Starting phenix.real_space_refine on Sat Feb 7 01:11:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vax_31869/02_2026/7vax_31869.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vax_31869/02_2026/7vax_31869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vax_31869/02_2026/7vax_31869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vax_31869/02_2026/7vax_31869.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vax_31869/02_2026/7vax_31869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vax_31869/02_2026/7vax_31869.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 105 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29553 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.18, per 1000 atoms: 0.21 Number of scatterers: 29553 At special positions: 0 Unit cell: (148.23, 147.42, 174.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 8 15.00 Mg 2 11.99 O 5572 8.00 N 5131 7.00 C 18735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.2 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: 143 helices and 26 sheets defined 47.5% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.914A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 3.970A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.562A pdb=" N TYR A 350 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 352 No H-bonds generated for 'chain 'A' and resid 351 through 352' 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: 3.631A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 4.072A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.592A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.712A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.642A pdb=" N TYR A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 272 removed outlier: 3.518A pdb=" N VAL B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.443A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.596A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 353 through 364 removed outlier: 3.624A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix removed outlier: 5.183A pdb=" N GLU B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 472 removed outlier: 4.477A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 494 removed outlier: 3.869A pdb=" N LEU B 482 " --> pdb=" O ASP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 533 Processing helix chain 'B' and resid 535 through 541 Processing helix chain 'B' and resid 543 through 552 removed outlier: 3.971A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 578 removed outlier: 4.027A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.031A 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: 4.165A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN C 316 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 342 Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.553A pdb=" N TYR C 350 " --> pdb=" O GLU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 364 removed outlier: 3.728A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 401 Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 3.829A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (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 removed outlier: 3.645A pdb=" N GLN C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 551 removed outlier: 3.989A pdb=" N GLU C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 558 through 576 removed outlier: 3.923A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.534A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.515A pdb=" N ARG D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.760A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.604A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.543A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.580A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.921A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.804A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 466 through 470 removed outlier: 3.680A pdb=" N GLU D 469 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.735A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 174 through 179 removed outlier: 4.658A pdb=" N SER E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.516A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.758A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.628A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.694A pdb=" N VAL E 366 " --> pdb=" O ASN E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 399 removed outlier: 3.642A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 422 Processing helix chain 'E' and resid 431 through 444 removed outlier: 3.534A pdb=" N SER E 435 " --> pdb=" O SER E 431 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 462 Processing helix chain 'F' and resid 85 through 90 removed outlier: 3.571A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 212 through 215 removed outlier: 4.017A pdb=" N SER F 215 " --> pdb=" O GLY F 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 212 through 215' Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.638A pdb=" N GLU F 230 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.942A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 4.259A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.627A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 removed outlier: 3.523A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 365 Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.821A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 470 Processing helix chain 'G' and resid 7 through 71 Processing helix chain 'G' and resid 72 through 82 removed outlier: 3.564A pdb=" N GLY G 82 " --> pdb=" O GLY G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 207 removed outlier: 4.501A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 6 through 17 Processing helix chain 'H' and resid 27 through 38 removed outlier: 4.110A pdb=" N SER H 31 " --> pdb=" O GLU H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 Processing helix chain 'H' and resid 78 through 83 Processing helix chain 'H' and resid 85 through 99 Processing helix chain 'I' and resid 82 through 106 removed outlier: 3.613A pdb=" N GLU I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 4.028A pdb=" N ALA I 110 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 93 Processing helix chain 'J' and resid 94 through 97 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.628A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 127 Processing helix chain 'J' and resid 128 through 139 removed outlier: 4.727A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.612A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 106 removed outlier: 3.628A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 119 Processing helix chain 'L' and resid 62 through 93 removed outlier: 3.556A pdb=" N ALA L 93 " --> pdb=" O GLU L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 128 through 130 No H-bonds generated for 'chain 'L' and resid 128 through 130' Processing helix chain 'L' and resid 131 through 139 Processing helix chain 'L' and resid 166 through 187 removed outlier: 5.287A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 10 removed outlier: 6.561A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.509A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 5.693A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 6.643A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 5.617A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 22 current: chain 'E' and resid 42 through 51 removed outlier: 5.791A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR E 54 " --> pdb=" O SER E 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 54 through 59 current: chain 'F' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 22 current: chain 'F' and resid 42 through 51 removed outlier: 5.673A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR F 54 " --> pdb=" O SER F 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 54 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 144 current: chain 'L' and resid 161 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 84 current: chain 'A' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 291 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.431A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.438A 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: 6.954A 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: 3.668A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.648A 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: 7.039A 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: 4.635A 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 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 84 current: chain 'C' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 291 current: chain 'C' and resid 375 through 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: 3.691A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 5.316A 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 Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.586A 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: 6.415A pdb=" N ARG D 91 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU D 221 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 257 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.566A 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 Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 93 removed outlier: 8.692A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASN E 222 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA E 193 " --> pdb=" O ASN E 222 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET E 194 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.681A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 313 through 315 Processing sheet with id=AC4, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC5, first strand: chain 'F' and resid 92 through 94 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 92 through 94 current: chain 'F' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 217 through 223 current: chain 'F' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 307 through 315 current: chain 'F' and resid 358 through 359 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.686A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 91 through 96 Processing sheet with id=AC8, first strand: chain 'H' and resid 2 through 3 removed outlier: 6.813A pdb=" N ALA H 2 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ASP H 48 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU H 72 " --> pdb=" O VAL H 45 " (cutoff:3.500A) 1296 hydrogen bonds defined for protein. 