Starting phenix.real_space_refine on Wed Jun 25 03:49:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gxz_34366/06_2025/8gxz_34366.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gxz_34366/06_2025/8gxz_34366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gxz_34366/06_2025/8gxz_34366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gxz_34366/06_2025/8gxz_34366.map" model { file = "/net/cci-nas-00/data/ceres_data/8gxz_34366/06_2025/8gxz_34366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gxz_34366/06_2025/8gxz_34366.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 18715 2.51 5 N 5121 2.21 5 O 5555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29499 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.80, per 1000 atoms: 0.60 Number of scatterers: 29499 At special positions: 0 Unit cell: (147.42, 148.23, 171.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 3 15.00 Mg 1 11.99 O 5555 8.00 N 5121 7.00 C 18715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.52 Conformation dependent library (CDL) restraints added in 4.0 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 29 sheets defined 47.9% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 4.427A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 317 removed outlier: 4.403A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.921A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.508A pdb=" N GLY A 389 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.716A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.696A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'A' and resid 535 through 540 Processing helix chain 'A' and resid 544 through 551 Processing helix chain 'A' and resid 558 through 577 removed outlier: 3.912A pdb=" N LEU A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 317 removed outlier: 4.760A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.501A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 464 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 477 through 494 removed outlier: 3.503A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 533 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 543 through 550 Processing helix chain 'B' and resid 558 through 576 removed outlier: 4.261A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 572 " --> pdb=" O LYS B 568 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.039A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.254A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 3.986A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 364 removed outlier: 3.776A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 401 Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.565A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.566A pdb=" N ASP C 436 " --> pdb=" O THR C 432 " (cutoff:3.500A) Proline residue: C 437 - end of helix removed outlier: 3.584A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 472 removed outlier: 3.992A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.515A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 549 removed outlier: 3.872A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 554 Processing helix chain 'C' and resid 558 through 578 removed outlier: 4.096A pdb=" N GLU C 564 " --> pdb=" O PRO C 560 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS C 575 " --> pdb=" O GLN C 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 175 through 178 Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.161A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.520A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.742A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.819A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 404 Processing helix chain 'D' and resid 405 through 422 removed outlier: 3.593A pdb=" N ASP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.645A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 467 through 472 Processing helix chain 'E' and resid 23 through 27 removed outlier: 4.590A pdb=" N ASP E 26 " --> pdb=" O ASN E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.623A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.516A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 179 removed outlier: 3.604A pdb=" N GLY E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 210 Processing helix chain 'E' and resid 212 through 215 Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.815A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.650A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 removed outlier: 3.557A pdb=" N ILE E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.557A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL E 366 " --> pdb=" O MET E 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 361 through 366' Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.569A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 404 removed outlier: 3.791A pdb=" N LEU E 404 " --> pdb=" O GLU E 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 401 through 404' Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.511A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 89' Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 179 removed outlier: 3.551A pdb=" N SER F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 212 through 215 removed outlier: 3.831A pdb=" N SER F 215 " --> pdb=" O GLY F 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 212 through 215' Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.669A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.541A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 361 through 365 Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.596A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.577A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 471 removed outlier: 3.970A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.726A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.595A pdb=" N LEU G 113 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 167 removed outlier: 3.822A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 209 Processing helix chain 'H' and resid 6 through 16 Processing helix chain 'H' and resid 25 through 39 Processing helix chain 'H' and resid 54 through 59 Processing helix chain 'H' and resid 59 through 66 Processing helix chain 'H' and resid 78 through 83 Processing helix chain 'H' and resid 85 through 98 Processing helix chain 'I' and resid 82 through 106 removed outlier: 3.568A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 62 through 94 Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.807A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.282A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 3.741A pdb=" N LEU J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP J 172 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG J 173 " --> pdb=" O ALA J 169 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 83 No H-bonds generated for 'chain 'K' and resid 81 through 83' Processing helix chain 'K' and resid 84 through 119 removed outlier: 3.791A pdb=" N TYR K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG K 100 " --> pdb=" O ALA K 96 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 93 removed outlier: 3.871A pdb=" N LEU L 66 " --> pdb=" O SER L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 128 through 130 No H-bonds generated for 'chain 'L' and resid 128 through 130' Processing helix chain 'L' and resid 131 through 139 Processing helix chain 'L' and resid 166 through 187 removed outlier: 3.799A pdb=" N ASP L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG L 173 " --> pdb=" O ALA L 169 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.574A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.659A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 6.144A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 6.467A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 5.590A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 