc_start: 0.8170 (mttm) cc_final: 0.7962 (mtmm) REVERT: G 175 GLN cc_start: 0.8659 (mt0) cc_final: 0.8422 (mt0) REVERT: J 81 GLU cc_start: 0.5552 (mm-30) cc_final: 0.4913 (tm-30) REVERT: L 88 ARG cc_start: 0.5435 (ttp80) cc_final: 0.4502 (ttp-110) outliers start: 83 outliers final: 41 residues processed: 443 average time/residue: 1.9565 time to fit residues: 977.9406 Evaluate side-chains 425 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 368 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 248 GLU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 37 ASP 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 258 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 393 ARG Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 122 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 334 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 370 optimal weight: 0.0770 chunk 201 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 469 GLN C 571 GLN D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN E 364 ASN E 428 GLN G 166 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124852 restraints weight = 34052.901| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.34 r_work: 0.3244 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30056 Z= 0.123 Angle : 0.526 9.003 40722 Z= 0.272 Chirality : 0.043 0.158 4564 Planarity : 0.005 0.061 5331 Dihedral : 5.204 71.764 4214 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.59 % Allowed : 16.28 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.14), residues: 3764 helix: 1.87 (0.13), residues: 1577 sheet: -0.12 (0.22), residues: 540 loop : 0.14 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 119 HIS 0.005 0.001 HIS A 185 PHE 0.013 0.002 PHE B 559 TYR 0.013 0.001 TYR D 29 ARG 0.006 0.000 ARG E 345 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 1376) hydrogen bonds : angle 4.68618 ( 3903) covalent geometry : bond 0.00282 (30056) covalent geometry : angle 0.52567 (40722) *********************** 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 461 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 381 time to evaluate : 3.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8398 (tp) REVERT: A 340 ARG cc_start: 0.7526 (tpp-160) cc_final: 0.7111 (tpp-160) REVERT: A 491 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7283 (mpt90) REVERT: A 517 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7942 (ttpt) REVERT: A 527 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6647 (mt-10) REVERT: A 530 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7240 (mt) REVERT: B 393 GLU cc_start: 0.6960 (tt0) cc_final: 0.6300 (pt0) REVERT: B 467 ILE cc_start: 0.8028 (tp) cc_final: 0.7678 (tt) REVERT: B 501 HIS cc_start: 0.7651 (t-90) cc_final: 0.7342 (t70) REVERT: B 502 GLU cc_start: 0.6381 (mp0) cc_final: 0.5535 (pm20) REVERT: C 53 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: C 54 ASP cc_start: 0.7988 (t0) cc_final: 0.7708 (t0) REVERT: C 92 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: C 133 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7887 (mtp) REVERT: C 161 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7947 (mttp) REVERT: C 177 ASP cc_start: 0.7866 (p0) cc_final: 0.7515 (p0) REVERT: C 342 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7623 (mm-30) REVERT: C 363 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7961 (tp30) REVERT: C 461 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: C 547 ARG cc_start: 0.6923 (tpp-160) cc_final: 0.6590 (ttm-80) REVERT: D 6 LYS cc_start: 0.6437 (tttm) cc_final: 0.6001 (tttt) REVERT: D 62 GLU cc_start: 0.6553 (pm20) cc_final: 0.6288 (mm-30) REVERT: D 162 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: D 280 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7342 (mtm110) REVERT: D 368 LYS cc_start: 0.7100 (ttpp) cc_final: 0.6873 (tmtt) REVERT: E 216 ARG cc_start: 0.7989 (ptt90) cc_final: 0.7633 (ptt90) REVERT: E 318 ASP cc_start: 0.7794 (t0) cc_final: 0.7384 (t0) REVERT: E 342 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: E 393 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7574 (ttp-170) REVERT: E 416 ASP cc_start: 0.7585 (t70) cc_final: 0.7291 (t0) REVERT: E 453 ARG cc_start: 0.7781 (mmt90) cc_final: 0.7132 (mpt180) REVERT: E 456 LYS cc_start: 0.6675 (mmmm) cc_final: 0.6292 (mmmt) REVERT: F 67 ASP cc_start: 0.7970 (p0) cc_final: 0.7667 (p0) REVERT: F 92 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7936 (mtt-85) REVERT: F 110 