3711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.21 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 10022 1.36 - 1.50: 7393 1.50 - 1.65: 12499 1.65 - 1.80: 119 1.80 - 1.95: 77 Bond restraints: 30110 Sorted by residual: bond pdb=" C4 ADP A 602 " pdb=" C5 ADP A 602 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C5 ADP A 602 " pdb=" C6 ADP A 602 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" O3B ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sigma weight residual 1.510 1.582 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" N GLU E 184 " pdb=" CA GLU E 184 " ideal model delta sigma weight residual 1.452 1.490 -0.037 1.25e-02 6.40e+03 8.89e+00 bond pdb=" N GLU E 182 " pdb=" CA GLU E 182 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.29e-02 6.01e+03 8.00e+00 ... (remaining 30105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 40557 2.69 - 5.38: 231 5.38 - 8.07: 13 8.07 - 10.76: 5 10.76 - 13.46: 1 Bond angle restraints: 40807 Sorted by residual: angle pdb=" N ALA E 188 " pdb=" CA ALA E 188 " pdb=" C ALA E 188 " ideal model delta sigma weight residual 110.17 101.72 8.45 1.61e+00 3.86e-01 2.75e+01 angle pdb=" O1B ADP A 602 " pdb=" PB ADP A 602 " pdb=" O3B ADP A 602 " ideal model delta sigma weight residual 119.90 106.44 13.46 3.00e+00 1.11e-01 2.01e+01 angle pdb=" CA ALA E 188 " pdb=" C ALA E 188 " pdb=" O ALA E 188 " ideal model delta sigma weight residual 121.28 116.47 4.81 1.18e+00 7.18e-01 1.66e+01 angle pdb=" C ALA E 188 " pdb=" N VAL E 189 " pdb=" CA VAL E 189 " ideal model delta sigma weight residual 123.17 118.47 4.70 1.28e+00 6.10e-01 1.35e+01 angle pdb=" CA GLU E 182 " pdb=" C GLU E 182 " pdb=" O GLU E 182 " ideal model delta sigma weight residual 121.40 117.39 4.01 1.13e+00 7.83e-01 1.26e+01 ... (remaining 40802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.16: 17606 26.16 - 52.32: 650 52.32 - 78.49: 79 78.49 - 104.65: 19 104.65 - 130.81: 1 Dihedral angle restraints: 18355 sinusoidal: 7533 harmonic: 10822 Sorted by residual: dihedral pdb=" C5' ADP A 602 " pdb=" O5' ADP A 602 " pdb=" PA ADP A 602 " pdb=" O2A ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 70.81 -130.81 1 2.00e+01 2.50e-03 3.97e+01 dihedral pdb=" CA THR E 371 " pdb=" C THR E 371 " pdb=" N ARG E 372 " pdb=" CA ARG E 372 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+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 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 18352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3677 0.051 - 0.102: 728 0.102 - 0.153: 162 0.153 - 0.204: 7 0.204 - 0.255: 2 Chirality restraints: 4576 Sorted by residual: chirality pdb=" CA GLU E 185 " pdb=" N GLU E 185 " pdb=" C GLU E 185 " pdb=" CB GLU E 185 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ALA E 188 " pdb=" N ALA E 188 " pdb=" C ALA E 188 " pdb=" CB ALA E 188 " both_signs ideal model delta sigma weight residual False 2.48 2.70 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE A 87 " pdb=" CA ILE A 87 " pdb=" CG1 ILE A 87 " pdb=" CG2 ILE A 87 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.61e-01 ... (remaining 4573 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 94 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO L 95 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 108 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO G 109 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO G 109 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 109 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO E 324 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.024 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 255 2.59 - 3.17: 24651 3.17 - 3.75: 47757 3.75 - 4.32: 66097 4.32 - 4.90: 110868 Nonbonded interactions: 249628 Sorted by model distance: nonbonded pdb=" OG SER A 235 " pdb="MG MG A 601 " model vdw 2.017 2.170 nonbonded pdb=" OG SER C 235 " pdb="MG MG C 601 " model vdw 2.027 2.170 nonbonded pdb="MG MG A 601 " pdb=" O3B ADP A 602 " model vdw 2.074 2.170 nonbonded pdb=" OH TYR F 263 " pdb=" OD2 ASP F 290 " model vdw 2.088 3.040 nonbonded pdb=" NH1 ARG A 258 " pdb="MG MG A 601 " model vdw 2.117 2.250 ... (remaining 249623 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = chain 'B' selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 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: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.970 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.003 0.106 30111 Z= 0.126 Angle : 0.509 13.456 40807 Z= 0.262 Chirality : 0.042 0.255 4576 Planarity : 0.004 0.047 5333 Dihedral : 13.522 130.812 11437 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.03 % Allowed : 0.39 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.14), residues: 3764 helix: 1.97 (0.14), residues: 1547 sheet: -0.16 (0.22), residues: 573 loop : 0.53 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 41 TYR 0.010 0.001 TYR D 13 PHE 0.014 0.001 PHE G 108 TRP 0.014 0.001 TRP E 440 HIS 0.003 0.000 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00250 (30110) covalent geometry : angle 0.50920 (40807) hydrogen bonds : bond 0.13528 ( 1296) hydrogen bonds : angle 5.66766 ( 3711) Misc. bond : bond 0.00050 ( 1) *********************** 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 594 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 593 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7308 (mm-30) REVERT: A 38 GLU cc_start: 0.7338 (tt0) cc_final: 0.7074 (tt0) REVERT: A 45 ASP cc_start: 0.7065 (t0) cc_final: 0.6769 (t70) REVERT: A 109 HIS cc_start: 0.7866 (m90) cc_final: 0.7388 (m170) REVERT: A 239 GLN cc_start: 0.7371 (mt0) cc_final: 0.7127 (mm-40) REVERT: A 248 ASP cc_start: 0.8470 (m-30) cc_final: 0.8263 (m-30) REVERT: A 262 MET cc_start: 0.8214 (mmp) cc_final: 0.7876 (mmp) REVERT: A 264 ASP cc_start: 0.7714 (t0) cc_final: 0.7162 (t0) REVERT: A 408 ARG cc_start: 0.8165 (ttt180) cc_final: 0.7877 (ttt90) REVERT: A 416 ARG cc_start: 0.7423 (mtp-110) cc_final: 0.7139 (mtp85) REVERT: A 466 GLU cc_start: 0.6731 (mp0) cc_final: 0.6517 (mp0) REVERT: A 491 ARG cc_start: 0.7096 (mtm-85) cc_final: 0.6794 (ttp-110) REVERT: A 524 LYS cc_start: 0.7114 (mmtt) cc_final: 0.6713 (ttmt) REVERT: A 541 GLN cc_start: 0.7271 (pt0) cc_final: 0.7018 (pt0) REVERT: A 550 ARG cc_start: 0.6671 (mmt180) cc_final: 0.6326 (mmm-85) REVERT: A 567 MET cc_start: 0.6870 (mmm) cc_final: 0.6442 (mmm) REVERT: B 19 MET cc_start: 0.8041 (ptm) cc_final: 0.7835 (ptm) REVERT: B 124 LYS cc_start: 0.7398 (ptpp) cc_final: 0.6829 (ptpt) REVERT: B 127 ASP cc_start: 0.7010 (m-30) cc_final: 0.6778 (m-30) REVERT: B 156 ARG cc_start: 0.7118 (mtp85) cc_final: 0.6899 (mtp-110) REVERT: B 166 TYR cc_start: 0.7838 (m-80) cc_final: 0.7265 (m-80) REVERT: B 200 ASP cc_start: 0.7014 (m-30) cc_final: 0.6501 (m-30) REVERT: B 220 MET cc_start: 0.6240 (tpp) cc_final: 0.5566 (mmm) REVERT: B 243 LYS cc_start: 0.7167 (tttm) cc_final: 0.5888 (mttm) REVERT: B 271 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7194 (tm-30) REVERT: B 342 GLU cc_start: 0.6727 (pt0) cc_final: 0.6454 (mt-10) REVERT: B 456 GLU cc_start: 0.6826 (tp30) cc_final: 0.6516 (tp30) REVERT: B 459 GLN cc_start: 0.7016 (tp40) cc_final: 0.6726 (tp40) REVERT: B 477 GLN cc_start: 0.5496 (pt0) cc_final: 0.4529 (tp40) REVERT: B 516 MET cc_start: 0.6877 (mtm) cc_final: 0.6675 (mtt) REVERT: B 563 PHE cc_start: 0.6919 (t80) cc_final: 0.6552 (t80) REVERT: C 1 MET cc_start: 0.6615 (mmt) cc_final: 0.6254 (pmm) REVERT: C 93 ARG cc_start: 0.7485 (mmm-85) cc_final: 0.6601 (mmm-85) REVERT: C 156 ARG cc_start: 0.6473 (ttt90) cc_final: 0.5834 (ttt180) REVERT: C 166 TYR cc_start: 0.8340 (m-80) cc_final: 0.7834 (m-80) REVERT: C 197 ARG cc_start: 0.7773 (ttp-110) cc_final: 0.7412 (ttt-90) REVERT: C 344 MET cc_start: 0.8208 (mmt) cc_final: 0.7955 (tpp) REVERT: C 374 GLU cc_start: 0.6371 (tp30) cc_final: 0.5929 (tp30) REVERT: C 433 SER cc_start: 0.8426 (p) cc_final: 0.8004 (m) REVERT: C 464 LEU cc_start: 0.7190 (mp) cc_final: 0.6866 (mp) REVERT: C 480 GLU cc_start: 0.5884 (mt-10) cc_final: 0.5674 (mm-30) REVERT: C 513 TYR cc_start: 0.8018 (t80) cc_final: 0.7691 (t80) REVERT: C 547 ARG cc_start: 0.6636 (mmm-85) cc_final: 0.6224 (ttm110) REVERT: D 52 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7625 (mm-30) REVERT: D 87 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7273 (mt-10) REVERT: D 98 LYS cc_start: 0.7483 (ttpp) cc_final: 0.6665 (mttm) REVERT: D 280 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7484 (mtm110) REVERT: D 401 GLU cc_start: 