6.087A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 21 current: chain 'F' and resid 42 through 51 removed outlier: 5.969A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 55 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 141 through 142 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 142 current: chain 'L' and resid 161 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 84 current: chain 'A' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 290 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 148 removed outlier: 3.667A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.924A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 288 current: chain 'B' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 148 removed outlier: 3.827A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.510A pdb=" N VAL B 173 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB2, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 382 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 117 through 119 Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.682A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL C 160 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL C 172 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.658A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AB7, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.564A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 92 through 93 removed outlier: 5.795A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL D 253 " --> pdb=" O THR D 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.533A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.515A pdb=" N LEU D 314 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AC3, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.583A pdb=" N MET E 194 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.560A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 313 through 315 Processing sheet with id=AC6, first strand: chain 'F' and resid 81 through 82 Processing sheet with id=AC7, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.587A pdb=" N ARG F 91 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU F 221 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE F 93 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.598A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR F 172 " --> pdb=" O GLN F 132 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 313 through 315 removed outlier: 6.480A pdb=" N ILE F 337 " --> pdb=" O PHE F 153 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 91 through 96 removed outlier: 3.508A pdb=" N SER G 99 " --> pdb=" O VAL G 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.800A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1303 hydrogen bonds defined for protein. 3738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.97 Time building geometry restraints manager: 9.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9960 1.34 - 1.46: 4580 1.46 - 1.57: 15313 1.57 - 1.69: 5 1.69 - 1.81: 194 Bond restraints: 30052 Sorted by residual: bond pdb=" CB ARG C 95 " pdb=" CG ARG C 95 " ideal model delta sigma weight residual 1.520 1.399 0.121 3.00e-02 1.11e+03 1.62e+01 bond pdb=" CG ARG C 95 " pdb=" CD ARG C 95 " ideal model delta sigma weight residual 1.520 1.405 0.115 3.00e-02 1.11e+03 1.47e+01 bond pdb=" O4 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.455 0.044 2.00e-02 2.50e+03 4.90e+00 bond pdb=" O3 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.455 0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" CA ARG C 95 " pdb=" CB ARG C 95 " ideal model delta sigma weight residual 1.531 1.498 0.034 1.57e-02 4.06e+03 4.60e+00 ... (remaining 30047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 39887 1.50 - 3.00: 628 3.00 - 4.50: 185 4.50 - 6.00: 13 6.00 - 7.50: 3 Bond angle restraints: 40716 Sorted by residual: angle pdb=" CG ARG C 95 " pdb=" CD ARG C 95 " pdb=" NE ARG C 95 " ideal model delta sigma weight residual 112.00 104.50 7.50 2.20e+00 2.07e-01 1.16e+01 angle pdb=" N HIS E 375 " pdb=" CA HIS E 375 " pdb=" C HIS E 375 " ideal model delta sigma weight residual 111.07 114.08 -3.01 1.07e+00 8.73e-01 7.89e+00 angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 113.20 110.56 2.64 9.60e-01 1.09e+00 7.54e+00 angle pdb=" C2' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O3' ATP C 601 " ideal model delta sigma weight residual 111.83 104.97 6.86 2.67e+00 1.40e-01 6.61e+00 angle pdb=" C GLU B 347 " pdb=" CA GLU B 347 " pdb=" CB GLU B 347 " ideal model delta sigma weight residual 110.42 115.22 -4.80 1.99e+00 2.53e-01 5.81e+00 ... (remaining 40711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 16690 17.91 - 35.82: 1335 35.82 - 53.73: 217 53.73 - 71.63: 57 71.63 - 89.54: 39 Dihedral angle restraints: 18338 sinusoidal: 7516 harmonic: 10822 Sorted by residual: dihedral pdb=" CA LEU F 257 " pdb=" C LEU F 257 " pdb=" N THR F 258 " pdb=" CA THR F 258 " ideal model delta harmonic sigma weight residual 180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU D 257 " pdb=" C LEU D 257 " pdb=" N THR D 258 " pdb=" CA THR D 258 " ideal model delta harmonic sigma weight residual 180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU L 128 " pdb=" C LEU L 128 " pdb=" N PRO L 129 " pdb=" CA PRO L 129 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 18335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3899 0.058 - 0.116: 593 0.116 - 0.174: 69 0.174 - 0.232: 0 0.232 - 0.290: 3 Chirality restraints: 4564 Sorted by residual: chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ATP C 601 " pdb=" C2' ATP C 601 " pdb=" C4' ATP C 601 " pdb=" O3' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C4' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" C5' ATP C 601 " pdb=" O4' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4561 not shown) Planarity restraints: 5331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 394 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 355 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO D 356 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 356 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 356 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 229 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " 0.022 5.00e-02 4.00e+02 ... (remaining 5328 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 117 2.44 - 3.06: 20498 3.06 - 3.67: 42898 3.67 - 4.29: 64431 4.29 - 4.90: 111267 Nonbonded interactions: 239211 Sorted by model distance: nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 1.826 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 1.888 2.170 nonbonded pdb=" O3B ATP C 601 " pdb="MG MG C 602 " model vdw 1.893 2.170 nonbonded pdb=" OG SER H 24 " pdb=" OE1 GLU H 28 " model vdw 1.939 3.040 nonbonded pdb=" O LYS D 370 " pdb=" OG1 THR D 371 " model vdw 1.953 3.040 ... (remaining 239206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = chain 'B' selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.030 Extract box with map and model: 1.330 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 70.280 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.150 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 30052 Z= 0.239 Angle : 0.536 7.501 40716 Z= 0.283 Chirality : 0.043 0.290 4564 Planarity : 0.004 0.058 5331 Dihedral : 13.924 89.543 11420 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3764 helix: 1.46 (0.13), residues: 1571 sheet: -1.06 (0.21), residues: 594 loop : -0.19 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 175 HIS 0.004 0.001 HIS B 145 PHE 0.018 0.001 PHE A 269 TYR 0.021 0.001 TYR D 331 ARG 0.004 0.000 ARG E 174 Details of bonding type rmsd hydrogen bonds : bond 0.15271 ( 1303) hydrogen bonds : angle 6.30966 ( 3738) covalent geometry : bond 0.00555 (30052) covalent geometry : angle 0.53582 (40716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 823 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 