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7731 (mttp) REVERT: F 342 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: F 376 LYS cc_start: 0.7933 (tptt) cc_final: 0.7662 (tptt) REVERT: F 452 LYS cc_start: 0.7745 (mttp) cc_final: 0.7525 (mttt) REVERT: G 10 ASN cc_start: 0.8149 (m-40) cc_final: 0.7798 (m-40) REVERT: G 30 LYS cc_start: 0.8125 (mttm) cc_final: 0.7902 (mtmm) REVERT: G 175 GLN cc_start: 0.8655 (mt0) cc_final: 0.8428 (mt0) REVERT: J 81 GLU cc_start: 0.5502 (mm-30) cc_final: 0.4862 (tm-30) REVERT: K 85 LEU cc_start: 0.5189 (OUTLIER) cc_final: 0.4896 (tt) REVERT: L 88 ARG cc_start: 0.5437 (ttp80) cc_final: 0.4481 (mtp85) outliers start: 80 outliers final: 40 residues processed: 440 average time/residue: 1.9298 time to fit residues: 961.1169 Evaluate side-chains 421 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 366 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 393 ARG Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 44 optimal weight: 0.8980 chunk 255 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 327 optimal weight: 0.0980 chunk 10 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN E 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.156211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123482 restraints weight = 34366.191| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.33 r_work: 0.3224 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30056 Z= 0.157 Angle : 0.575 9.391 40722 Z= 0.297 Chirality : 0.045 0.180 4564 Planarity : 0.005 0.063 5331 Dihedral : 5.335 70.933 4214 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.66 % Allowed : 16.67 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.14), residues: 3764 helix: 1.70 (0.13), residues: 1591 sheet: -0.14 (0.22), residues: 540 loop : 0.10 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 100 HIS 0.005 0.001 HIS A 185 PHE 0.015 0.002 PHE A 230 TYR 0.017 0.002 TYR D 29 ARG 0.006 0.001 ARG D 91 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 1376) hydrogen bonds : angle 4.83260 ( 3903) covalent geometry : bond 0.00367 (30056) covalent geometry : angle 0.57507 (40722) *********************** 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 459 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 377 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8342 (tp) REVERT: A 274 ASP cc_start: 0.7520 (t0) cc_final: 0.7306 (t0) REVERT: A 340 ARG cc_start: 0.7529 (tpp-160) cc_final: 0.7129 (tpp-160) REVERT: A 491 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7279 (mpt90) REVERT: A 517 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7995 (ttpt) REVERT: A 530 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7233 (mt) REVERT: B 124 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.6111 (mmmm) REVERT: B 393 GLU cc_start: 0.6955 (tt0) cc_final: 0.6295 (pt0) REVERT: B 467 ILE cc_start: 0.8012 (tp) cc_final: 0.7592 (tt) REVERT: B 501 HIS cc_start: 0.7580 (t-90) cc_final: 0.7302 (t70) REVERT: B 502 GLU cc_start: 0.6377 (mp0) cc_final: 0.5523 (pm20) REVERT: B 552 ARG cc_start: 0.6705 (mtp180) cc_final: 0.6369 (mtm110) REVERT: C 53 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: C 54 ASP cc_start: 0.8058 (t0) cc_final: 0.7769 (t0) REVERT: C 92 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: C 133 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7912 (mtp) REVERT: C 154 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6971 (ttm-80) REVERT: C 161 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7950 (mttp) REVERT: C 170 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6241 (tp30) REVERT: C 177 ASP cc_start: 0.7918 (p0) cc_final: 0.7566 (p0) REVERT: C 342 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7631 (mm-30) REVERT: C 363 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7983 (tp30) REVERT: C 461 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7020 (tm-30) REVERT: C 547 ARG cc_start: 0.6985 (tpp-160) cc_final: 0.6501 (ttm-80) REVERT: C 569 GLU cc_start: 0.6671 (tt0) cc_final: 0.6397 (tt0) REVERT: D 6 LYS cc_start: 0.6435 (tttm) cc_final: 0.5984 (tttt) REVERT: D 62 GLU cc_start: 0.6617 (pm20) cc_final: 0.6328 (mm-30) REVERT: D 162 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7190 (mt-10) REVERT: D 177 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6972 (mp) REVERT: D 280 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7362 (mtm110) REVERT: D 368 LYS cc_start: 0.7107 (ttpp) cc_final: 0.6863 (tmtt) REVERT: E 216 ARG cc_start: 0.7981 (ptt90) cc_final: 0.7614 (ptt90) REVERT: E 237 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8360 (mtt) REVERT: E 318 ASP cc_start: 0.7812 (t0) cc_final: 0.7415 (t0) REVERT: E 393 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7566 (ttp-170) REVERT: E 416 ASP cc_start: 0.7611 (t70) cc_final: 0.7326 (t0) REVERT: E 453 ARG cc_start: 0.7790 (mmt90) cc_final: 0.7124 (mpt180) REVERT: F 67 ASP cc_start: 0.8001 (p0) cc_final: 0.7689 (p0) REVERT: F 92 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7939 (mtt-85) REVERT: F 110 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7775 (mttp) REVERT: F 342 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: F 376 LYS cc_start: 0.7987 (tptt) cc_final: 0.7708 (tptt) REVERT: F 452 LYS cc_start: 0.7742 (mttp) cc_final: 0.7509 (mttt) REVERT: G 10 ASN cc_start: 0.8171 (m-40) cc_final: 0.7819 (m-40) REVERT: G 30 LYS cc_start: 0.8230 (mttm) cc_final: 0.7998 (mtmm) REVERT: G 138 ILE cc_start: 0.6086 (OUTLIER) cc_final: 0.5880 (tp) REVERT: G 175 GLN cc_start: 0.8667 (mt0) cc_final: 0.8430 (mt0) REVERT: J 81 GLU cc_start: 0.5455 (mm-30) cc_final: 0.4812 (tm-30) REVERT: J 160 LYS cc_start: 0.6047 (mmtm) cc_final: 0.5753 (mttp) REVERT: K 85 LEU cc_start: 0.5204 (OUTLIER) cc_final: 0.4913 (tt) REVERT: L 88 ARG cc_start: 0.5437 (ttp80) cc_final: 0.4486 (mtp85) REVERT: L 168 LEU cc_start: 0.5658 (OUTLIER) cc_final: 0.5164 (mt) REVERT: L 178 LEU cc_start: 0.6023 (mt) cc_final: 0.5629 (mm) outliers start: 82 outliers final: 44 residues processed: 433 average time/residue: 1.9390 time to fit residues: 949.0240 Evaluate side-chains 427 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 363 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 37 ASP 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 258 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 393 ARG Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL 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 42 optimal weight: 0.8980 chunk 320 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 304 optimal weight: 0.9990 chunk 358 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 335 optimal weight: 10.0000 chunk 349 optimal weight: 0.9990 chunk 84 optimal weight: 0.0000 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN E 428 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.157473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125090 restraints weight = 34033.773| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.29 r_work: 0.3245 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30056 Z= 0.120 Angle : 0.527 9.314 40722 Z= 0.271 Chirality : 0.043 0.169 4564 Planarity : 0.005 0.061 5331 Dihedral : 5.124 66.927 4214 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.27 % Allowed : 17.26 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.14), residues: 3764 helix: 1.88 (0.13), residues: 1578 sheet: -0.10 (0.22), residues: 540 loop : 0.16 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 100 HIS 0.004 0.001 HIS A 185 PHE 0.013 0.001 PHE B 559 TYR 0.014 0.001 TYR D 29 ARG 0.005 0.000 ARG E 345 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 1376) hydrogen bonds : angle 4.65544 ( 3903) covalent geometry : bond 0.00274 (30056) covalent geometry : angle 0.52677 (40722) *********************** 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 442 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 372 time to evaluate : 3.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8417 (tp) REVERT: A 274 ASP cc_start: 0.7528 (t0) cc_final: 0.7294 (t0) REVERT: A 340 ARG cc_start: 0.7525 (tpp-160) cc_final: 0.7111 (tpp-160) REVERT: A 491 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7294 (mpt90) REVERT: A 517 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7925 (ttpt) REVERT: A 530 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7217 (mt) REVERT: A 537 ASP cc_start: 0.5747 (OUTLIER) cc_final: 0.5492 (t0) REVERT: B 393 GLU cc_start: 0.6959 (tt0) cc_final: 0.6302 (pt0) REVERT: B 467 ILE cc_start: 0.7994 (tp) cc_final: 0.7647 (tt) REVERT: B 501 HIS cc_start: 0.7543 (t-90) cc_final: 0.7337 (t70) REVERT: B 502 GLU cc_start: 0.6396 (mp0) cc_final: 0.5661 (pm20) REVERT: C 54 ASP cc_start: 0.8040 (t0) cc_final: 0.7750 (t0) REVERT: C 92 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: C 133 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7912 (mtp) REVERT: C 154 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6976 (ttm-80) REVERT: C 161 LYS cc_start: 0.8212 (mtpp) cc_final: 0.7947 (mttp) REVERT: C 170 