0.7321 (pt0) cc_final: 0.7010 (pt0) REVERT: D 420 ARG cc_start: 0.7544 (mmm160) cc_final: 0.6781 (mmt180) REVERT: D 434 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7170 (mt-10) REVERT: D 466 LYS cc_start: 0.7078 (mtmm) cc_final: 0.6690 (mmmm) REVERT: E 25 LYS cc_start: 0.7752 (ptpt) cc_final: 0.7475 (mtpt) REVERT: E 52 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7718 (mt-10) REVERT: E 77 GLU cc_start: 0.6644 (pt0) cc_final: 0.5990 (mt-10) REVERT: E 110 LYS cc_start: 0.7183 (tttt) cc_final: 0.6925 (tttm) REVERT: E 139 ASP cc_start: 0.7494 (m-30) cc_final: 0.7200 (m-30) REVERT: E 174 ARG cc_start: 0.6729 (mmm-85) cc_final: 0.6202 (ttm-80) REVERT: E 210 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7458 (ttt180) REVERT: E 216 ARG cc_start: 0.5801 (ttp80) cc_final: 0.5340 (ttp-110) REVERT: E 353 ASP cc_start: 0.7027 (t0) cc_final: 0.6794 (t0) REVERT: E 362 MET cc_start: 0.7983 (ttp) cc_final: 0.7686 (ttp) REVERT: E 368 LYS cc_start: 0.6420 (mmmt) cc_final: 0.5080 (mppt) REVERT: E 452 LYS cc_start: 0.6173 (ptpt) cc_final: 0.5935 (mptt) REVERT: F 6 LYS cc_start: 0.7621 (tppp) cc_final: 0.6553 (mttp) REVERT: F 78 ASP cc_start: 0.7114 (m-30) cc_final: 0.6909 (m-30) REVERT: F 98 LYS cc_start: 0.7715 (mptt) cc_final: 0.7306 (mmmt) REVERT: F 264 CYS cc_start: 0.8143 (m) cc_final: 0.7858 (m) REVERT: F 302 GLU cc_start: 0.7090 (tt0) cc_final: 0.6881 (mt-10) REVERT: F 373 GLU cc_start: 0.7807 (pm20) cc_final: 0.7500 (pt0) REVERT: F 394 LYS cc_start: 0.7398 (ttmt) cc_final: 0.7027 (mtpt) REVERT: G 17 GLN cc_start: 0.7089 (mm110) cc_final: 0.6855 (mm-40) REVERT: G 30 LYS cc_start: 0.7188 (mtpp) cc_final: 0.6908 (mtpp) REVERT: G 38 GLU cc_start: 0.7167 (tp30) cc_final: 0.6775 (tt0) REVERT: G 152 GLU cc_start: 0.6197 (mm-30) cc_final: 0.5856 (mt-10) REVERT: G 159 ARG cc_start: 0.6795 (mtm180) cc_final: 0.6356 (mtm-85) REVERT: G 181 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7093 (mt0) REVERT: G 187 GLU cc_start: 0.7449 (pp20) cc_final: 0.7226 (tm-30) REVERT: G 205 GLU cc_start: 0.3838 (tm-30) cc_final: 0.3285 (tt0) REVERT: H 38 GLU cc_start: 0.4660 (mm-30) cc_final: 0.4286 (mt-10) REVERT: H 90 MET cc_start: 0.7086 (tpp) cc_final: 0.6425 (ttm) REVERT: I 104 MET cc_start: 0.4136 (mtp) cc_final: 0.3934 (mpt) REVERT: J 66 LEU cc_start: 0.5784 (mt) cc_final: 0.5485 (mp) REVERT: J 78 GLU cc_start: 0.4292 (tt0) cc_final: 0.3928 (tt0) REVERT: J 79 VAL cc_start: 0.6331 (t) cc_final: 0.5741 (t) REVERT: L 105 ARG cc_start: 0.6160 (mtm-85) cc_final: 0.5939 (mtm-85) REVERT: L 126 GLU cc_start: 0.5250 (mp0) cc_final: 0.5012 (mp0) REVERT: L 181 LYS cc_start: 0.5799 (mttp) cc_final: 0.5456 (mmpt) outliers start: 1 outliers final: 0 residues processed: 594 average time/residue: 0.8411 time to fit residues: 564.9681 Evaluate side-chains 379 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN C 571 GLN D 377 GLN D 437 GLN E 142 ASN E 222 ASN E 364 ASN E 424 ASN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 166 GLN L 124 ASN L 162 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.107548 restraints weight = 39826.598| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.84 r_work: 0.3131 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30111 Z= 0.211 Angle : 0.621 7.914 40807 Z= 0.317 Chirality : 0.046 0.205 4576 Planarity : 0.005 0.065 5333 Dihedral : 5.529 103.845 4231 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.34 % Allowed : 9.54 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.14), residues: 3764 helix: 1.56 (0.13), residues: 1549 sheet: -0.25 (0.22), residues: 563 loop : 0.19 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 154 TYR 0.022 0.002 TYR B 562 PHE 0.016 0.002 PHE C 559 TRP 0.017 0.002 TRP C 119 HIS 0.006 0.001 HIS E 375 Details of bonding type rmsd covalent geometry : bond 0.00503 (30110) covalent geometry : angle 0.62075 (40807) hydrogen bonds : bond 0.04564 ( 1296) hydrogen bonds : angle 4.83690 ( 3711) Misc. bond : bond 0.00057 ( 1) *********************** 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 463 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 391 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8026 (mm-30) REVERT: A 109 HIS cc_start: 0.8399 (m90) cc_final: 0.8076 (m90) REVERT: A 262 MET cc_start: 0.8687 (mmp) cc_final: 0.8484 (mmp) REVERT: A 400 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8869 (mp) REVERT: A 408 ARG cc_start: 0.8647 (ttt180) cc_final: 0.8394 (ttt90) REVERT: A 416 ARG cc_start: 0.8212 (mtp-110) cc_final: 0.7951 (mtp85) REVERT: A 491 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7854 (ttp-110) REVERT: A 541 GLN cc_start: 0.7636 (pt0) cc_final: 0.7390 (pt0) REVERT: A 550 ARG cc_start: 0.7338 (mmt180) cc_final: 0.7009 (mmm-85) REVERT: A 567 MET cc_start: 0.7691 (mmm) cc_final: 0.7378 (mmm) REVERT: B 32 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: B 124 LYS cc_start: 0.7621 (ptpp) cc_final: 0.7075 (ptpt) REVERT: B 166 TYR cc_start: 0.8028 (m-80) cc_final: 0.7601 (m-80) REVERT: B 271 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7401 (tm-30) REVERT: B 456 GLU cc_start: 0.7072 (tp30) cc_final: 0.6854 (tp30) REVERT: B 459 GLN cc_start: 0.7600 (tp40) cc_final: 0.7289 (tp40) REVERT: B 481 ARG cc_start: 0.7823 (tmt-80) cc_final: 0.7214 (tmm-80) REVERT: B 563 PHE cc_start: 0.7325 (t80) cc_final: 0.6966 (t80) REVERT: C 1 MET cc_start: 0.7134 (mmt) cc_final: 0.6891 (mmp) REVERT: C 93 ARG cc_start: 0.8248 (mmm-85) cc_final: 0.7363 (mmm-85) REVERT: C 156 ARG cc_start: 0.7326 (ttt90) cc_final: 0.6854 (ttt180) REVERT: C 166 TYR cc_start: 0.8776 (m-80) cc_final: 0.8159 (m-80) REVERT: C 344 MET cc_start: 0.8663 (mmt) cc_final: 0.8395 (tpp) REVERT: C 433 SER cc_start: 0.8628 (p) cc_final: 0.8287 (m) REVERT: C 480 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6509 (mt-10) REVERT: C 565 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: D 49 GLU cc_start: 0.8463 (tt0) cc_final: 0.8261 (tt0) REVERT: D 52 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8039 (mm-30) REVERT: D 185 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7086 (mt-10) REVERT: D 280 ARG cc_start: 0.8464 (mtp-110) cc_final: 0.8001 (mtm110) REVERT: D 456 LYS cc_start: 0.7773 (mmmt) cc_final: 0.7365 (mmtt) REVERT: D 466 LYS cc_start: 0.7131 (mtmm) cc_final: 0.6929 (mmmm) REVERT: E 77 GLU cc_start: 0.7458 (pt0) cc_final: 0.6667 (mt-10) REVERT: E 88 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7894 (ttt) REVERT: E 96 ILE cc_start: 0.8312 (tp) cc_final: 0.8051 (tt) REVERT: E 110 LYS cc_start: 0.7555 (tttt) cc_final: 0.7314 (tttm) REVERT: E 139 ASP cc_start: 0.7917 (m-30) cc_final: 0.7416 (m-30) REVERT: E 174 ARG cc_start: 0.7069 (mmm-85) cc_final: 0.6638 (ttm-80) REVERT: E 216 ARG cc_start: 0.6646 (ttp80) cc_final: 0.5988 (ttp-110) REVERT: E 353 ASP cc_start: 0.7439 (t0) cc_final: 0.7084 (t0) REVERT: E 368 LYS cc_start: 0.6500 (mmmt) cc_final: 0.5193 (mppt) REVERT: E 452 LYS cc_start: 0.6567 (ptpt) cc_final: 0.6063 (pmtt) REVERT: F 6 LYS cc_start: 0.7874 (tppp) cc_final: 0.7064 (mttp) REVERT: F 275 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: F 302 GLU cc_start: 0.8082 (tt0) cc_final: 0.7768 (mt-10) REVERT: F 373 GLU cc_start: 0.8136 (pm20) cc_final: 0.7873 (pt0) REVERT: F 394 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7880 (mttm) REVERT: F 406 GLU cc_start: 0.7187 (tp30) cc_final: 0.6845 (tt0) REVERT: F 420 ARG cc_start: 0.8659 (mmm160) cc_final: 0.8138 (mpp80) REVERT: G 38 GLU cc_start: 0.8063 (tp30) cc_final: 0.7723 (tt0) REVERT: G 45 GLU cc_start: 0.6698 (tm-30) cc_final: 0.6350 (tt0) REVERT: G 152 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6335 (mt-10) REVERT: G 159 ARG cc_start: 0.7739 (mtm180) cc_final: 0.7388 (mtm-85) REVERT: G 181 GLN cc_start: 0.8450 (mm-40) cc_final: 0.7899 (mt0) REVERT: H 19 GLU cc_start: 0.3670 (OUTLIER) cc_final: 0.2061 (pp20) REVERT: H 38 GLU cc_start: 0.4385 (mm-30) cc_final: 0.4043 (mt-10) REVERT: H 90 MET cc_start: 0.7055 (tpp) cc_final: 0.6461 (mtp) REVERT: H 92 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6819 (tp30) REVERT: J 66 LEU cc_start: 0.5932 (mt) cc_final: 0.5612 (mp) REVERT: J 79 VAL cc_start: 0.6397 (t) cc_final: 0.5832 (t) REVERT: J 82 GLU cc_start: 0.5034 (OUTLIER) cc_final: 0.4336 (mt-10) REVERT: J 138 ARG cc_start: 0.3433 (mmt-90) cc_final: 0.2569 (tpp-160) REVERT: L 126 GLU cc_start: 0.5490 (mp0) cc_final: 0.5178 (mp0) REVERT: L 181 LYS cc_start: 0.6354 (mttp) cc_final: 0.5835 (mmpt) outliers start: 72 outliers final: 20 residues processed: 432 average time/residue: 0.7905 time to fit residues: 390.1298 Evaluate side-chains 376 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 347 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 180 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 281 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 270 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 307 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN C 425 ASN C 571 GLN E 424 ASN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN G 166 GLN L 130 HIS L 162 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.141074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.107077 restraints weight = 40029.368| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.92 r_work: 0.3122 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30111 Z= 0.215 Angle : 0.605 7.382 40807 Z= 0.309 Chirality : 0.046 0.176 4576 Planarity : 0.005 0.051 5333 Dihedral : 5.571 84.334 4231 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.66 % Allowed : 12.46 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3764 helix: 1.30 (0.13), residues: 1561 sheet: -0.46 (0.22), residues: 563 loop : -0.06 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 130 TYR 0.014 0.002 TYR B 562 PHE 0.017 0.002 PHE C 559 TRP 0.017 0.002 TRP A 119 HIS 0.004 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00515 (30110) covalent geometry : angle 0.60489 (40807) hydrogen bonds : bond 0.04669 ( 1296) hydrogen bonds : angle 4.83631 ( 3711) Misc. bond : bond 0.00017 ( 1) *********************** 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 440 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 358 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8052 (mm-30) REVERT: A 323 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8149 (mpp) REVERT: A 470 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7765 (tm) REVERT: A 491 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7866 (ttp-110) REVERT: A 541 GLN cc_start: 0.7719 (pt0) cc_final: 0.7494 (pt0) REVERT: A 550 ARG cc_start: 0.7416 (mmt180) cc_final: 0.7063 (mmm-85) REVERT: A 567 MET cc_start: 0.7696 (mmm) cc_final: 0.7380 (mmm) REVERT: B 32 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: B 120 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8391 (t) REVERT: B 166 TYR cc_start: 0.8011 (m-80) cc_final: 0.7567 (m-80) REVERT: B 209 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7286 (mtt) REVERT: B 459 GLN cc_start: 0.7641 (tp40) cc_final: 0.7317 (tp40) REVERT: B 547 ARG cc_start: 0.5052 (OUTLIER) cc_final: 0.4597 (ttm-80) REVERT: B 558 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.4785 (mt-10) REVERT: B 563 PHE cc_start: 0.7361 (t80) cc_final: 0.6998 (t80) REVERT: B 567 MET cc_start: 0.5311 (OUTLIER) cc_final: 0.4494 (tmm) REVERT: C 1 MET cc_start: 0.7198 (mmt) cc_final: 0.6938 (mmp) REVERT: C 93 ARG cc_start: 0.8292 (mmm-85) cc_final: 0.7396 (mmm-85) REVERT: C 156 ARG cc_start: 0.7327 (ttt90) cc_final: 0.6981 (ttt180) REVERT: C 344 MET cc_start: 0.8627 (mmt) cc_final: 0.8358 (tpp) REVERT: C 433 SER cc_start: 0.8653 (p) cc_final: 0.8304 (m) REVERT: C 464 LEU cc_start: 0.7793 (mp) cc_final: 0.7550 (mp) REVERT: C 480 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6538 (mt-10) REVERT: C 513 TYR cc_start: 0.8685 (t80) cc_final: 0.8302 (t80) REVERT: C 565 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: D 52 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8047 (mm-30) REVERT: D 185 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7112 (mt-10) REVERT: D 268 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8071 (ttm170) REVERT: D 280 ARG cc_start: 0.8493 (mtp-110) cc_final: 0.8171 (mtm180) REVERT: D 456 LYS cc_start: 0.7790 (mmmt) cc_final: 0.7346 (mmtt) REVERT: D 466 LYS cc_start: 0.7200 (mtmm) cc_final: 0.6911 (mmmm) REVERT: E 77 GLU cc_start: 0.7562 (pt0) cc_final: 0.6705 (mt-10) REVERT: E 88 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7924 (ttt) REVERT: E 96 ILE cc_start: 0.8420 (tp) cc_final: 0.8129 (tt) REVERT: E 139 ASP cc_start: 0.7947 (m-30) cc_final: 0.7487 (m-30) REVERT: E 174 ARG cc_start: 0.7032 (mmm-85) cc_final: 0.6562 (ttt-90) REVERT: E 216 ARG cc_start: 0.6672 (ttp80) cc_final: 0.5999 (ttp-110) REVERT: E 353 ASP cc_start: 0.7492 (t0) cc_final: 0.7155 (t0) REVERT: E 368 LYS cc_start: 0.6494 (mmmt) cc_final: 0.5142 (tppt) REVERT: E 443 LEU cc_start: 0.5423 (mp) cc_final: 0.4750 (tp) REVERT: E 452 LYS cc_start: 0.6524 (ptpt) cc_final: 0.5740 (pttm) REVERT: E 461 LYS cc_start: 0.7104 (tmtt) cc_final: 0.6845 (tmtm) REVERT: F 6 LYS cc_start: 0.7937 (tppp) cc_final: 0.7192 (mttp) REVERT: F 275 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: F 302 GLU cc_start: 0.8114 (tt0) cc_final: 0.7799 (mt-10) REVERT: F 373 GLU cc_start: 0.8208 (pm20) cc_final: 0.7959 (pt0) REVERT: F 394 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7954 (mttm) REVERT: F 406 GLU cc_start: 0.7209 (tp30) cc_final: 0.6815 (tt0) REVERT: F 420 ARG cc_start: 0.8616 (mmm160) cc_final: 0.8279 (mtm110) REVERT: G 38 GLU cc_start: 0.8106 (tp30) cc_final: 0.7857 (tt0) REVERT: G 159 ARG cc_start: 0.7803 (mtm180) cc_final: 0.7527 (ttp-170) REVERT: G 181 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7894 (mt0) REVERT: H 19 GLU cc_start: 0.3946 (OUTLIER) cc_final: 0.2374 (pp20) REVERT: H 38 GLU cc_start: 0.4343 (mm-30) cc_final: 0.3990 (mt-10) REVERT: H 90 MET cc_start: 0.7060 (tpp) cc_final: 0.6533 (mtp) REVERT: J 66 LEU cc_start: 0.5970 (mt) cc_final: 0.5637 (mp) REVERT: J 79 VAL cc_start: 0.6250 (t) cc_final: 0.5863 (t) REVERT: J 82 GLU cc_start: 0.5002 (OUTLIER) cc_final: 0.4735 (mt-10) REVERT: J 138 ARG cc_start: 0.3127 (mmt-90) cc_final: 0.2339 (tpp-160) REVERT: L 126 GLU cc_start: 0.5557 (mp0) cc_final: 0.5263 (mp0) REVERT: L 181 LYS cc_start: 0.6310 (mttp) cc_final: 0.5750 (mmpt) outliers start: 82 outliers final: 34 residues processed: 406 average time/residue: 0.8272 time to fit residues: 384.7872 Evaluate side-chains 365 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 316 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 166 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 280 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 294 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 325 optimal weight: 5.9990 chunk 202 optimal weight: 0.8980 chunk 224 optimal weight: 0.8980 chunk 260 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN A 469 GLN B 425 ASN B 465 GLN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN C 425 ASN C 571 GLN ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 HIS F 437 GLN F 465 GLN G 17 GLN G 142 ASN G 166 GLN L 130 HIS ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.140983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.106558 restraints weight = 39928.269| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.86 r_work: 0.3124 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30111 Z= 0.206 Angle : 0.594 7.080 40807 Z= 0.303 Chirality : 0.046 0.174 4576 Planarity : 0.005 0.051 5333 Dihedral : 5.530 75.867 4231 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.21 % Allowed : 13.98 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3764 helix: 1.29 (0.13), residues: 1563 sheet: -0.61 (0.21), residues: 568 loop : -0.12 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 130 TYR 0.016 0.002 TYR D 411 PHE 0.018 0.002 PHE C 559 TRP 0.015 0.002 TRP A 119 HIS 0.004 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00491 (30110) covalent geometry : angle 0.59400 (40807) hydrogen bonds : bond 0.04480 ( 1296) hydrogen bonds : angle 4.80784 ( 3711) Misc. bond : bond 0.00030 ( 1) *********************** 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 434 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 335 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8051 (mm-30) REVERT: A 122 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7356 (mtm) REVERT: A 323 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8129 (mpp) REVERT: A 470 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7808 (tm) REVERT: A 491 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7885 (ttp-110) REVERT: A 541 GLN cc_start: 0.7661 (pt0) cc_final: 0.7424 (pt0) REVERT: A 550 ARG cc_start: 0.7414 (mmt180) cc_final: 0.7077 (mmm-85) REVERT: B 32 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: B 120 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8366 (t) REVERT: B 166 TYR cc_start: 0.8000 (m-80) cc_final: 0.7535 (m-80) REVERT: B 459 GLN cc_start: 0.7626 (tp40) cc_final: 0.7295 (tp40) REVERT: B 547 ARG cc_start: 0.5113 (OUTLIER) cc_final: 0.4426 (ttm170) REVERT: B 563 PHE cc_start: 0.7113 (t80) cc_final: 0.6767 (t80) REVERT: B 567 MET cc_start: 0.5314 (OUTLIER) cc_final: 0.4520 (tmm) REVERT: C 1 MET cc_start: 0.7218 (mmt) cc_final: 0.6977 (mmp) REVERT: C 93 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.7396 (mmm-85) REVERT: C 264 ASP cc_start: 0.7749 (m-30) cc_final: 0.7505 (t70) REVERT: C 268 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7670 (mt-10) REVERT: C 344 MET cc_start: 0.8638 (mmt) cc_final: 0.8356 (tpp) REVERT: C 433 SER cc_start: 0.8732 (p) cc_final: 0.8394 (m) REVERT: C 464 LEU cc_start: 0.7730 (mp) cc_final: 0.7512 (mp) REVERT: C 565 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: D 52 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8072 (mm-30) REVERT: D 185 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: D 268 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8053 (ttm170) REVERT: D 280 ARG cc_start: 0.8501 (mtp-110) cc_final: 0.8183 (mtm180) REVERT: D 456 LYS cc_start: 0.7776 (mmmt) cc_final: 0.7346 (mmtt) REVERT: D 466 LYS cc_start: 0.7243 (mtmm) cc_final: 0.6974 (mmmm) REVERT: E 77 GLU cc_start: 0.7609 (pt0) cc_final: 0.6773 (mt-10) REVERT: E 88 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7998 (ttt) REVERT: E 96 ILE cc_start: 0.8433 (tp) cc_final: 0.8157 (tt) REVERT: E 139 ASP cc_start: 0.7912 (m-30) cc_final: 0.7453 (m-30) REVERT: E 174 ARG cc_start: 0.7063 (mmm-85) cc_final: 0.6327 (ttt-90) REVERT: E 216 ARG cc_start: 0.6635 (ttp80) cc_final: 0.5942 (ttp-110) REVERT: E 353 ASP cc_start: 0.7612 (t0) cc_final: 0.7380 (t0) REVERT: E 368 LYS cc_start: 0.6507 (mmmt) cc_final: 0.5175 (tppt) REVERT: E 413 GLN cc_start: 0.5710 (mp10) cc_final: 0.5341 (mp10) REVERT: E 420 ARG cc_start: 0.8155 (mmt180) cc_final: 0.7849 (tpp-160) REVERT: E 443 LEU cc_start: 0.5559 (mp) cc_final: 0.4867 (tp) REVERT: E 452 LYS cc_start: 0.6364 (ptpt) cc_final: 0.5939 (pmtt) REVERT: F 6 LYS cc_start: 0.7939 (tppp) cc_final: 0.7190 (mttp) REVERT: F 275 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: F 302 GLU cc_start: 0.8116 (tt0) cc_final: 0.7803 (mt-10) REVERT: F 373 GLU cc_start: 0.8241 (pm20) cc_final: 0.7977 (pt0) REVERT: F 394 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7872 (mttm) REVERT: F 405 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7932 (p) REVERT: F 406 GLU cc_start: 0.7216 (tp30) cc_final: 0.6685 (tt0) REVERT: F 420 ARG cc_start: 0.8592 (mmm160) cc_final: 0.8236 (mtm110) REVERT: G 9 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7451 (ttt) REVERT: G 38 GLU cc_start: 0.8063 (tp30) cc_final: 0.7688 (tt0) REVERT: G 45 GLU cc_start: 0.6699 (tm-30) cc_final: 0.6315 (tt0) REVERT: G 181 GLN cc_start: 0.8446 (mm-40) cc_final: 0.7877 (mt0) REVERT: H 19 GLU cc_start: 0.3931 (OUTLIER) cc_final: 0.2241 (pp20) REVERT: H 38 GLU cc_start: 0.4346 (mm-30) cc_final: 0.4071 (mt-10) REVERT: H 90 MET cc_start: 0.7065 (tpp) cc_final: 0.6751 (mmm) REVERT: J 66 LEU cc_start: 0.5983 (mt) cc_final: 0.5627 (mp) REVERT: J 82 GLU cc_start: 0.4891 (OUTLIER) cc_final: 0.4683 (mt-10) REVERT: J 138 ARG cc_start: 0.3192 (mmt-90) cc_final: 0.2430 (tpp-160) REVERT: L 126 GLU cc_start: 0.5505 (mp0) cc_final: 0.5203 (mp0) REVERT: L 181 LYS cc_start: 0.6344 (mttp) cc_final: 0.5749 (mmpt) outliers start: 99 outliers final: 45 residues processed: 401 average time/residue: 0.8251 time to fit residues: 379.7410 Evaluate side-chains 371 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 310 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 180 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 39 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 330 optimal weight: 9.9990 chunk 274 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 348 optimal weight: 2.9990 chunk 230 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 469 GLN B 202 ASN B 425 ASN B 469 GLN B 497 GLN B 498 ASN C 425 ASN C 571 GLN ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN L 162 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.108707 restraints weight = 39915.730| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.90 r_work: 0.3153 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30111 Z= 0.124 Angle : 0.523 6.945 40807 Z= 0.266 Chirality : 0.043 0.201 4576 Planarity : 0.004 0.049 5333 Dihedral : 5.219 68.547 4231 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.85 % Allowed : 15.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.14), residues: 3764 helix: 1.56 (0.13), residues: 1561 sheet: -0.62 (0.21), residues: 570 loop : -0.02 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 130 TYR 0.014 0.001 TYR B 513 PHE 0.015 0.001 PHE F 414 TRP 0.014 0.001 TRP A 119 HIS 0.003 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00281 (30110) covalent geometry : angle 0.52276 (40807) hydrogen bonds : bond 0.03801 ( 1296) hydrogen bonds : angle 4.62374 ( 3711) Misc. bond : bond 0.00025 ( 1) *********************** 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 443 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 355 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8003 (mm-30) REVERT: A 122 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7272 (mtm) REVERT: A 323 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8112 (mpp) REVERT: A 344 MET cc_start: 0.8324 (mmm) cc_final: 0.7932 (ttm) REVERT: A 416 ARG cc_start: 0.8163 (mtp-110) cc_final: 0.7896 (mtp85) REVERT: A 470 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7847 (tm) REVERT: A 491 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7842 (ttp-110) REVERT: A 541 GLN cc_start: 0.7708 (pt0) cc_final: 0.7465 (pt0) REVERT: A 550 ARG cc_start: 0.7438 (mmt180) cc_final: 0.7093 (mmm-85) REVERT: B 32 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: B 120 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8292 (t) REVERT: B 133 MET cc_start: 0.7992 (ttm) cc_final: 0.7698 (ttt) REVERT: B 166 TYR cc_start: 0.7933 (m-80) cc_final: 0.7456 (m-80) REVERT: B 200 ASP cc_start: 0.7355 (m-30) cc_final: 0.7127 (m-30) REVERT: B 257 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.7083 (mm-30) REVERT: B 347 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: B 459 GLN cc_start: 0.7641 (tp40) cc_final: 0.7314 (tp40) REVERT: B 491 ARG cc_start: 0.7044 (mtm-85) cc_final: 0.6670 (mtm-85) REVERT: B 547 ARG cc_start: 0.4965 (OUTLIER) cc_final: 0.4532 (ttm-80) REVERT: B 558 GLU cc_start: 0.5640 (OUTLIER) cc_final: 0.4563 (mt-10) REVERT: B 563 PHE cc_start: 0.7100 (t80) cc_final: 0.6684 (t80) REVERT: B 567 MET cc_start: 0.5306 (OUTLIER) cc_final: 0.4607 (tmm) REVERT: C 1 MET cc_start: 0.7202 (mmt) cc_final: 0.6940 (mmp) REVERT: C 93 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.7413 (mmm-85) REVERT: C 156 ARG cc_start: 0.7594 (ttp-110) cc_final: 0.7157 (ttt180) REVERT: C 268 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7533 (mt-10) REVERT: C 433 SER cc_start: 0.8719 (p) cc_final: 0.8365 (m) REVERT: C 464 LEU cc_start: 0.7632 (mp) cc_final: 0.7384 (mp) REVERT: C 513 TYR cc_start: 0.8604 (t80) cc_final: 0.8255 (t80) REVERT: C 565 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7398 (mm-30) REVERT: D 52 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8044 (mm-30) REVERT: D 236 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8303 (mmt180) REVERT: D 280 ARG cc_start: 0.8470 (mtp-110) cc_final: 0.8080 (mtm110) REVERT: D 456 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7370 (mmtt) REVERT: D 466 LYS cc_start: 0.7157 (mtmm) cc_final: 0.6881 (mmmm) REVERT: E 77 GLU cc_start: 0.7537 (pt0) cc_final: 0.6739 (mt-10) REVERT: E 88 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8232 (ttm) REVERT: E 96 ILE cc_start: 0.8319 (tp) cc_final: 0.8070 (tt) REVERT: E 139 ASP cc_start: 0.7804 (m-30) cc_final: 0.7360 (m-30) REVERT: E 174 ARG cc_start: 0.7026 (mmm-85) cc_final: 0.6416 (ttt-90) REVERT: E 216 ARG cc_start: 0.6577 (ttp80) cc_final: 0.5862 (ttp-110) REVERT: E 368 LYS cc_start: 0.6584 (mmmt) cc_final: 0.5141 (tppt) REVERT: E 410 ARG cc_start: 0.5017 (ttp-110) cc_final: 0.3541 (tmm-80) REVERT: E 413 GLN cc_start: 0.5675 (mp10) cc_final: 0.5306 (mp10) REVERT: E 420 ARG cc_start: 0.8074 (mmt180) cc_final: 0.7832 (tpp-160) REVERT: E 452 LYS cc_start: 0.6276 (ptpt) cc_final: 0.5852 (pmtt) REVERT: F 6 LYS cc_start: 0.7866 (tppp) cc_final: 0.7030 (mttp) REVERT: F 275 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: F 302 GLU cc_start: 0.8120 (tt0) cc_final: 0.7819 (mt-10) REVERT: F 373 GLU cc_start: 0.8193 (pm20) cc_final: 0.7926 (pt0) REVERT: F 394 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7946 (mttm) REVERT: F 405 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7809 (p) REVERT: F 406 GLU cc_start: 0.7219 (tp30) cc_final: 0.6700 (tt0) REVERT: F 420 ARG cc_start: 0.8556 (mmm160) cc_final: 0.8196 (mtm110) REVERT: G 38 GLU cc_start: 0.8049 (tp30) cc_final: 0.7785 (tt0) REVERT: G 45 GLU cc_start: 0.6678 (tm-30) cc_final: 0.6254 (tt0) REVERT: G 133 TYR cc_start: 0.6314 (t80) cc_final: 0.6058 (t80) REVERT: G 159 ARG cc_start: 0.7978 (mtm180) cc_final: 0.7667 (mtm-85) REVERT: G 181 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7932 (mt0) REVERT: H 19 GLU cc_start: 0.3915 (OUTLIER) cc_final: 0.2299 (pp20) REVERT: H 38 GLU cc_start: 0.4373 (mm-30) cc_final: 0.4057 (mt-10) REVERT: H 56 GLU cc_start: 0.4446 (pp20) cc_final: 0.4240 (pm20) REVERT: H 90 MET cc_start: 0.7060 (tpp) cc_final: 0.6795 (mmm) REVERT: J 66 LEU cc_start: 0.5957 (mt) cc_final: 0.5596 (mp) REVERT: J 79 VAL cc_start: 0.6435 (t) cc_final: 0.6094 (t) REVERT: J 82 GLU cc_start: 0.4884 (OUTLIER) cc_final: 0.4469 (mt-10) REVERT: L 113 GLU cc_start: 0.5654 (pt0) cc_final: 0.5079 (pp20) REVERT: L 126 GLU cc_start: 0.5531 (mp0) cc_final: 0.5264 (mp0) REVERT: L 181 LYS cc_start: 0.6301 (mttp) cc_final: 0.5736 (mmpt) outliers start: 88 outliers final: 34 residues processed: 412 average time/residue: 0.8445 time to fit residues: 398.6134 Evaluate side-chains 372 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 321 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain L residue 166 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 119 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 236 optimal weight: 0.7980 chunk 283 optimal weight: 9.9990 chunk 238 optimal weight: 3.9990 chunk 349 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 353 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 340 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 202 ASN B 425 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN C 425 ASN C 571 GLN ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN F 363 ASN G 166 GLN ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106118 restraints weight = 39743.592| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.73 r_work: 0.3081 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 30111 Z= 0.307 Angle : 0.683 8.289 40807 Z= 0.349 Chirality : 0.049 0.211 4576 Planarity : 0.006 0.055 5333 Dihedral : 5.759 67.808 4231 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.99 % Allowed : 15.05 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3764 helix: 1.12 (0.13), residues: 1553 sheet: -0.73 (0.21), residues: 570 loop : -0.28 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 105 TYR 0.020 0.002 TYR B 513 PHE 0.020 0.002 PHE C 559 TRP 0.013 0.002 TRP E 440 HIS 0.006 0.002 HIS E 252 Details of bonding type rmsd covalent geometry : bond 0.00740 (30110) covalent geometry : angle 0.68258 (40807) hydrogen bonds : bond 0.05103 ( 1296) hydrogen bonds : angle 4.94596 ( 3711) Misc. bond : bond 0.00017 ( 1) *********************** 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 442 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 319 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8050 (mm-30) REVERT: A 161 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7907 (mmtt) REVERT: A 262 MET cc_start: 0.8760 (mmp) cc_final: 0.8513 (mmm) REVERT: A 323 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8171 (mpp) REVERT: A 344 MET cc_start: 0.8311 (mmm) cc_final: 0.8052 (ttm) REVERT: A 470 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7780 (tm) REVERT: A 491 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7894 (ttp-110) REVERT: A 541 GLN cc_start: 0.7591 (pt0) cc_final: 0.7354 (pt0) REVERT: A 550 ARG cc_start: 0.7513 (mmt180) cc_final: 0.7133 (mmm-85) REVERT: B 133 MET cc_start: 0.8097 (ttm) cc_final: 0.7872 (ttt) REVERT: B 166 TYR cc_start: 0.8068 (m-80) cc_final: 0.7560 (m-80) REVERT: B 347 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: B 397 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: B 459 GLN cc_start: 0.7652 (tp40) cc_final: 0.7374 (tp40) REVERT: B 491 ARG cc_start: 0.7185 (mtm-85) cc_final: 0.6448 (mtm-85) REVERT: B 502 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6599 (pp20) REVERT: B 547 ARG cc_start: 0.5004 (OUTLIER) cc_final: 0.4366 (ttm170) REVERT: B 558 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.4712 (mt-10) REVERT: B 563 PHE cc_start: 0.7146 (t80) cc_final: 0.6893 (t80) REVERT: B 567 MET cc_start: 0.5386 (OUTLIER) cc_final: 0.4588 (tmm) REVERT: C 1 MET cc_start: 0.7431 (mmt) cc_final: 0.7131 (mmp) REVERT: C 93 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7414 (mmm-85) REVERT: C 156 ARG cc_start: 0.7747 (ttp-110) cc_final: 0.7332 (ttt180) REVERT: C 344 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8276 (tpp) REVERT: C 433 SER cc_start: 0.8768 (p) cc_final: 0.8434 (m) REVERT: C 513 TYR cc_start: 0.8683 (t80) cc_final: 0.8323 (t80) REVERT: D 52 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8123 (mm-30) REVERT: D 268 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8051 (ttm170) REVERT: D 280 ARG cc_start: 0.8531 (mtp-110) cc_final: 0.8214 (mtm180) REVERT: E 3 LEU cc_start: 0.5057 (mp) cc_final: 0.4847 (mp) REVERT: E 77 GLU cc_start: 0.7756 (pt0) cc_final: 0.6897 (mt-10) REVERT: E 88 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7975 (ttt) REVERT: E 96 ILE cc_start: 0.8457 (tp) cc_final: 0.8196 (tt) REVERT: E 139 ASP cc_start: 0.8002 (m-30) cc_final: 0.7534 (m-30) REVERT: E 174 ARG cc_start: 0.7150 (mmm-85) cc_final: 0.6458 (ttt-90) REVERT: E 216 ARG cc_start: 0.6762 (ttp80) cc_final: 0.5932 (ttp-110) REVERT: E 313 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8576 (mt) REVERT: E 368 LYS cc_start: 0.6609 (mmmt) cc_final: 0.5156 (tppt) REVERT: E 413 GLN cc_start: 0.5801 (mp10) cc_final: 0.5359 (mp10) REVERT: E 452 LYS cc_start: 0.6489 (ptpt) cc_final: 0.5925 (pttp) REVERT: F 6 LYS cc_start: 0.7882 (tppp) cc_final: 0.7223 (mttp) REVERT: F 275 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: F 302 GLU cc_start: 0.8165 (tt0) cc_final: 0.7844 (mt-10) REVERT: F 373 GLU cc_start: 0.8266 (pm20) cc_final: 0.8016 (pt0) REVERT: F 394 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7944 (mttm) REVERT: F 406 GLU cc_start: 0.7274 (tp30) cc_final: 0.6838 (tt0) REVERT: F 420 ARG cc_start: 0.8635 (mmm160) cc_final: 0.8297 (mtt90) REVERT: F 467 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.5867 (mt) REVERT: G 9 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7891 (ttp) REVERT: G 38 GLU cc_start: 0.8112 (tp30) cc_final: 0.7868 (tt0) REVERT: G 159 ARG cc_start: 0.7994 (mtm180) cc_final: 0.7709 (ttp-170) REVERT: G 181 GLN cc_start: 0.8492 (mm-40) cc_final: 0.7961 (mt0) REVERT: H 38 GLU cc_start: 0.4409 (mm-30) cc_final: 0.4128 (mt-10) REVERT: H 63 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.4695 (pmm) REVERT: H 90 MET cc_start: 0.7074 (tpp) cc_final: 0.6785 (mmm) REVERT: I 84 LEU cc_start: 0.3956 (OUTLIER) cc_final: 0.3627 (mm) REVERT: J 66 LEU cc_start: 0.6100 (mt) cc_final: 0.5738 (mp) REVERT: J 82 GLU cc_start: 0.4931 (OUTLIER) cc_final: 0.4374 (mt-10) REVERT: L 126 GLU cc_start: 0.5576 (mp0) cc_final: 0.5310 (mp0) REVERT: L 181 LYS cc_start: 0.6391 (mttp) cc_final: 0.5807 (mmpt) outliers start: 123 outliers final: 48 residues processed: 404 average time/residue: 0.8248 time to fit residues: 383.3598 Evaluate side-chains 370 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 304 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 180 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 276 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 76 optimal weight: 0.0270 chunk 228 optimal weight: 0.5980 chunk 213 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 202 ASN B 425 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN C 425 ASN C 571 GLN ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 ASN F 437 GLN F 465 GLN G 22 GLN L 162 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.143901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.109955 restraints weight = 39883.454| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.92 r_work: 0.3170 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30111 Z= 0.106 Angle : 0.524 8.533 40807 Z= 0.265 Chirality : 0.043 0.155 4576 Planarity : 0.004 0.052 5333 Dihedral : 5.175 60.556 4231 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.43 % Allowed : 16.74 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 3764 helix: 1.56 (0.14), residues: 1556 sheet: -0.69 (0.21), residues: 573 loop : -0.09 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 130 TYR 0.016 0.001 TYR B 513 PHE 0.014 0.001 PHE F 414 TRP 0.019 0.001 TRP B 424 HIS 0.002 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00230 (30110) covalent geometry : angle 0.52370 (40807) hydrogen bonds : bond 0.03592 ( 1296) hydrogen bonds : angle 4.60520 ( 3711) Misc. bond : bond 0.00032 ( 1) *********************** 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 418 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 343 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8025 (mm-30) REVERT: A 161 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7882 (mmtt) REVERT: A 323 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8063 (mpp) REVERT: A 344 MET cc_start: 0.8261 (mmm) cc_final: 0.7955 (ttm) REVERT: A 416 ARG cc_start: 0.8138 (mtp-110) cc_final: 0.7879 (mtp85) REVERT: A 491 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7843 (ttp-110) REVERT: A 541 GLN cc_start: 0.7589 (pt0) cc_final: 0.7347 (pt0) REVERT: A 550 ARG cc_start: 0.7451 (mmt180) cc_final: 0.7104 (mmm-85) REVERT: B 32 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: B 120 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8246 (t) REVERT: B 133 MET cc_start: 0.8009 (ttm) cc_final: 0.7808 (ttt) REVERT: B 166 TYR cc_start: 0.7897 (m-80) cc_final: 0.7425 (m-80) REVERT: B 200 ASP cc_start: 0.7313 (m-30) cc_final: 0.7095 (m-30) REVERT: B 257 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7103 (mm-30) REVERT: B 347 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: B 459 GLN cc_start: 0.7659 (tp40) cc_final: 0.7328 (tp40) REVERT: B 491 ARG cc_start: 0.6918 (mtm-85) cc_final: 0.6370 (mtm-85) REVERT: B 502 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6632 (pp20) REVERT: B 547 ARG cc_start: 0.5035 (OUTLIER) cc_final: 0.4707 (ttm-80) REVERT: B 563 PHE cc_start: 0.7113 (t80) cc_final: 0.6721 (t80) REVERT: C 1 MET cc_start: 0.7296 (mmt) cc_final: 0.6969 (mmp) REVERT: C 93 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.7424 (mmm-85) REVERT: C 156 ARG cc_start: 0.7592 (ttp-110) cc_final: 0.7146 (ttt180) REVERT: C 423 ASN cc_start: 0.8878 (t0) cc_final: 0.8545 (t0) REVERT: C 433 SER cc_start: 0.8721 (p) cc_final: 0.8345 (m) REVERT: C 464 LEU cc_start: 0.7648 (mp) cc_final: 0.7359 (mp) REVERT: C 480 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6422 (mt-10) REVERT: C 513 TYR cc_start: 0.8601 (t80) cc_final: 0.8280 (t80) REVERT: C 565 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7413 (mm-30) REVERT: D 52 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7994 (mm-30) REVERT: D 280 ARG cc_start: 0.8474 (mtp-110) cc_final: 0.8096 (mtm110) REVERT: E 77 GLU cc_start: 0.7598 (pt0) cc_final: 0.6751 (mt-10) REVERT: E 96 ILE cc_start: 0.8282 (tp) cc_final: 0.8043 (tt) REVERT: E 139 ASP cc_start: 0.7790 (m-30) cc_final: 0.7330 (m-30) REVERT: E 174 ARG cc_start: 0.7134 (mmm-85) cc_final: 0.6587 (ttt-90) REVERT: E 216 ARG cc_start: 0.6597 (ttp80) cc_final: 0.5917 (ttp-110) REVERT: E 368 LYS cc_start: 0.6591 (mmmt) cc_final: 0.5132 (tppt) REVERT: E 372 ARG cc_start: 0.5296 (OUTLIER) cc_final: 0.5052 (ttt-90) REVERT: E 445 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.5937 (tmm) REVERT: E 452 LYS cc_start: 0.6478 (ptpt) cc_final: 0.5997 (pttp) REVERT: F 6 LYS cc_start: 0.7539 (tppp) cc_final: 0.6941 (mttp) REVERT: F 275 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: F 302 GLU cc_start: 0.8112 (tt0) cc_final: 0.7786 (mt-10) REVERT: F 373 GLU cc_start: 0.8153 (pm20) cc_final: 0.7911 (pt0) REVERT: F 394 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7785 (mtmt) REVERT: F 420 ARG cc_start: 0.8566 (mmm160) cc_final: 0.8248 (mtm110) REVERT: G 9 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7284 (ttt) REVERT: G 38 GLU cc_start: 0.8097 (tp30) cc_final: 0.7672 (tt0) REVERT: G 181 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7941 (mt0) REVERT: G 205 GLU cc_start: 0.4112 (tm-30) cc_final: 0.3285 (tt0) REVERT: H 38 GLU cc_start: 0.4224 (mm-30) cc_final: 0.4014 (mt-10) REVERT: H 63 MET cc_start: 0.5343 (OUTLIER) cc_final: 0.4614 (pmm) REVERT: J 66 LEU cc_start: 0.5986 (mt) cc_final: 0.5629 (mp) REVERT: J 79 VAL cc_start: 0.6122 (t) cc_final: 0.5875 (t) REVERT: J 82 