95 ARG cc_start: 0.6391 (tpt-90) cc_final: 0.6012 (tpt-90) REVERT: A 96 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6398 (pt0) REVERT: A 129 VAL cc_start: 0.7083 (t) cc_final: 0.6662 (m) REVERT: A 143 PHE cc_start: 0.7299 (m-80) cc_final: 0.6979 (m-80) REVERT: A 156 ARG cc_start: 0.5953 (mtp-110) cc_final: 0.5209 (ttp-170) REVERT: A 174 VAL cc_start: 0.7585 (t) cc_final: 0.7216 (p) REVERT: A 182 LYS cc_start: 0.6738 (mtmm) cc_final: 0.6368 (mptt) REVERT: A 323 MET cc_start: 0.8377 (mmt) cc_final: 0.8068 (mmm) REVERT: A 337 ILE cc_start: 0.7042 (mm) cc_final: 0.6587 (mt) REVERT: A 340 ARG cc_start: 0.6537 (tpp-160) cc_final: 0.5995 (mpt180) REVERT: A 348 GLU cc_start: 0.7167 (mt-10) cc_final: 0.5920 (tt0) REVERT: A 374 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6043 (tt0) REVERT: A 375 GLU cc_start: 0.6368 (tt0) cc_final: 0.6057 (tt0) REVERT: A 416 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.6309 (mtp85) REVERT: A 481 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6650 (mtp-110) REVERT: A 492 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6996 (tt0) REVERT: A 517 LYS cc_start: 0.6952 (mmtp) cc_final: 0.6710 (mtpt) REVERT: A 518 MET cc_start: 0.8303 (mtp) cc_final: 0.8051 (mtm) REVERT: A 541 GLN cc_start: 0.6311 (mt0) cc_final: 0.5858 (pt0) REVERT: A 546 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6170 (mm-30) REVERT: A 550 ARG cc_start: 0.6935 (mtm-85) cc_final: 0.6555 (tpp-160) REVERT: A 557 GLU cc_start: 0.7214 (pm20) cc_final: 0.6413 (tp30) REVERT: A 558 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7085 (mt-10) REVERT: A 565 GLU cc_start: 0.7347 (tp30) cc_final: 0.6834 (mt-10) REVERT: A 567 MET cc_start: 0.6993 (mmm) cc_final: 0.6690 (mmm) REVERT: B 3 GLN cc_start: 0.7514 (tt0) cc_final: 0.6932 (mt0) REVERT: B 29 LYS cc_start: 0.7039 (mtpt) cc_final: 0.6664 (mttt) REVERT: B 59 LYS cc_start: 0.7602 (mtpp) cc_final: 0.7089 (mttp) REVERT: B 93 ARG cc_start: 0.6342 (mtm-85) cc_final: 0.6125 (mtm180) REVERT: B 130 ARG cc_start: 0.5639 (ttm-80) cc_final: 0.5288 (tpt170) REVERT: B 133 MET cc_start: 0.6094 (mmm) cc_final: 0.5823 (mmt) REVERT: B 134 VAL cc_start: 0.7311 (m) cc_final: 0.7072 (t) REVERT: B 159 GLU cc_start: 0.7268 (tt0) cc_final: 0.6060 (tp30) REVERT: B 166 TYR cc_start: 0.7004 (m-10) cc_final: 0.5893 (m-80) REVERT: B 197 ARG cc_start: 0.6468 (ttp80) cc_final: 0.6115 (ttp-110) REVERT: B 200 ASP cc_start: 0.6602 (m-30) cc_final: 0.6366 (m-30) REVERT: B 220 MET cc_start: 0.7641 (tpp) cc_final: 0.7379 (ttm) REVERT: B 236 VAL cc_start: 0.7230 (t) cc_final: 0.7006 (p) REVERT: B 243 LYS cc_start: 0.7176 (mtpp) cc_final: 0.6917 (mtpp) REVERT: B 264 ASP cc_start: 0.6515 (m-30) cc_final: 0.6230 (m-30) REVERT: B 340 ARG cc_start: 0.6820 (tpp-160) cc_final: 0.6513 (tpt-90) REVERT: B 374 GLU cc_start: 0.6185 (mt-10) cc_final: 0.5722 (mm-30) REVERT: B 480 GLU cc_start: 0.6331 (mp0) cc_final: 0.5936 (mt-10) REVERT: B 481 ARG cc_start: 0.6785 (mmm-85) cc_final: 0.5968 (mmm160) REVERT: B 553 TYR cc_start: 0.7670 (m-10) cc_final: 0.7419 (m-10) REVERT: C 5 VAL cc_start: 0.8148 (t) cc_final: 0.7911 (m) REVERT: C 24 MET cc_start: 0.8053 (mtp) cc_final: 0.7730 (mmm) REVERT: C 69 LEU cc_start: 0.7718 (mt) cc_final: 0.7448 (mp) REVERT: C 84 TYR cc_start: 0.8652 (m-80) cc_final: 0.8437 (m-80) REVERT: C 124 LYS cc_start: 0.7262 (mttt) cc_final: 0.6930 (mtmm) REVERT: C 125 PRO cc_start: 0.7245 (Cg_exo) cc_final: 0.6763 (Cg_endo) REVERT: C 183 MET cc_start: 0.8416 (mtp) cc_final: 0.8203 (mtm) REVERT: C 191 ARG cc_start: 0.7840 (mtp180) cc_final: 0.7503 (ttp80) REVERT: C 197 ARG cc_start: 0.7495 (mtm110) cc_final: 0.7275 (ptm-80) REVERT: C 198 LYS cc_start: 0.7288 (mmtp) cc_final: 0.7047 (mmmt) REVERT: C 268 GLU cc_start: 0.6702 (mt-10) cc_final: 0.5867 (tp30) REVERT: C 272 LEU cc_start: 0.7520 (mt) cc_final: 0.7316 (mt) REVERT: C 338 SER cc_start: 0.7704 (t) cc_final: 0.7232 (p) REVERT: C 344 MET cc_start: 0.7786 (mmm) cc_final: 0.7529 (mmt) REVERT: C 367 LYS cc_start: 0.7633 (ttpp) cc_final: 0.7269 (ttpp) REVERT: C 374 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6663 (mm-30) REVERT: C 393 GLU cc_start: 0.6565 (tm-30) cc_final: 0.6317 (tm-30) REVERT: C 416 ARG cc_start: 0.7325 (mtm110) cc_final: 0.6653 (mtm180) REVERT: C 442 ASN cc_start: 0.8212 (m-40) cc_final: 0.7812 (m-40) REVERT: C 452 ASP cc_start: 0.7241 (m-30) cc_final: 0.6879 (m-30) REVERT: C 460 ARG cc_start: 0.7080 (mtm180) cc_final: 0.6850 (mtm-85) REVERT: C 513 TYR cc_start: 0.7369 (t80) cc_final: 0.6959 (t80) REVERT: C 518 MET cc_start: 0.7998 (mtp) cc_final: 0.7693 (mtm) REVERT: C 524 LYS cc_start: 0.6951 (mtpp) cc_final: 0.6547 (ttpp) REVERT: C 525 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6234 (mt-10) REVERT: C 547 ARG cc_start: 0.6217 (mtp85) cc_final: 0.5803 (mtp85) REVERT: C 550 ARG cc_start: 0.6744 (ttm-80) cc_final: 0.6400 (mtm110) REVERT: D 22 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6928 (mt-10) REVERT: D 51 SER cc_start: 0.7670 (t) cc_final: 0.7406 (p) REVERT: D 52 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7075 (mt-10) REVERT: D 92 ARG cc_start: 0.7576 (mtm110) cc_final: 0.6990 (mtm-85) REVERT: D 111 ARG cc_start: 0.7359 (mtp-110) cc_final: 0.7026 (mmm-85) REVERT: D 199 ARG cc_start: 0.6475 (ttp80) cc_final: 0.6116 (ttp80) REVERT: D 231 ARG cc_start: 0.7450 (ttm170) cc_final: 0.7236 (ttm170) REVERT: D 232 ILE cc_start: 0.7456 (mm) cc_final: 0.7174 (mt) REVERT: D 250 ASP cc_start: 0.7756 (m-30) cc_final: 0.7547 (m-30) REVERT: D 269 GLU cc_start: 0.6088 (tt0) cc_final: 0.5757 (mt-10) REVERT: D 280 ARG cc_start: 0.7016 (mtp85) cc_final: 0.6387 (mtp-110) REVERT: D 302 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6552 (mm-30) REVERT: D 305 LYS cc_start: 0.6868 (mtmm) cc_final: 0.6115 (mtpp) REVERT: D 337 ILE cc_start: 0.8288 (mt) cc_final: 0.8076 (mm) REVERT: D 338 GLN cc_start: 0.8540 (tt0) cc_final: 0.8031 (tp40) REVERT: D 376 LYS cc_start: 0.6549 (tppt) cc_final: 0.5787 (tttm) REVERT: D 406 GLU cc_start: 0.6061 (tp30) cc_final: 0.5379 (pm20) REVERT: D 409 ARG cc_start: 0.6647 (ttm-80) cc_final: 0.6269 (mtt90) REVERT: D 416 ASP cc_start: 0.7040 (t0) cc_final: 0.6240 (m-30) REVERT: D 461 LYS cc_start: 0.6961 (tttt) cc_final: 0.6754 (ttmt) REVERT: D 463 TYR cc_start: 0.7646 (t80) cc_final: 0.7394 (t80) REVERT: D 465 GLN cc_start: 0.6690 (mm-40) cc_final: 0.6374 (mp10) REVERT: E 25 LYS cc_start: 0.7336 (ttmm) cc_final: 0.7055 (mtpp) REVERT: E 128 GLU cc_start: 0.7079 (pt0) cc_final: 0.6701 (pt0) REVERT: E 228 THR cc_start: 0.8009 (t) cc_final: 0.7392 (m) REVERT: E 251 TYR cc_start: 0.7793 (m-80) cc_final: 0.7274 (m-80) REVERT: E 252 HIS cc_start: 0.8169 (m-70) cc_final: 0.7881 (m170) REVERT: E 302 GLU cc_start: 0.6980 (tt0) cc_final: 0.5904 (tp30) REVERT: E 345 ARG cc_start: 0.6305 (mtm110) cc_final: 0.6068 (mtm-85) REVERT: E 394 LYS cc_start: 0.6768 (tptp) cc_final: 0.6283 (tttm) REVERT: E 410 ARG cc_start: 0.4761 (mtm180) cc_final: 0.4097 (mmp80) REVERT: E 420 ARG cc_start: 0.7440 (mtm110) cc_final: 0.7236 (mtm-85) REVERT: E 445 MET cc_start: 0.7298 (mtp) cc_final: 0.7016 (mtt) REVERT: E 450 GLU cc_start: 0.5914 (mm-30) cc_final: 0.5698 (mt-10) REVERT: F 6 LYS cc_start: 0.6096 (tptm) cc_final: 0.5689 (mtpp) REVERT: F 7 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6813 (mt-10) REVERT: F 13 TYR cc_start: 0.8585 (t80) cc_final: 0.8252 (t80) REVERT: F 53 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6390 (mm-30) REVERT: F 77 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6940 (pt0) REVERT: F 81 ARG cc_start: 0.7387 (mtt-85) cc_final: 0.6880 (mtm-85) REVERT: F 98 LYS cc_start: 0.7429 (mttt) cc_final: 0.7055 (mmtm) REVERT: F 207 GLU cc_start: 0.6592 (mm-30) cc_final: 0.5996 (tm-30) REVERT: F 209 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6725 (mt-10) REVERT: F 210 ARG cc_start: 0.6282 (ttp80) cc_final: 0.5322 (ttm110) REVERT: F 230 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6928 (mt-10) REVERT: F 280 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7365 (mtt180) REVERT: F 302 GLU cc_start: 0.7292 (tt0) cc_final: 0.6717 (mm-30) REVERT: F 305 LYS cc_start: 0.7994 (mttt) cc_final: 0.7787 (mttm) REVERT: F 362 MET cc_start: 0.8007 (ttp) cc_final: 0.7771 (ttt) REVERT: F 409 ARG cc_start: 0.6795 (ttm110) cc_final: 0.6117 (mtt90) REVERT: F 412 LEU cc_start: 0.7402 (tp) cc_final: 0.7183 (tp) REVERT: F 453 ARG cc_start: 0.6971 (mmt90) cc_final: 0.6716 (mmm-85) REVERT: G 17 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6570 (mm-40) REVERT: G 38 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6467 (tp30) REVERT: G 47 MET cc_start: 0.5255 (mmm) cc_final: 0.4213 (ttm) REVERT: G 177 ARG cc_start: 0.6645 (mtp85) cc_final: 0.6267 (mtm-85) REVERT: G 180 GLN cc_start: 0.7189 (mt0) cc_final: 0.6964 (mt0) REVERT: G 198 LYS cc_start: 0.6461 (tttm) cc_final: 0.6256 (ttmm) REVERT: H 63 MET cc_start: 0.3761 (mmm) cc_final: 0.2141 (ttp) REVERT: J 65 GLU cc_start: 0.4107 (mt-10) cc_final: 0.3655 (mm-30) REVERT: J 86 ARG cc_start: 0.4035 (mmp80) cc_final: 0.3396 (ttm-80) REVERT: J 105 ARG cc_start: 0.3493 (mtt-85) cc_final: 0.3235 (mtt-85) REVERT: J 112 LEU cc_start: 0.4601 (mp) cc_final: 0.4061 (tt) REVERT: J 158 GLU cc_start: 0.5277 (mp0) cc_final: 0.4537 (mt-10) REVERT: J 182 VAL cc_start: 0.3334 (t) cc_final: 0.3066 (p) REVERT: L 86 ARG cc_start: 0.5163 (mtt180) cc_final: 0.4852 (mtp180) REVERT: L 102 GLU cc_start: 0.5661 (mp0) cc_final: 0.4687 (tp30) REVERT: L 153 ARG cc_start: 0.3855 (ttm170) cc_final: 0.3545 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 823 average time/residue: 0.5199 time to fit residues: 623.7052 Evaluate side-chains 506 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 96 optimal weight: 0.4980 chunk 190 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 338 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 442 ASN A 571 GLN B 145 HIS B 185 HIS B 571 GLN C 81 ASN C 145 HIS C 283 HIS C 316 GLN C 397 GLN C 418 HIS C 459 GLN C 496 GLN D 252 HIS ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 HIS D 448 GLN E 58 GLN E 148 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN F 206 GLN F 388 ASN F 413 GLN F 427 GLN G 180 GLN L 130 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.152400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.119502 restraints weight = 34325.949| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.33 r_work: 0.3055 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 30052 Z= 0.160 Angle : 0.570 10.127 40716 Z= 0.296 Chirality : 0.045 0.212 4564 Planarity : 0.005 0.041 5331 Dihedral : 5.120 82.881 4214 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.53 % Rotamer: Outliers : 1.49 % Allowed : 9.80 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3764 helix: 1.68 (0.13), residues: 1597 sheet: -0.72 (0.22), residues: 570 loop : 0.06 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 175 HIS 0.005 0.001 HIS C 283 PHE 0.017 0.002 PHE F 130 TYR 0.016 0.001 TYR H 89 ARG 0.014 0.001 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 1303) hydrogen bonds : angle 4.85082 ( 3738) covalent geometry : bond 0.00364 (30052) covalent geometry : angle 0.56958 (40716) *********************** 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 573 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 527 time to evaluate : 3.310 Fit side-chains REVERT: A 95 ARG cc_start: 0.7184 (tpt-90) cc_final: 0.6720 (tpt-90) REVERT: A 154 ARG cc_start: 0.7186 (mtp85) cc_final: 0.6879 (mtp180) REVERT: A 156 ARG cc_start: 0.6257 (mtp-110) cc_final: 0.5718 (ttp-170) REVERT: A 169 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7287 (mm-30) REVERT: A 174 VAL cc_start: 0.8079 (t) cc_final: 0.7744 (p) REVERT: A 200 ASP cc_start: 0.7219 (m-30) cc_final: 0.6810 (m-30) REVERT: A 243 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8569 (mtpt) REVERT: A 262 MET cc_start: 0.8690 (mmp) cc_final: 0.8000 (mmt) REVERT: A 340 ARG cc_start: 0.7470 (tpp-160) cc_final: 0.7032 (mmp80) REVERT: A 348 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6271 (tt0) REVERT: A 374 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6919 (tt0) REVERT: A 416 ARG cc_start: 0.7790 (mtm-85) cc_final: 0.7251 (mtp85) REVERT: A 481 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7276 (mtp-110) REVERT: A 492 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7394 (pt0) REVERT: A 518 MET cc_start: 0.8845 (mtp) cc_final: 0.8613 (mtm) REVERT: A 541 GLN cc_start: 0.6597 (mt0) cc_final: 0.6130 (pt0) REVERT: A 546 GLU cc_start: 0.7714 (mt-10) cc_final: 0.6887 (mm-30) REVERT: A 557 GLU cc_start: 0.7301 (pm20) cc_final: 0.6785 (tp30) REVERT: A 567 MET cc_start: 0.7561 (mmm) cc_final: 0.7347 (mmm) REVERT: B 156 ARG cc_start: 0.7100 (ttp-170) cc_final: 0.6178 (mpt-90) REVERT: B 159 GLU cc_start: 0.7390 (tt0) cc_final: 0.6624 (tp30) REVERT: B 166 TYR cc_start: 0.7185 (m-10) cc_final: 0.6332 (m-80) REVERT: B 197 ARG cc_start: 0.7268 (ttp80) cc_final: 0.7036 (ttp-110) REVERT: B 220 MET cc_start: 0.8257 (tpp) cc_final: 0.7981 (ttm) REVERT: B 241 LEU cc_start: 0.8426 (mp) cc_final: 0.7934 (tt) REVERT: B 243 LYS cc_start: 0.7756 (mtpp) cc_final: 0.7517 (mtpt) REVERT: B 449 GLU cc_start: 0.6372 (mm-30) cc_final: 0.5983 (mp0) REVERT: B 452 ASP cc_start: 0.7876 (m-30) cc_final: 0.7639 (m-30) REVERT: B 480 GLU cc_start: 0.6660 (mp0) cc_final: 0.5927 (mt-10) REVERT: B 481 ARG cc_start: 0.7163 (mmm-85) cc_final: 0.6564 (ttt-90) REVERT: B 570 ILE cc_start: 0.6028 (tt) cc_final: 0.5749 (mt) REVERT: C 101 TYR cc_start: 0.8034 (m-80) cc_final: 0.7589 (m-80) REVERT: C 183 MET cc_start: 0.8784 (mtp) cc_final: 0.8499 (mtm) REVERT: C 374 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7706 (mm-30) REVERT: C 416 ARG cc_start: 0.7933 (mtm110) cc_final: 0.7400 (mtm180) REVERT: C 442 ASN cc_start: 0.8757 (m-40) cc_final: 0.8403 (m-40) REVERT: C 452 ASP cc_start: 0.7691 (m-30) cc_final: 0.7445 (m-30) REVERT: C 460 ARG cc_start: 0.7668 (mtm180) cc_final: 0.7457 (mtp180) REVERT: C 518 MET cc_start: 0.8499 (mtp) cc_final: 0.8259 (mtm) REVERT: C 524 LYS cc_start: 0.7309 (mtpp) cc_final: 0.7090 (ttpp) REVERT: C 547 ARG cc_start: 0.6490 (mtp85) cc_final: 0.6019 (mtp85) REVERT: C 550 ARG cc_start: 0.7071 (ttm-80) cc_final: 0.6777 (mtm110) REVERT: D 34 ASP cc_start: 0.7405 (m-30) cc_final: 0.6953 (t0) REVERT: D 52 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7098 (mt-10) REVERT: D 280 ARG cc_start: 0.7775 (mtp85) cc_final: 0.7416 (mtp-110) REVERT: D 305 LYS cc_start: 0.7397 (mtmm) cc_final: 0.6496 (tttt) REVERT: D 322 THR cc_start: 0.8138 (p) cc_final: 0.7930 (p) REVERT: D 376 LYS cc_start: 0.7314 (tppt) cc_final: 0.6974 (tttm) REVERT: D 406 GLU cc_start: 0.5847 (tp30) cc_final: 0.5594 (pm20) REVERT: D 409 ARG cc_start: 0.6949 (ttm-80) cc_final: 0.6595 (mtt90) REVERT: D 461 LYS cc_start: 0.7456 (tttt) cc_final: 0.7229 (tttp) REVERT: D 463 TYR cc_start: 0.7843 (t80) cc_final: 0.7425 (t80) REVERT: E 128 GLU cc_start: 0.6971 (pt0) cc_final: 0.6660 (pt0) REVERT: E 194 MET cc_start: 0.8807 (mtm) cc_final: 0.8524 (mtm) REVERT: E 209 GLU cc_start: 0.6352 (mt-10) cc_final: 0.6068 (mm-30) REVERT: E 259 ASP cc_start: 0.7030 (m-30) cc_final: 0.6646 (m-30) REVERT: E 278 PRO cc_start: 0.8619 (Cg_endo) cc_final: 0.8222 (Cg_exo) REVERT: E 302 GLU cc_start: 0.6946 (tt0) cc_final: 0.6406 (tp30) REVERT: E 360 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7779 (mtt90) REVERT: E 445 MET cc_start: 0.7321 (mtp) cc_final: 0.7028 (mtt) REVERT: F 6 LYS cc_start: 0.6429 (tptm) cc_final: 0.5785 (mtpp) REVERT: F 7 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7034 (mt-10) REVERT: F 74 SER cc_start: 0.8614 (p) cc_final: 0.8078 (t) REVERT: F 109 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6509 (mm-30) REVERT: F 207 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7430 (tm-30) REVERT: F 210 ARG cc_start: 0.6972 (ttp80) cc_final: 0.6184 (ttm110) REVERT: F 302 GLU cc_start: 0.8096 (tt0) cc_final: 0.7783 (mm-30) REVERT: F 399 ILE cc_start: 0.6556 (mm) cc_final: 0.6008 (mt) REVERT: G 47 MET cc_start: 0.5237 (mmm) cc_final: 0.4590 (ttm) REVERT: G 59 GLU cc_start: 0.5485 (pp20) cc_final: 0.4390 (tp30) REVERT: G 180 GLN cc_start: 0.8119 (mt0) cc_final: 0.7881 (mt0) REVERT: G 197 ILE cc_start: 0.6398 (pt) cc_final: 0.5901 (mm) REVERT: H 63 MET cc_start: 0.4079 (mmm) cc_final: 0.2306 (ttp) REVERT: J 65 GLU cc_start: 0.4199 (mt-10) cc_final: 0.3774 (tt0) REVERT: J 81 GLU cc_start: 0.4501 (tt0) cc_final: 0.4131 (tp30) REVERT: J 86 ARG cc_start: 0.4243 (mmp80) cc_final: 0.3537 (ttm-80) REVERT: J 112 LEU cc_start: 0.4564 (mp) cc_final: 0.3993 (tt) REVERT: J 162 GLN cc_start: 0.6317 (tt0) cc_final: 0.5996 (tt0) REVERT: J 164 GLU cc_start: 0.5367 (tp30) cc_final: 0.4822 (mt-10) REVERT: K 102 LYS cc_start: 0.6005 (tptp) cc_final: 0.4313 (mmtt) REVERT: L 86 ARG cc_start: 0.5598 (mtt180) cc_final: 0.5161 (mtp180) REVERT: L 102 GLU cc_start: 0.5535 (mp0) cc_final: 0.4679 (tp30) REVERT: L 141 GLU cc_start: 0.5174 (tt0) cc_final: 0.4215 (mm-30) REVERT: L 153 ARG cc_start: 0.4237 (ttm170) cc_final: 0.3653 (ttm-80) outliers start: 46 outliers final: 27 residues processed: 552 average time/residue: 0.5459 time to fit residues: 441.8104 Evaluate side-chains 471 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 444 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 413 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 0.1980 chunk 131 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 230 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN A 498 ASN B 246 ASN D 170 GLN D 310 GLN D 323 HIS D 338 GLN D 364 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS F 249 HIS F 381 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.151862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.116601 restraints weight = 34511.473| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.43 r_work: 0.3056 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 30052 Z= 0.177 Angle : 0.571 10.503 40716 Z= 0.296 Chirality : 0.046 0.217 4564 Planarity : 0.005 0.043 5331 Dihedral : 5.177 80.590 4214 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Rotamer: Outliers : 2.21 % Allowed : 10.87 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.14), residues: 3764 helix: 1.60 (0.13), residues: 1584 sheet: -0.74 (0.21), residues: 565 loop : -0.03 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 119 HIS 0.008 0.001 HIS B 145 PHE 0.020 0.002 PHE E 130 TYR 0.017 0.002 TYR C 562 ARG 0.007 0.001 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 1303) hydrogen bonds : angle 4.73589 ( 3738) covalent geometry : bond 0.00431 (30052) covalent geometry : angle 0.57102 (40716) *********************** 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 520 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 452 time to evaluate : 3.002 Fit side-chains REVERT: A 93 ARG cc_start: 0.7859 (mmm160) cc_final: 0.7539 (mpt180) REVERT: A 95 ARG cc_start: 0.7329 (tpt-90) cc_final: 0.6852 (tpt-90) REVERT: A 154 ARG cc_start: 0.7216 (mtp85) cc_final: 0.6912 (mtp180) REVERT: A 156 ARG cc_start: 0.6252 (mtp-110) cc_final: 0.5679 (ttp-170) REVERT: A 169 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7119 (mt-10) REVERT: A 174 VAL cc_start: 0.8023 (t) cc_final: 0.7654 (p) REVERT: A 340 ARG cc_start: 0.7492 (tpp-160) cc_final: 0.7036 (mmt180) REVERT: A 348 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6316 (tt0) REVERT: A 374 GLU cc_start: 0.7541 (mt-10) cc_final: 0.6950 (tt0) REVERT: A 416 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7277 (mtp85) REVERT: A 481 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7329 (mtp-110) REVERT: A 518 MET cc_start: 0.8893 (mtp) cc_final: 0.8619 (mtm) REVERT: A 541 GLN cc_start: 0.6544 (mt0) cc_final: 0.6054 (pt0) REVERT: A 546 GLU cc_start: 0.7823 (mt-10) cc_final: 0.6967 (mm-30) REVERT: A 557 GLU cc_start: 0.7244 (pm20) cc_final: 0.6763 (tp30) REVERT: B 154 ARG cc_start: 0.6640 (ptp90) cc_final: 0.6388 (ptt-90) REVERT: B 156 ARG cc_start: 0.7241 (ttp-170) cc_final: 0.6298 (mpt-90) REVERT: B 166 TYR cc_start: 0.7235 (m-80) cc_final: 0.6380 (m-80) REVERT: B 197 ARG cc_start: 0.7412 (ttp80) cc_final: 0.7047 (ttp-110) REVERT: B 241 LEU cc_start: 0.8409 (mp) cc_final: 0.7995 (tt) REVERT: B 449 GLU cc_start: 0.6361 (mm-30) cc_final: 0.5992 (mp0) REVERT: B 452 ASP cc_start: 0.7795 (m-30) cc_final: 0.7360 (m-30) REVERT: B 477 GLN cc_start: 0.6497 (pm20) cc_final: 0.6228 (mp10) REVERT: B 480 GLU cc_start: 0.6819 (mp0) cc_final: 0.6045 (mt-10) REVERT: B 481 ARG cc_start: 0.7189 (mmm-85) cc_final: 0.6481 (ttt-90) REVERT: C 183 MET cc_start: 0.8778 (mtp) cc_final: 0.8514 (mtm) REVERT: C 416 ARG cc_start: 0.7987 (mtm110) cc_final: 0.7422 (mtm180) REVERT: C 518 MET cc_start: 0.8658 (mtp) cc_final: 0.8453 (mtm) REVERT: C 547 ARG cc_start: 0.6439 (mtp85) cc_final: 0.5905 (mtp85) REVERT: C 550 ARG cc_start: 0.7296 (ttm-80) cc_final: 0.6722 (mtm110) REVERT: D 34 ASP cc_start: 0.7431 (m-30) cc_final: 0.6961 (t0) REVERT: D 52 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7151 (mt-10) REVERT: D 305 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.6824 (mtpt) REVERT: D 362 MET cc_start: 0.8328 (ttp) cc_final: 0.8111 (ttt) REVERT: D 409 ARG cc_start: 0.6838 (ttm-80) cc_final: 0.6409 (mtt90) REVERT: D 420 ARG cc_start: 0.7589 (mtp-110) cc_final: 0.7236 (mtp-110) REVERT: D 461 LYS cc_start: 0.7527 (tttt) cc_final: 0.7301 (tttp) REVERT: D 463 TYR cc_start: 0.7950 (t80) cc_final: 0.7513 (t80) REVERT: E 26 ASP cc_start: 0.7066 (t0) cc_final: 0.6820 (t0) REVERT: E 89 LEU cc_start: 0.8389 (mt) cc_final: 0.8121 (mt) REVERT: E 110 LYS cc_start: 0.7472 (ttmm) cc_final: 0.6934 (mtpp) REVERT: E 259 ASP cc_start: 0.7107 (m-30) cc_final: 0.6715 (m-30) REVERT: E 278 PRO cc_start: 0.8683 (Cg_endo) cc_final: 0.8304 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7121 (tt0) cc_final: 0.6839 (tt0) REVERT: E 380 ASP cc_start: 0.6512 (t0) cc_final: 0.6220 (t0) REVERT: E 445 MET cc_start: 0.7392 (mtp) cc_final: 0.6978 (mtt) REVERT: E 448 GLN cc_start: 0.5676 (OUTLIER) cc_final: 0.5204 (mm110) REVERT: F 6 LYS cc_start: 0.6458 (tptm) cc_final: 0.6184 (mtpp) REVERT: F 7 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7284 (mt-10) REVERT: F 109 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6408 (mm-30) REVERT: F 207 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7412 (tm-30) REVERT: F 210 ARG cc_start: 0.7044 (ttp80) cc_final: 0.6201 (ttm110) REVERT: F 302 GLU cc_start: 0.8168 (tt0) cc_final: 0.7921 (tt0) REVERT: F 305 LYS cc_start: 0.8535 (mttm) cc_final: 0.8230 (mmtp) REVERT: F 399 ILE cc_start: 0.6592 (mm) cc_final: 0.6025 (mt) REVERT: F 409 ARG cc_start: 0.7215 (ttm110) cc_final: 0.6941 (ttm170) REVERT: G 47 MET cc_start: 0.5469 (mmm) cc_final: 0.4932 (ttm) REVERT: G 59 GLU cc_start: 0.5456 (pp20) cc_final: 0.4498 (tp30) REVERT: G 139 ARG cc_start: 0.5418 (ttp80) cc_final: 0.4509 (ptm-80) REVERT: G 197 ILE cc_start: 0.6294 (pt) cc_final: 0.5787 (mm) REVERT: H 63 MET cc_start: 0.3997 (mmm) cc_final: 0.2472 (ttp) REVERT: H 77 LEU cc_start: 0.3965 (mm) cc_final: 0.3644 (mt) REVERT: J 65 GLU cc_start: 0.4464 (mt-10) cc_final: 0.4201 (mt-10) REVERT: J 86 ARG cc_start: 0.4557 (mmp80) cc_final: 0.3623 (ttm-80) REVERT: J 112 LEU cc_start: 0.4639 (OUTLIER) cc_final: 0.4070 (tt) REVERT: J 162 GLN cc_start: 0.6180 (tt0) cc_final: 0.5862 (tt0) REVERT: J 173 ARG cc_start: 0.3627 (ttt-90) cc_final: 0.3274 (mtp85) REVERT: K 102 LYS cc_start: 0.5990 (tptp) cc_final: 0.4256 (mmtt) REVERT: L 86 ARG cc_start: 0.5662 (mtt180) cc_final: 0.5197 (mtp180) REVERT: L 102 GLU cc_start: 0.5498 (mp0) cc_final: 0.4632 (tp30) REVERT: L 113 GLU cc_start: 0.5771 (mm-30) cc_final: 0.5376 (mp0) REVERT: L 153 ARG cc_start: 0.4159 (ttm170) cc_final: 0.3622 (ttm-80) outliers start: 68 outliers final: 46 residues processed: 497 average time/residue: 0.5023 time to fit residues: 370.3467 Evaluate side-chains 450 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 401 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain L residue 134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 