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6258 (tp30) REVERT: C 177 ASP cc_start: 0.7853 (p0) cc_final: 0.7518 (p0) REVERT: C 342 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7646 (mm-30) REVERT: C 363 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7969 (tp30) REVERT: C 461 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: C 547 ARG cc_start: 0.6930 (tpp-160) cc_final: 0.6320 (ttm-80) REVERT: C 569 GLU cc_start: 0.6734 (tt0) cc_final: 0.6486 (tt0) REVERT: D 6 LYS cc_start: 0.6433 (tttm) cc_final: 0.5999 (tttt) REVERT: D 62 GLU cc_start: 0.6591 (pm20) cc_final: 0.6319 (mm-30) REVERT: D 162 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: D 280 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7335 (mtm110) REVERT: D 368 LYS cc_start: 0.7085 (ttpp) cc_final: 0.6852 (tmtt) REVERT: E 216 ARG cc_start: 0.7996 (ptt90) cc_final: 0.7643 (ptt90) REVERT: E 318 ASP cc_start: 0.7803 (t0) cc_final: 0.7391 (t0) REVERT: E 342 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7439 (tm-30) REVERT: E 416 ASP cc_start: 0.7586 (t70) cc_final: 0.7282 (t0) REVERT: E 453 ARG cc_start: 0.7764 (mmt90) cc_final: 0.7125 (mpt180) REVERT: F 67 ASP cc_start: 0.7941 (p0) cc_final: 0.7641 (p0) REVERT: F 92 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7940 (mtt-85) REVERT: F 110 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7708 (mttp) REVERT: F 342 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: F 376 LYS cc_start: 0.7938 (tptt) cc_final: 0.7669 (tptt) REVERT: F 452 LYS cc_start: 0.7723 (mttp) cc_final: 0.7500 (mttt) REVERT: G 10 ASN cc_start: 0.8162 (m-40) cc_final: 0.7806 (m-40) REVERT: G 30 LYS cc_start: 0.8125 (mttm) cc_final: 0.7905 (mtmm) REVERT: G 175 GLN cc_start: 0.8666 (mt0) cc_final: 0.8439 (mt0) REVERT: J 81 GLU cc_start: 0.5459 (mm-30) cc_final: 0.4831 (tm-30) REVERT: J 160 LYS cc_start: 0.6069 (mmtm) cc_final: 0.5755 (mttp) REVERT: K 85 LEU cc_start: 0.5205 (OUTLIER) cc_final: 0.4908 (tt) REVERT: L 88 ARG cc_start: 0.5517 (ttp80) cc_final: 0.4600 (mtp85) REVERT: L 168 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5331 (mt) outliers start: 70 outliers final: 38 residues processed: 420 average time/residue: 2.0978 time to fit residues: 1020.3179 Evaluate side-chains 419 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 365 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL 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 259 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 246 optimal weight: 0.0060 chunk 284 optimal weight: 4.9990 chunk 313 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 322 optimal weight: 0.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 260 ASN D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN D 413 GLN E 58 GLN E 428 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.156318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123731 restraints weight = 34225.809| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.47 r_work: 0.3237 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30056 Z= 0.155 Angle : 0.577 9.538 40722 Z= 0.297 Chirality : 0.045 0.211 4564 Planarity : 0.005 0.062 5331 Dihedral : 5.282 65.225 4214 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.08 % Allowed : 17.52 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.14), residues: 3764 helix: 1.72 (0.13), residues: 1584 sheet: -0.15 (0.22), residues: 540 loop : 0.13 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 100 HIS 0.005 0.001 HIS A 185 PHE 0.015 0.002 PHE A 230 TYR 0.019 0.002 TYR D 29 ARG 0.006 0.001 ARG D 91 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 1376) hydrogen bonds : angle 4.80526 ( 3903) covalent geometry : bond 0.00362 (30056) covalent geometry : angle 0.57740 (40722) ********************** 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 435 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 371 time to evaluate : 3.