GLU cc_start: 0.4695 (OUTLIER) cc_final: 0.4270 (mt-10) REVERT: L 113 GLU cc_start: 0.5411 (pt0) cc_final: 0.4870 (pp20) REVERT: L 126 GLU cc_start: 0.5602 (mp0) cc_final: 0.5338 (mp0) REVERT: L 181 LYS cc_start: 0.6300 (mttp) cc_final: 0.5735 (mmpt) outliers start: 75 outliers final: 29 residues processed: 389 average time/residue: 0.8284 time to fit residues: 369.5929 Evaluate side-chains 360 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 317 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 445 MET Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain L residue 166 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 260 optimal weight: 9.9990 chunk 359 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 182 optimal weight: 8.9990 chunk 265 optimal weight: 0.8980 chunk 348 optimal weight: 6.9990 chunk 237 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 chunk 333 optimal weight: 20.0000 chunk 295 optimal weight: 4.9990 chunk 350 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 202 ASN B 425 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN C 316 GLN C 425 ASN C 571 GLN ** E 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN F 437 GLN F 465 GLN G 22 GLN G 166 GLN L 130 HIS L 162 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.141631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107850 restraints weight = 39776.644| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.76 r_work: 0.3110 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30111 Z= 0.212 Angle : 0.603 9.870 40807 Z= 0.306 Chirality : 0.046 0.190 4576 Planarity : 0.005 0.047 5333 Dihedral : 5.440 62.098 4231 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.76 % Allowed : 17.35 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3764 helix: 1.41 (0.13), residues: 1547 sheet: -0.76 (0.21), residues: 583 loop : -0.14 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 130 TYR 0.018 0.002 TYR B 513 PHE 0.019 0.002 PHE C 559 TRP 0.012 0.002 TRP B 424 HIS 0.006 0.001 HIS B 501 Details of bonding type rmsd covalent geometry : bond 0.00504 (30110) covalent geometry : angle 0.60288 (40807) hydrogen bonds : bond 0.04376 ( 1296) hydrogen bonds : angle 4.75251 ( 3711) Misc. bond : bond 0.00028 ( 1) *********************** 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 395 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 310 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8068 (mm-30) REVERT: A 161 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7870 (mmtt) REVERT: A 323 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8165 (mpp) REVERT: A 344 MET cc_start: 0.8272 (mmm) cc_final: 0.8052 (ttm) REVERT: A 491 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7891 (ttp-110) REVERT: A 541 GLN cc_start: 0.7584 (pt0) cc_final: 0.7346 (pt0) REVERT: A 550 ARG cc_start: 0.7472 (mmt180) cc_final: 0.7127 (mmm-85) REVERT: B 32 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: B 120 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8328 (t) REVERT: B 257 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7057 (mm-30) REVERT: B 347 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: B 397 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: B 459 GLN cc_start: 0.7677 (tp40) cc_final: 0.7384 (tp40) REVERT: B 491 ARG cc_start: 0.7049 (mtm-85) cc_final: 0.6448 (mtm-85) REVERT: B 563 PHE cc_start: 0.7102 (t80) cc_final: 0.6797 (t80) REVERT: C 1 MET cc_start: 0.7418 (mmt) cc_final: 0.7093 (mmp) REVERT: C 93 ARG cc_start: 0.8289 (mmm-85) cc_final: 0.7444 (mmm-85) REVERT: C 156 ARG cc_start: 0.7650 (ttp-110) cc_final: 0.7197 (ttt180) REVERT: C 433 SER cc_start: 0.8753 (p) cc_final: 0.8411 (m) REVERT: C 464 LEU cc_start: 0.7717 (mp) cc_final: 0.7449 (mp) REVERT: C 480 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6506 (mt-10) REVERT: D 52 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8087 (mm-30) REVERT: D 268 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8075 (ttm170) REVERT: D 280 ARG cc_start: 0.8498 (mtp-110) cc_final: 0.8083 (mtm110) REVERT: D 314 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8699 (pt) REVERT: E 77 GLU cc_start: 0.7709 (pt0) cc_final: 0.6872 (mt-10) REVERT: E 96 ILE cc_start: 0.8378 (tp) cc_final: 0.8126 (tt) REVERT: E 139 ASP cc_start: 0.7944 (m-30) cc_final: 0.7491 (m-30) REVERT: E 174 ARG cc_start: 0.7189 (mmm-85) cc_final: 0.6491 (ttt-90) REVERT: E 313 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8575 (mt) REVERT: E 368 LYS cc_start: 0.6578 (mmmt) cc_final: 0.5081 (tppt) REVERT: E 372 ARG cc_start: 0.5192 (OUTLIER) cc_final: 0.4911 (ttt-90) REVERT: F 6 LYS cc_start: 0.7733 (tppp) cc_final: 0.7112 (mttp) REVERT: F 275 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: F 302 GLU cc_start: 0.8156 (tt0) cc_final: 0.7828 (mt-10) REVERT: F 373 GLU cc_start: 0.8244 (pm20) cc_final: 0.7983 (pt0) REVERT: F 394 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7985 (mttm) REVERT: F 406 GLU cc_start: 0.7290 (tp30) cc_final: 0.6847 (tt0) REVERT: F 420 ARG cc_start: 0.8638 (mmm160) cc_final: 0.8292 (mtt90) REVERT: G 9 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7816 (ttp) REVERT: G 38 GLU cc_start: 0.8099 (tp30) cc_final: 0.7807 (tp30) REVERT: G 45 GLU cc_start: 0.6785 (tm-30) cc_final: 0.6384 (tt0) REVERT: G 159 ARG cc_start: 0.7991 (mtm180) cc_final: 0.7706 (ttp-170) REVERT: G 181 GLN cc_start: 0.8473 (mm-40) cc_final: 0.7971 (mt0) REVERT: G 205 GLU cc_start: 0.4169 (tm-30) cc_final: 0.3305 (tt0) REVERT: H 63 MET cc_start: 0.5461 (OUTLIER) cc_final: 0.4641 (pmm) REVERT: H 90 MET cc_start: 0.6378 (mmm) cc_final: 0.5702 (mmm) REVERT: H 92 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7370 (pt0) REVERT: J 66 LEU cc_start: 0.6082 (mt) cc_final: 0.5700 (mp) REVERT: L 126 GLU cc_start: 0.5548 (mp0) cc_final: 0.5298 (mp0) REVERT: L 181 LYS cc_start: 0.6325 (mttp) cc_final: 0.5740 (mmpt) outliers start: 85 outliers final: 39 residues processed: 366 average time/residue: 0.7643 time to fit residues: 321.7382 Evaluate side-chains 357 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 303 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 166 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 175 optimal weight: 5.9990 chunk 364 optimal weight: 8.9990 chunk 153 optimal weight: 0.0670 chunk 123 optimal weight: 0.9980 chunk 305 optimal weight: 0.7980 chunk 190 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 341 optimal weight: 20.0000 chunk 301 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 202 ASN B 425 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN C 571 GLN E 428 GLN G 142 ASN L 162 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.110008 restraints weight = 39794.312| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.88 r_work: 0.3164 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30111 Z= 0.109 Angle : 0.529 10.379 40807 Z= 0.267 Chirality : 0.043 0.153 4576 Planarity : 0.004 0.050 5333 Dihedral : 5.102 58.651 4231 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.01 % Allowed : 18.10 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.14), residues: 3764 helix: 1.67 (0.14), residues: 1544 sheet: -0.74 (0.21), residues: 578 loop : -0.02 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 130 TYR 0.017 0.001 TYR B 513 PHE 0.015 0.001 PHE F 414 TRP 0.016 0.001 TRP A 119 HIS 0.002 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00243 (30110) covalent geometry : angle 0.52900 (40807) hydrogen bonds : bond 0.03535 ( 1296) hydrogen bonds : angle 4.55471 ( 3711) Misc. bond : bond 0.00034 ( 1) *********************** 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 399 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 337 time to evaluate : 0.876 Fit side-chains REVERT: A 32 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8031 (mm-30) REVERT: A 161 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7880 (mmtt) REVERT: A 261 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: A 323 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8086 (mpp) REVERT: A 344 MET cc_start: 0.8219 (mmm) cc_final: 0.7990 (ttm) REVERT: A 416 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7869 (mtp85) REVERT: A 491 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7875 (ttp-110) REVERT: A 541 GLN cc_start: 0.7596 (pt0) cc_final: 0.7363 (pt0) REVERT: A 550 ARG cc_start: 0.7407 (mmt180) cc_final: 0.7092 (mmm-85) REVERT: B 32 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: B 120 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8254 (t) REVERT: B 166 TYR cc_start: 0.8011 (m-80) cc_final: 0.7543 (m-80) REVERT: B 200 ASP cc_start: 0.7301 (m-30) cc_final: 0.7092 (m-30) REVERT: B 257 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7092 (mm-30) REVERT: B 347 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7455 (mt-10) REVERT: B 392 SER cc_start: 0.7591 (m) cc_final: 0.6900 (t) REVERT: B 459 GLN cc_start: 0.7657 (tp40) cc_final: 0.7324 (tp40) REVERT: B 491 ARG cc_start: 0.6939 (mtm-85) cc_final: 0.6525 (mtm-85) REVERT: B 563 PHE cc_start: 0.7146 (t80) cc_final: 0.6798 (t80) REVERT: C 1 MET cc_start: 0.7278 (mmt) cc_final: 0.6958 (mmp) REVERT: C 93 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.7434 (mmm-85) REVERT: C 156 ARG cc_start: 0.7615 (ttp-110) cc_final: 0.7150 (ttt180) REVERT: C 338 SER cc_start: 0.8937 (t) cc_final: 0.8667 (m) REVERT: C 423 ASN cc_start: 0.8897 (t0) cc_final: 0.8538 (t0) REVERT: C 433 SER cc_start: 0.8720 (p) cc_final: 0.8361 (m) REVERT: C 464 LEU cc_start: 0.7576 (mp) cc_final: 0.7265 (mp) REVERT: C 480 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6436 (mt-10) REVERT: C 513 TYR cc_start: 0.8616 (t80) cc_final: 0.8304 (t80) REVERT: C 565 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7347 (mm-30) REVERT: D 52 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8074 (mm-30) REVERT: D 280 ARG cc_start: 0.8465 (mtp-110) cc_final: 0.8089 (mtm110) REVERT: E 77 GLU cc_start: 0.7630 (pt0) cc_final: 0.6762 (mt-10) REVERT: E 96 ILE cc_start: 0.8280 (tp) cc_final: 0.8035 (tt) REVERT: E 139 ASP cc_start: 0.7782 (m-30) cc_final: 0.7307 (m-30) REVERT: E 174 ARG cc_start: 0.7168 (mmm-85) cc_final: 0.6468 (ttt-90) REVERT: E 216 ARG cc_start: 0.6580 (ttp80) cc_final: 0.5922 (ttp-110) REVERT: E 368 LYS cc_start: 0.6595 (mmmt) cc_final: 0.5221 (tppt) REVERT: E 372 ARG cc_start: 0.5241 (OUTLIER) cc_final: 0.4924 (ttt-90) REVERT: E 410 ARG cc_start: 0.5039 (ttp-110) cc_final: 0.3557 (tmm-80) REVERT: E 413 GLN cc_start: 0.5853 (mp10) cc_final: 0.5496 (mp10) REVERT: F 6 LYS cc_start: 0.7575 (tppp) cc_final: 0.6967 (mttp) REVERT: F 275 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: F 302 GLU cc_start: 0.8118 (tt0) cc_final: 0.7798 (mt-10) REVERT: F 373 GLU cc_start: 0.8169 (pm20) cc_final: 0.7928 (pt0) REVERT: F 394 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7798 (mtmt) REVERT: F 406 GLU cc_start: 0.7244 (tp30) cc_final: 0.6841 (tt0) REVERT: F 420 ARG cc_start: 0.8553 (mmm160) cc_final: 0.8256 (mtm110) REVERT: G 9 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7318 (ttt) REVERT: G 38 GLU cc_start: 0.8094 (tp30) cc_final: 0.7849 (tt0) REVERT: G 159 ARG cc_start: 0.7938 (mtm180) cc_final: 0.7651 (mtm-85) REVERT: G 181 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7960 (mt0) REVERT: G 205 GLU cc_start: 0.4059 (tm-30) cc_final: 0.3301 (tt0) REVERT: H 63 MET cc_start: 0.5329 (OUTLIER) cc_final: 0.4497 (pmm) REVERT: H 90 MET cc_start: 0.6391 (mmm) cc_final: 0.5701 (mmm) REVERT: H 92 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7035 (pt0) REVERT: J 66 LEU cc_start: 0.5989 (mt) cc_final: 0.5616 (mp) REVERT: L 113 GLU cc_start: 0.5542 (pt0) cc_final: 0.5021 (pp20) REVERT: L 126 GLU cc_start: 0.5631 (mp0) cc_final: 0.5330 (mp0) REVERT: L 181 LYS cc_start: 0.6318 (mttp) cc_final: 0.5745 (mmpt) outliers start: 62 outliers final: 33 residues processed: 378 average time/residue: 0.7590 time to fit residues: 329.2197 Evaluate side-chains 360 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 315 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 166 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 270 optimal weight: 4.9990 chunk 240 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 192 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 271 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 216 optimal weight: 0.2980 chunk 252 optimal weight: 0.0040 chunk 140 optimal weight: 0.9990 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS A 469 GLN B 202 ASN B 425 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN C 571 GLN F 363 ASN G 22 GLN L 162 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109126 restraints weight = 39900.136| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.84 r_work: 0.3162 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30111 Z= 0.125 Angle : 0.543 10.130 40807 Z= 0.273 Chirality : 0.043 0.157 4576 Planarity : 0.004 0.056 5333 Dihedral : 5.055 55.114 4231 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.72 % Allowed : 18.78 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3764 helix: 1.72 (0.13), residues: 1543 sheet: -0.70 (0.21), residues: 578 loop : -0.01 (0.16), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 156 TYR 0.017 0.001 TYR B 513 PHE 0.016 0.001 PHE C 559 TRP 0.014 0.001 TRP B 424 HIS 0.003 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00289 (30110) covalent geometry : angle 0.54272 (40807) hydrogen bonds : bond 0.03665 ( 1296) hydrogen bonds : angle 4.53983 ( 3711) Misc. bond : bond 0.00020 ( 1) ********************** 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 374 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 321 time to evaluate : 1.210 Fit side-chains REVERT: A 32 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8032 (mm-30) REVERT: A 161 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7874 (mmtt) REVERT: A 261 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: A 323 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8071 (mpp) REVERT: A 344 MET cc_start: 0.8235 (mmm) cc_final: 0.7971 (ttm) REVERT: A 491 ARG cc_start: 0.8122 (mtm-85) cc_final: 0.7852 (ttp-110) REVERT: A 541 GLN cc_start: 0.7664 (pt0) cc_final: 0.7436 (pt0) REVERT: A 550 ARG cc_start: 0.7443 (mmt180) cc_final: 0.7121 (mmm-85) REVERT: B 32 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7767 (mt-10) REVERT: B 120 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8261 (t) REVERT: B 257 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.7040 (mm-30) REVERT: B 392 SER cc_start: 0.7554 (m) cc_final: 0.6869 (t) REVERT: B 459 GLN cc_start: 0.7655 (tp40) cc_final: 0.7317 (tp40) REVERT: B 491 ARG cc_start: 0.6928 (mtm-85) cc_final: 0.6493 (mtm-85) REVERT: B 563 PHE cc_start: 0.7203 (t80) cc_final: 0.6866 (t80) REVERT: C 1 MET cc_start: 0.7324 (mmt) cc_final: 0.6998 (mmp) REVERT: C 93 ARG cc_start: 0.8270 (mmm-85) cc_final: 0.7404 (mmm-85) REVERT: C 156 ARG cc_start: 0.7623 (ttp-110) cc_final: 0.7393 (ttm-80) REVERT: C 338 SER cc_start: 0.8942 (t) cc_final: 0.8666 (m) REVERT: C 433 SER cc_start: 0.8726 (p) cc_final: 0.8409 (m) REVERT: C 464 LEU cc_start: 0.7568 (mp) cc_final: 0.7296 (mp) REVERT: C 480 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6465 (mt-10) REVERT: C 513 TYR cc_start: 0.8654 (t80) cc_final: 0.8411 (t80) REVERT: C 565 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7304 (mm-30) REVERT: D 52 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8027 (mm-30) REVERT: D 280 ARG cc_start: 0.8459 (mtp-110) cc_final: 0.8072 (mtm110) REVERT: E 77 GLU cc_start: 0.7648 (pt0) cc_final: 0.6773 (mt-10) REVERT: E 139 ASP cc_start: 0.7822 (m-30) cc_final: 0.7345 (m-30) REVERT: E 174 ARG cc_start: 0.7196 (mmm-85) cc_final: 0.6518 (ttt-90) REVERT: E 216 ARG cc_start: 0.6611 (ttp80) cc_final: 0.5944 (ttp-110) REVERT: E 368 LYS cc_start: 0.6612 (mmmt) cc_final: 0.5196 (tppt) REVERT: E 372 ARG cc_start: 0.5199 (OUTLIER) cc_final: 0.4894 (ttt-90) REVERT: E 410 ARG cc_start: 0.5042 (ttp-110) cc_final: 0.3740 (tmm-80) REVERT: E 413 GLN cc_start: 0.5829 (mp10) cc_final: 0.5524 (mp10) REVERT: E 442 LEU cc_start: 0.6156 (mt) cc_final: 0.5649 (mm) REVERT: F 6 LYS cc_start: 0.7559 (tppp) cc_final: 0.6954 (mttp) REVERT: F 275 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: F 302 GLU cc_start: 0.8088 (tt0) cc_final: 0.7758 (mt-10) REVERT: F 373 GLU cc_start: 0.8153 (pm20) cc_final: 0.7898 (pt0) REVERT: F 394 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7785 (mtmt) REVERT: F 406 GLU cc_start: 0.7277 (tp30) cc_final: 0.6821 (tt0) REVERT: F 420 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8251 (mtm110) REVERT: G 38 GLU cc_start: 0.8094 (tp30) cc_final: 0.7845 (tt0) REVERT: G 45 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6328 (tt0) REVERT: G 159 ARG cc_start: 0.7926 (mtm180) cc_final: 0.7634 (mtm-85) REVERT: G 181 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7896 (mt0) REVERT: G 205 GLU cc_start: 0.4032 (tm-30) cc_final: 0.3279 (tt0) REVERT: H 63 MET cc_start: 0.5308 (OUTLIER) cc_final: 0.4473 (pmm) REVERT: H 90 MET cc_start: 0.6382 (mmm) cc_final: 0.5689 (mmm) REVERT: H 92 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7048 (pt0) REVERT: J 66 LEU cc_start: 0.5999 (mt) cc_final: 0.5623 (mp) REVERT: L 113 GLU cc_start: 0.5571 (pt0) cc_final: 0.5018 (pp20) REVERT: L 126 GLU cc_start: 0.5632 (mp0) cc_final: 0.5334 (mp0) REVERT: L 181 LYS cc_start: 0.6304 (mttp) cc_final: 0.5733 (mmpt) outliers start: 53 outliers final: 35 residues processed: 355 average time/residue: 0.7770 time to fit residues: 316.5852 Evaluate side-chains 356 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 311 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain L residue 166 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 267 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 362 optimal weight: 0.7980 chunk 225 optimal weight: 10.0000 chunk 356 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 358 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 425 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN C 571 GLN G 22 GLN L 162 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.142251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.108764 restraints weight = 40024.850| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.02 r_work: 0.3142 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30111 Z= 0.170 Angle : 0.580 10.273 40807 Z= 0.293 Chirality : 0.045 0.190 4576 Planarity : 0.005 0.065 5333 Dihedral : 5.194 59.191 4231 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.08 % Allowed : 18.65 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.14), residues: 3764 helix: 1.59 (0.13), residues: 1545 sheet: -0.74 (0.21), residues: 582 loop : -0.05 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 156 TYR 0.018 0.001 TYR B 513 PHE 0.016 0.002 PHE C 559 TRP 0.014 0.001 TRP B 424 HIS 0.004 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00404 (30110) covalent geometry : angle 0.57976 (40807) hydrogen bonds : bond 0.04012 ( 1296) hydrogen bonds : angle 4.62236 ( 3711) Misc. bond : bond 0.00015 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11624.81 seconds wall clock time: 198 minutes 13.55 seconds (11893.55 seconds total)