324 optimal weight: 0.4980 chunk 191 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 247 optimal weight: 0.5980 chunk 359 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 351 optimal weight: 0.0970 chunk 80 optimal weight: 0.8980 chunk 363 optimal weight: 3.9990 chunk 258 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN E 161 ASN E 364 ASN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 HIS G 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.157470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.126234 restraints weight = 34482.381| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.74 r_work: 0.3101 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 30052 Z= 0.102 Angle : 0.469 8.165 40716 Z= 0.243 Chirality : 0.042 0.187 4564 Planarity : 0.004 0.046 5331 Dihedral : 4.755 82.065 4214 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.59 % Favored : 98.38 % Rotamer: Outliers : 1.33 % Allowed : 12.81 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3764 helix: 1.84 (0.13), residues: 1602 sheet: -0.65 (0.21), residues: 581 loop : 0.12 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 119 HIS 0.005 0.001 HIS F 249 PHE 0.019 0.001 PHE E 130 TYR 0.008 0.001 TYR H 89 ARG 0.008 0.000 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 1303) hydrogen bonds : angle 4.42756 ( 3738) covalent geometry : bond 0.00229 (30052) covalent geometry : angle 0.46853 (40716) *********************** 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 490 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 449 time to evaluate : 3.180 Fit side-chains REVERT: A 95 ARG cc_start: 0.7238 (tpt-90) cc_final: 0.6759 (tpt-90) REVERT: A 156 ARG cc_start: 0.6245 (mtp-110) cc_final: 0.5665 (ttp-170) REVERT: A 169 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7170 (mt-10) REVERT: A 174 VAL cc_start: 0.7977 (t) cc_final: 0.7622 (p) REVERT: A 340 ARG cc_start: 0.7423 (tpp-160) cc_final: 0.6950 (mmt180) REVERT: A 374 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6913 (tt0) REVERT: A 416 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7147 (mtp85) REVERT: A 481 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7283 (mtp-110) REVERT: A 541 GLN cc_start: 0.6656 (mt0) cc_final: 0.6254 (pt0) REVERT: A 546 GLU cc_start: 0.7714 (mt-10) cc_final: 0.6868 (mm-30) REVERT: A 547 ARG cc_start: 0.7322 (ttm110) cc_final: 0.6913 (ttm110) REVERT: A 557 GLU cc_start: 0.7226 (pm20) cc_final: 0.6792 (tp30) REVERT: B 156 ARG cc_start: 0.7207 (ttp-170) cc_final: 0.6278 (mpt-90) REVERT: B 166 TYR cc_start: 0.7167 (m-80) cc_final: 0.6292 (m-80) REVERT: B 197 ARG cc_start: 0.7333 (ttp80) cc_final: 0.7020 (ttp-110) REVERT: B 241 LEU cc_start: 0.8360 (mp) cc_final: 0.8063 (tt) REVERT: B 315 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: B 340 ARG cc_start: 0.7561 (tpp-160) cc_final: 0.7138 (tpt-90) REVERT: B 449 GLU cc_start: 0.6438 (mm-30) cc_final: 0.6147 (mp0) REVERT: B 477 GLN cc_start: 0.6520 (pm20) cc_final: 0.6201 (mp10) REVERT: B 480 GLU cc_start: 0.6695 (mp0) cc_final: 0.5952 (mt-10) REVERT: B 481 ARG cc_start: 0.7109 (mmm-85) cc_final: 0.6594 (ttt-90) REVERT: B 547 ARG cc_start: 0.5766 (mmm-85) cc_final: 0.5275 (ttm-80) REVERT: B 570 ILE cc_start: 0.6176 (tt) cc_final: 0.5874 (mt) REVERT: C 32 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7590 (mt-10) REVERT: C 115 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7928 (tttm) REVERT: C 183 MET cc_start: 0.8688 (mtp) cc_final: 0.8418 (mtt) REVERT: C 312 TYR cc_start: 0.8859 (t80) cc_final: 0.8598 (t80) REVERT: C 344 MET cc_start: 0.8075 (mmt) cc_final: 0.7540 (mmm) REVERT: C 416 ARG cc_start: 0.7912 (mtm110) cc_final: 0.7405 (mtm180) REVERT: C 452 ASP cc_start: 0.7565 (m-30) cc_final: 0.7240 (m-30) REVERT: C 460 ARG cc_start: 0.7623 (mtm180) cc_final: 0.7384 (mtp180) REVERT: C 518 MET cc_start: 0.8560 (mtp) cc_final: 0.8335 (mtm) REVERT: C 547 ARG cc_start: 0.6328 (mtp85) cc_final: 0.5935 (mtp85) REVERT: C 550 ARG cc_start: 0.7178 (ttm-80) cc_final: 0.6751 (mtm110) REVERT: D 34 ASP cc_start: 0.7320 (m-30) cc_final: 0.6880 (t0) REVERT: D 52 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7152 (mt-10) REVERT: D 305 LYS cc_start: 0.7456 (mtmm) cc_final: 0.6598 (tttt) REVERT: D 409 ARG cc_start: 0.6785 (ttm-80) cc_final: 0.6503 (mtt90) REVERT: D 420 ARG cc_start: 0.7419 (mtp-110) cc_final: 0.7062 (mtp-110) REVERT: D 461 LYS cc_start: 0.7574 (tttt) cc_final: 0.7341 (tttp) REVERT: D 463 TYR cc_start: 0.7932 (t80) cc_final: 0.7526 (t80) REVERT: E 89 LEU cc_start: 0.8346 (mt) cc_final: 0.8060 (mt) REVERT: E 110 LYS cc_start: 0.7299 (ttmm) cc_final: 0.6782 (mtpp) REVERT: E 259 ASP cc_start: 0.6874 (m-30) cc_final: 0.6505 (m-30) REVERT: E 278 PRO cc_start: 0.8618 (Cg_endo) cc_final: 0.8271 (Cg_exo) REVERT: E 302 GLU cc_start: 0.6958 (tt0) cc_final: 0.6427 (tp30) REVERT: E 433 GLU cc_start: 0.7176 (mp0) cc_final: 0.6884 (mp0) REVERT: E 445 MET cc_start: 0.7340 (mtp) cc_final: 0.7112 (mtt) REVERT: F 6 LYS cc_start: 0.6432 (tptm) cc_final: 0.5908 (mtpp) REVERT: F 7 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7183 (mt-10) REVERT: F 74 SER cc_start: 0.8630 (p) cc_final: 0.8068 (t) REVERT: F 94 ASN cc_start: 0.8422 (p0) cc_final: 0.8187 (p0) REVERT: F 109 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6369 (mm-30) REVERT: F 210 ARG cc_start: 0.6926 (ttp80) cc_final: 0.6149 (mtm110) REVERT: F 302 GLU cc_start: 0.8132 (tt0) cc_final: 0.7900 (tt0) REVERT: F 445 MET cc_start: 0.7197 (mtm) cc_final: 0.6872 (mtp) REVERT: G 47 MET cc_start: 0.5440 (mmm) cc_final: 0.5022 (ttm) REVERT: G 59 GLU cc_start: 0.5343 (pp20) cc_final: 0.4173 (tp30) REVERT: G 197 ILE cc_start: 0.6306 (pt) cc_final: 0.6044 (mm) REVERT: H 63 MET cc_start: 0.3981 (mmm) cc_final: 0.2425 (ttp) REVERT: H 77 LEU cc_start: 0.4085 (mm) cc_final: 0.3557 (mt) REVERT: J 65 GLU cc_start: 0.4577 (mt-10) cc_final: 0.4043 (tt0) REVERT: J 86 ARG cc_start: 0.4619 (mmp80) cc_final: 0.3638 (ttm-80) REVERT: J 112 LEU cc_start: 0.4499 (mp) cc_final: 0.3934 (tt) REVERT: J 173 ARG cc_start: 0.3657 (ttt-90) cc_final: 0.3334 (mtp85) REVERT: J 182 VAL cc_start: 0.3514 (t) cc_final: 0.3146 (p) REVERT: K 102 LYS cc_start: 0.6055 (tptp) cc_final: 0.5174 (mmtt) REVERT: L 86 ARG cc_start: 0.5805 (mtt180) cc_final: 0.5378 (mtp180) REVERT: L 102 GLU cc_start: 0.5486 (mp0) cc_final: 0.4610 (tp30) REVERT: L 113 GLU cc_start: 0.5764 (mm-30) cc_final: 0.5256 (mp0) REVERT: L 141 GLU cc_start: 0.5073 (tt0) cc_final: 0.4192 (mm-30) REVERT: L 153 ARG cc_start: 0.4097 (ttm170) cc_final: 0.3591 (ttm-80) outliers start: 41 outliers final: 30 residues processed: 476 average time/residue: 0.5009 time to fit residues: 353.9594 Evaluate side-chains 442 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 410 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 128 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 297 optimal weight: 7.9990 chunk 142 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 148 optimal weight: 0.0070 chunk 256 optimal weight: 9.9990 chunk 303 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN G 166 GLN G 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.153978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.121248 restraints weight = 34382.834| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.32 r_work: 0.3045 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 30052 Z= 0.148 Angle : 0.520 8.997 40716 Z= 0.267 Chirality : 0.044 0.206 4564 Planarity : 0.005 0.063 5331 Dihedral : 4.945 81.520 4214 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.27 % Allowed : 12.94 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3764 helix: 1.75 (0.13), residues: 1592 sheet: -0.68 (0.21), residues: 581 loop : 0.08 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 119 HIS 0.005 0.001 HIS D 375 PHE 0.019 0.002 PHE E 130 TYR 0.013 0.001 TYR C 562 ARG 0.009 0.000 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 1303) hydrogen bonds : angle 4.47358 ( 3738) covalent geometry : bond 0.00360 (30052) covalent geometry : angle 0.51983 (40716) *********************** 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 488 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 418 time to evaluate : 3.328 Fit side-chains REVERT: A 95 ARG cc_start: 0.7293 (tpt-90) cc_final: 0.6693 (tpt-90) REVERT: A 156 ARG cc_start: 0.6301 (mtp-110) cc_final: 0.5709 (ttp-170) REVERT: A 169 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7222 (mt-10) REVERT: A 374 GLU cc_start: 0.7574 (mt-10) cc_final: 0.6998 (tt0) REVERT: A 416 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7177 (mtp85) REVERT: A 481 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7306 (mtp-110) REVERT: A 541 GLN cc_start: 0.6759 (mt0) cc_final: 0.6262 (pt0) REVERT: A 546 GLU cc_start: 0.7757 (mt-10) cc_final: 0.6926 (mm-30) REVERT: A 547 ARG cc_start: 0.7280 (ttm110) cc_final: 0.6920 (ttm110) REVERT: A 557 GLU cc_start: 0.7152 (pm20) cc_final: 0.6759 (tp30) REVERT: B 166 TYR cc_start: 0.7236 (m-80) cc_final: 0.6404 (m-80) REVERT: B 197 ARG cc_start: 0.7413 (ttp80) cc_final: 0.7054 (ttp-110) REVERT: B 241 LEU cc_start: 0.8430 (mp) cc_final: 0.8135 (tt) REVERT: B 340 ARG cc_start: 0.7602 (tpp-160) cc_final: 0.7195 (tpt-90) REVERT: B 449 GLU cc_start: 0.6417 (mm-30) cc_final: 0.6096 (mp0) REVERT: B 477 GLN cc_start: 0.6647 (pm20) cc_final: 0.6297 (mp10) REVERT: B 480 GLU cc_start: 0.6727 (mp0) cc_final: 0.5969 (mt-10) REVERT: B 481 ARG cc_start: 0.7064 (mmm-85) cc_final: 0.6475 (ttt-90) REVERT: B 547 ARG cc_start: 0.5796 (mmm-85) cc_final: 0.5529 (mmm160) REVERT: C 1 MET cc_start: 0.5898 (mmm) cc_final: 0.5248 (mmp) REVERT: C 115 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7867 (tttm) REVERT: C 183 MET cc_start: 0.8709 (mtp) cc_final: 0.8485 (mtt) REVERT: C 416 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7387 (mtm180) REVERT: C 518 MET cc_start: 0.8644 (mtp) cc_final: 0.8444 (mtm) REVERT: C 547 ARG cc_start: 0.6392 (mtp85) cc_final: 0.5883 (mtp85) REVERT: C 550 ARG cc_start: 0.7218 (ttm-80) cc_final: 0.6624 (mtm110) REVERT: D 34 ASP cc_start: 0.7394 (m-30) cc_final: 0.6894 (t0) REVERT: D 52 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7205 (mt-10) REVERT: D 305 LYS cc_start: 0.7471 (mtmm) cc_final: 0.7166 (mtpt) REVERT: D 409 ARG cc_start: 0.6816 (ttm-80) cc_final: 0.6428 (mtt90) REVERT: D 420 ARG cc_start: 0.7498 (mtp-110) cc_final: 0.7161 (mtp-110) REVERT: D 461 LYS cc_start: 0.7415 (tttt) cc_final: 0.7193 (tttp) REVERT: D 463 TYR cc_start: 0.7938 (t80) cc_final: 0.7450 (t80) REVERT: E 88 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7542 (mtt) REVERT: E 110 LYS cc_start: 0.7274 (ttmm) cc_final: 0.6850 (mtpp) REVERT: E 259 ASP cc_start: 0.7136 (m-30) cc_final: 0.6736 (m-30) REVERT: E 278 PRO cc_start: 0.8669 (Cg_endo) cc_final: 0.8324 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7107 (tt0) cc_final: 0.6501 (tp30) REVERT: E 433 GLU cc_start: 0.7275 (mp0) cc_final: 0.6947 (mp0) REVERT: E 445 MET cc_start: 0.7461 (mtp) cc_final: 0.7136 (mtt) REVERT: E 448 GLN cc_start: 0.5678 (OUTLIER) cc_final: 0.5062 (mm110) REVERT: F 6 LYS cc_start: 0.6405 (tptm) cc_final: 0.6171 (mtpp) REVERT: F 7 GLU cc_start: 0.7665 (mt-10) cc_final: 0.6819 (mt-10) REVERT: F 109 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6397 (mm-30) REVERT: F 210 ARG cc_start: 0.6913 (ttp80) cc_final: 0.6151 (ttm110) REVERT: F 302 GLU cc_start: 0.8153 (tt0) cc_final: 0.7903 (tt0) REVERT: G 9 MET cc_start: 0.7496 (ttp) cc_final: 0.7086 (ptm) REVERT: G 47 MET cc_start: 0.5463 (mmm) cc_final: 0.5030 (ttm) REVERT: G 59 GLU cc_start: 0.5500 (pp20) cc_final: 0.4311 (tp30) REVERT: G 197 ILE cc_start: 0.6369 (pt) cc_final: 0.5884 (mm) REVERT: G 200 LYS cc_start: 0.5697 (OUTLIER) cc_final: 0.5065 (mttt) REVERT: H 63 MET cc_start: 0.3968 (mmm) cc_final: 0.2477 (ttp) REVERT: H 77 LEU cc_start: 0.4118 (mm) cc_final: 0.3574 (mt) REVERT: J 86 ARG cc_start: 0.4543 (mmp80) cc_final: 0.3560 (ttm-80) REVERT: J 162 GLN cc_start: 0.6161 (tt0) cc_final: 0.5925 (tt0) REVERT: J 173 ARG cc_start: 0.3640 (ttt-90) cc_final: 0.3334 (mtp85) REVERT: K 102 LYS cc_start: 0.6062 (tptp) cc_final: 0.4421 (mmtt) REVERT: L 86 ARG cc_start: 0.5743 (mtt180) cc_final: 0.5279 (mtp180) REVERT: L 102 GLU cc_start: 0.5620 (mp0) cc_final: 0.4708 (tp30) REVERT: L 113 GLU cc_start: 0.5695 (mm-30) cc_final: 0.5296 (mp0) REVERT: L 153 ARG cc_start: 0.4045 (ttm170) cc_final: 0.3392 (ttm-80) REVERT: L 164 GLU cc_start: 0.5928 (tp30) cc_final: 0.5008 (mt-10) outliers start: 70 outliers final: 48 residues processed: 464 average time/residue: 0.5190 time to fit residues: 357.1286 Evaluate side-chains 456 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 404 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 200 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 159 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 344 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN G 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.155832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.134347 restraints weight = 34488.317| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 0.84 r_work: 0.3112 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 30052 Z= 0.160 Angle : 0.537 9.673 40716 Z= 0.277 Chirality : 0.044 0.210 4564 Planarity : 0.005 0.083 5331 Dihedral : 5.049 80.039 4214 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.69 % Allowed : 13.56 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3764 helix: 1.63 (0.13), residues: 1572 sheet: -0.72 (0.20), residues: 591 loop : -0.01 (0.16), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 119 HIS 0.006 0.001 HIS D 375 PHE 0.020 0.002 PHE E 130 TYR 0.013 0.001 TYR C 312 ARG 0.013 0.001 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 1303) hydrogen bonds : angle 4.51332 ( 3738) covalent geometry : bond 0.00388 (30052) covalent geometry : angle 0.53748 (40716) *********************** 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 496 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 413 time to evaluate : 3.453 Fit side-chains REVERT: A 53 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7441 (mt-10) REVERT: A 95 ARG cc_start: 0.7167 (tpt-90) cc_final: 0.6582 (tpt-90) REVERT: A 169 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7168 (mt-10) REVERT: A 374 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7102 (tt0) REVERT: A 416 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7124 (mtp85) REVERT: A 481 ARG cc_start: 0.7576 (mtm-85) cc_final: 0.7300 (mtp-110) REVERT: A 541 GLN cc_start: 0.6537 (mt0) cc_final: 0.6100 (pt0) REVERT: A 546 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6847 (mm-30) REVERT: A 547 ARG cc_start: 0.7291 (ttm110) cc_final: 0.6898 (ttm110) REVERT: B 166 TYR cc_start: 0.7229 (m-80) cc_final: 0.6463 (m-80) REVERT: B 197 ARG cc_start: 0.7453 (ttp80) cc_final: 0.7086 (ttp-110) REVERT: B 340 ARG cc_start: 0.7465 (tpp-160) cc_final: 0.7049 (tpt-90) REVERT: B 449 GLU cc_start: 0.6395 (mm-30) cc_final: 0.6158 (mp0) REVERT: B 477 GLN cc_start: 0.6683 (pm20) cc_final: 0.6397 (mp10) REVERT: B 480 GLU cc_start: 0.6746 (mp0) cc_final: 0.6031 (mt-10) REVERT: B 481 ARG cc_start: 0.7050 (mmm-85) cc_final: 0.6465 (ttt-90) REVERT: C 115 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7936 (tttm) REVERT: C 125 PRO cc_start: 0.7522 (Cg_exo) cc_final: 0.7095 (Cg_endo) REVERT: C 183 MET cc_start: 0.8644 (mtp) cc_final: 0.8415 (mtt) REVERT: C 344 MET cc_start: 0.7918 (mmp) cc_final: 0.7499 (mmm) REVERT: C 416 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7305 (mtm180) REVERT: C 547 ARG cc_start: 0.6366 (mtp85) cc_final: 0.5931 (mtp85) REVERT: C 550 ARG cc_start: 0.7333 (ttm-80) cc_final: 0.6860 (mtm110) REVERT: D 34 ASP cc_start: 0.7243 (m-30) cc_final: 0.6736 (t0) REVERT: D 42 VAL cc_start: 0.7608 (t) cc_final: 0.7306 (m) REVERT: D 52 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7158 (mt-10) REVERT: D 305 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6766 (mtpt) REVERT: D 409 ARG cc_start: 