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8301 (tp) REVERT: A 340 ARG cc_start: 0.7520 (tpp-160) cc_final: 0.7149 (tpp-160) REVERT: A 491 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7285 (mpt90) REVERT: A 517 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7989 (ttpt) REVERT: A 530 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7225 (mt) REVERT: A 537 ASP cc_start: 0.5741 (OUTLIER) cc_final: 0.5511 (t0) REVERT: B 124 LYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6184 (mmmm) REVERT: B 393 GLU cc_start: 0.6964 (tt0) cc_final: 0.6331 (pt0) REVERT: B 467 ILE cc_start: 0.8019 (tp) cc_final: 0.7646 (tt) REVERT: B 502 GLU cc_start: 0.6454 (mp0) cc_final: 0.5586 (pm20) REVERT: B 552 ARG cc_start: 0.6703 (mtp180) cc_final: 0.6365 (mtm110) REVERT: C 54 ASP cc_start: 0.8038 (t0) cc_final: 0.7744 (t0) REVERT: C 92 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: C 133 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7916 (mtp) REVERT: C 154 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6947 (ttm-80) REVERT: C 161 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7964 (mttp) REVERT: C 170 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6236 (tp30) REVERT: C 177 ASP cc_start: 0.7836 (p0) cc_final: 0.7504 (p0) REVERT: C 342 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7669 (mm-30) REVERT: C 363 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7981 (tp30) REVERT: C 461 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: C 547 ARG cc_start: 0.6982 (tpp-160) cc_final: 0.6363 (ttm-80) REVERT: C 569 GLU cc_start: 0.6744 (tt0) cc_final: 0.6510 (tt0) REVERT: D 6 LYS cc_start: 0.6443 (tttm) cc_final: 0.6008 (tttt) REVERT: D 62 GLU cc_start: 0.6640 (pm20) cc_final: 0.6362 (mm-30) REVERT: D 162 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: D 280 ARG cc_start: 0.7660 (mtp85) cc_final: 0.7346 (mtm110) REVERT: D 368 LYS cc_start: 0.7057 (ttpp) cc_final: 0.6849 (tmtt) REVERT: E 216 ARG cc_start: 0.7948 (ptt90) cc_final: 0.7590 (ptt90) REVERT: E 318 ASP cc_start: 0.7719 (t0) cc_final: 0.7329 (t0) REVERT: E 416 ASP cc_start: 0.7591 (t70) cc_final: 0.7306 (t0) REVERT: E 453 ARG cc_start: 0.7787 (mmt90) cc_final: 0.7149 (mpt180) REVERT: F 67 ASP cc_start: 0.7954 (p0) cc_final: 0.7655 (p0) REVERT: F 92 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7922 (mtt-85) REVERT: F 110 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7749 (mttp) REVERT: F 342 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: F 376 LYS cc_start: 0.7971 (tptt) cc_final: 0.7701 (tptt) REVERT: F 452 LYS cc_start: 0.7719 (mttp) cc_final: 0.7487 (mttt) REVERT: G 10 ASN cc_start: 0.8172 (m-40) cc_final: 0.7829 (m-40) REVERT: G 30 LYS cc_start: 0.8217 (mttm) cc_final: 0.8002 (mtmm) REVERT: G 175 GLN cc_start: 0.8656 (mt0) cc_final: 0.8425 (mt0) REVERT: J 81 GLU cc_start: 0.5470 (mm-30) cc_final: 0.4845 (tm-30) REVERT: J 158 GLU cc_start: 0.5980 (pm20) cc_final: 0.5726 (pm20) REVERT: J 160 LYS cc_start: 0.5996 (mmtm) cc_final: 0.5760 (mttp) REVERT: K 85 LEU cc_start: 0.5173 (OUTLIER) cc_final: 0.4870 (tt) REVERT: L 88 ARG cc_start: 0.5503 (ttp80) cc_final: 0.4547 (mtp85) REVERT: L 164 GLU cc_start: 0.6331 (tt0) cc_final: 0.6091 (tt0) REVERT: L 168 LEU cc_start: 0.5735 (OUTLIER) cc_final: 0.5315 (mt) outliers start: 64 outliers final: 39 residues processed: 413 average time/residue: 2.0922 time to fit residues: 976.1190 Evaluate side-chains 420 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 365 time to evaluate : 6.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 81 PHE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 152 VAL 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 346 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 365 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 249 optimal weight: 0.0870 chunk 279 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 342 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 501 HIS D 206 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN D 413 GLN E 58 GLN E 428 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.156546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124240 restraints weight = 34097.997| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.29 r_work: 0.3230 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30056 Z= 0.146 Angle : 0.564 9.479 40722 Z= 0.291 Chirality : 0.044 0.191 4564 Planarity : 0.005 0.061 5331 Dihedral : 5.259 61.534 4214 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.04 % Allowed : 17.74 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3764 helix: 1.72 (0.13), residues: 1584 sheet: -0.15 (0.22), residues: 540 loop : 0.13 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 100 HIS 0.007 0.001 HIS B 501 PHE 0.013 0.002 PHE A 230 TYR 0.018 0.002 TYR D 29 ARG 0.005 0.001 ARG D 91 Details of bonding type rmsd hydrogen bonds : bond 0.04473 ( 1376) hydrogen bonds : angle 4.78003 ( 3903) covalent geometry : bond 0.00340 (30056) covalent geometry : angle 0.56405 (40722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33980.05 seconds wall clock time: 593 minutes 37.46 seconds (35617.46 seconds total)