0.6702 (ttm-80) cc_final: 0.6388 (mtt90) REVERT: D 420 ARG cc_start: 0.7431 (mtp-110) cc_final: 0.7081 (mtp-110) REVERT: D 461 LYS cc_start: 0.7491 (tttt) cc_final: 0.7272 (tttp) REVERT: D 463 TYR cc_start: 0.7959 (t80) cc_final: 0.7484 (t80) REVERT: E 88 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7552 (mtt) REVERT: E 110 LYS cc_start: 0.7318 (ttmm) cc_final: 0.6930 (mtpp) REVERT: E 259 ASP cc_start: 0.6906 (m-30) cc_final: 0.6536 (m-30) REVERT: E 278 PRO cc_start: 0.8554 (Cg_endo) cc_final: 0.8140 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7061 (tt0) cc_final: 0.6612 (pt0) REVERT: E 410 ARG cc_start: 0.5765 (mtm-85) cc_final: 0.4561 (mmp80) REVERT: E 445 MET cc_start: 0.7388 (mtp) cc_final: 0.7001 (mtt) REVERT: E 448 GLN cc_start: 0.5546 (OUTLIER) cc_final: 0.5170 (mm110) REVERT: F 6 LYS cc_start: 0.6405 (tptm) cc_final: 0.6153 (mtpp) REVERT: F 7 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7040 (mt-10) REVERT: F 109 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6277 (mm-30) REVERT: F 210 ARG cc_start: 0.6856 (ttp80) cc_final: 0.6060 (ttm110) REVERT: F 302 GLU cc_start: 0.7940 (tt0) cc_final: 0.7712 (tt0) REVERT: F 410 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6739 (mtm-85) REVERT: G 9 MET cc_start: 0.7336 (ttp) cc_final: 0.7003 (ptm) REVERT: G 47 MET cc_start: 0.5597 (mmm) cc_final: 0.5081 (ttm) REVERT: G 59 GLU cc_start: 0.5508 (OUTLIER) cc_final: 0.4312 (tp30) REVERT: G 197 ILE cc_start: 0.6473 (pt) cc_final: 0.5900 (mm) REVERT: G 200 LYS cc_start: 0.5807 (OUTLIER) cc_final: 0.5209 (mttt) REVERT: H 63 MET cc_start: 0.4016 (mmm) cc_final: 0.2498 (ttp) REVERT: H 77 LEU cc_start: 0.4184 (mm) cc_final: 0.3624 (mt) REVERT: J 162 GLN cc_start: 0.6170 (tt0) cc_final: 0.5939 (tt0) REVERT: K 102 LYS cc_start: 0.5981 (tptp) cc_final: 0.4272 (mmtt) REVERT: L 86 ARG cc_start: 0.5761 (mtt180) cc_final: 0.5417 (mtp180) REVERT: L 102 GLU cc_start: 0.5607 (mp0) cc_final: 0.4693 (tp30) REVERT: L 113 GLU cc_start: 0.5669 (mm-30) cc_final: 0.5279 (mp0) REVERT: L 141 GLU cc_start: 0.5051 (OUTLIER) cc_final: 0.4272 (mm-30) REVERT: L 153 ARG cc_start: 0.4140 (ttm170) cc_final: 0.3582 (ttm-80) outliers start: 83 outliers final: 54 residues processed: 469 average time/residue: 0.5146 time to fit residues: 359.8706 Evaluate side-chains 463 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 400 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 170 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 299 optimal weight: 1.9990 chunk 368 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS A 423 ASN A 498 ASN B 246 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN F 413 GLN G 180 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.151643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.118886 restraints weight = 34581.087| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.39 r_work: 0.3004 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30052 Z= 0.219 Angle : 0.614 8.806 40716 Z= 0.317 Chirality : 0.047 0.290 4564 Planarity : 0.006 0.048 5331 Dihedral : 5.365 80.418 4214 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.92 % Allowed : 13.85 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3764 helix: 1.29 (0.13), residues: 1592 sheet: -0.77 (0.20), residues: 588 loop : -0.23 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 97 HIS 0.008 0.001 HIS D 375 PHE 0.021 0.002 PHE E 130 TYR 0.016 0.002 TYR C 562 ARG 0.008 0.001 ARG G 159 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 1303) hydrogen bonds : angle 4.70391 ( 3738) covalent geometry : bond 0.00541 (30052) covalent geometry : angle 0.61386 (40716) *********************** 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 497 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 407 time to evaluate : 3.516 Fit side-chains REVERT: A 53 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: A 95 ARG cc_start: 0.7087 (tpt-90) cc_final: 0.6578 (tmt170) REVERT: A 156 ARG cc_start: 0.6251 (mtp-110) cc_final: 0.5768 (ttp-170) REVERT: A 169 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7051 (mt-10) REVERT: A 354 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7857 (tp) REVERT: A 374 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7011 (tt0) REVERT: A 416 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7168 (mtp85) REVERT: A 481 ARG cc_start: 0.7613 (mtm-85) cc_final: 0.7148 (mtp-110) REVERT: A 541 GLN cc_start: 0.6613 (mt0) cc_final: 0.6084 (pt0) REVERT: A 546 GLU cc_start: 0.7551 (mt-10) cc_final: 0.6682 (mm-30) REVERT: A 547 ARG cc_start: 0.7295 (ttm110) cc_final: 0.6884 (tpp80) REVERT: B 166 TYR cc_start: 0.7323 (m-80) cc_final: 0.6439 (m-80) REVERT: B 197 ARG cc_start: 0.7351 (ttp80) cc_final: 0.6934 (ttp-110) REVERT: B 340 ARG cc_start: 0.7517 (tpp-160) cc_final: 0.7130 (tpt-90) REVERT: B 449 GLU cc_start: 0.6431 (mm-30) cc_final: 0.6091 (mp0) REVERT: B 477 GLN cc_start: 0.6698 (pm20) cc_final: 0.6464 (mp10) REVERT: B 480 GLU cc_start: 0.6656 (mp0) cc_final: 0.5875 (mt-10) REVERT: B 481 ARG cc_start: 0.6937 (mmm-85) cc_final: 0.6369 (ttt-90) REVERT: C 1 MET cc_start: 0.5987 (mmm) cc_final: 0.5274 (mmp) REVERT: C 115 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7968 (tttm) REVERT: C 125 PRO cc_start: 0.7482 (Cg_exo) cc_final: 0.6945 (Cg_endo) REVERT: C 183 MET cc_start: 0.8703 (mtp) cc_final: 0.8497 (mtt) REVERT: C 344 MET cc_start: 0.8061 (mmp) cc_final: 0.7757 (mmm) REVERT: C 416 ARG cc_start: 0.7809 (mtm110) cc_final: 0.7203 (mtm180) REVERT: C 547 ARG cc_start: 0.6529 (mtp85) cc_final: 0.6234 (mtp180) REVERT: C 550 ARG cc_start: 0.7332 (ttm-80) cc_final: 0.6597 (mtm110) REVERT: D 34 ASP cc_start: 0.7455 (m-30) cc_final: 0.6988 (t0) REVERT: D 42 VAL cc_start: 0.7644 (t) cc_final: 0.7407 (m) REVERT: D 206 GLN cc_start: 0.6987 (tp40) cc_final: 0.6679 (mm-40) REVERT: D 305 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.6813 (mtpt) REVERT: D 376 LYS cc_start: 0.7274 (tppt) cc_final: 0.7070 (tttm) REVERT: D 420 ARG cc_start: 0.7493 (mtp-110) cc_final: 0.7134 (mtp-110) REVERT: D 444 SER cc_start: 0.8284 (p) cc_final: 0.8038 (m) REVERT: D 463 TYR cc_start: 0.7975 (t80) cc_final: 0.7426 (t80) REVERT: E 88 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7564 (mtt) REVERT: E 110 LYS cc_start: 0.7283 (ttmm) cc_final: 0.6891 (mtpp) REVERT: E 259 ASP cc_start: 0.7156 (m-30) cc_final: 0.6728 (m-30) REVERT: E 278 PRO cc_start: 0.8544 (Cg_endo) cc_final: 0.8193 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7426 (tt0) cc_final: 0.6599 (tp30) REVERT: E 380 ASP cc_start: 0.6269 (t0) cc_final: 0.6035 (t0) REVERT: E 410 ARG cc_start: 0.5857 (mtm-85) cc_final: 0.4635 (mmp80) REVERT: E 445 MET cc_start: 0.7461 (mtp) cc_final: 0.6930 (mtt) REVERT: F 6 LYS cc_start: 0.6444 (tptm) cc_final: 0.6160 (mtpp) REVERT: F 7 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7159 (mt-10) REVERT: F 109 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6402 (mm-30) REVERT: F 210 ARG cc_start: 0.6748 (ttp80) cc_final: 0.6514 (ttp80) REVERT: F 302 GLU cc_start: 0.8076 (tt0) cc_final: 0.7796 (tt0) REVERT: F 410 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6663 (mtm-85) REVERT: G 9 MET cc_start: 0.7558 (ttp) cc_final: 0.7148 (ptm) REVERT: G 47 MET cc_start: 0.5379 (mmm) cc_final: 0.4840 (ttm) REVERT: G 59 GLU cc_start: 0.5562 (OUTLIER) cc_final: 0.4290 (tp30) REVERT: G 200 LYS cc_start: 0.5612 (OUTLIER) cc_final: 0.5225 (mttt) REVERT: H 63 MET cc_start: 0.3874 (mmm) cc_final: 0.2438 (ttp) REVERT: H 77 LEU cc_start: 0.4158 (mm) cc_final: 0.3644 (mt) REVERT: J 112 LEU cc_start: 0.4386 (OUTLIER) cc_final: 0.4115 (mp) REVERT: J 162 GLN cc_start: 0.5962 (tt0) cc_final: 0.5579 (tt0) REVERT: K 102 LYS cc_start: 0.5579 (tptp) cc_final: 0.3984 (mmtt) REVERT: L 86 ARG cc_start: 0.5711 (mtt180) cc_final: 0.5226 (mtp180) REVERT: L 102 GLU cc_start: 0.5585 (mp0) cc_final: 0.4650 (tp30) REVERT: L 138 ARG cc_start: 0.4439 (mtt180) cc_final: 0.3718 (mtt90) REVERT: L 141 GLU cc_start: 0.5091 (OUTLIER) cc_final: 0.4367 (mm-30) REVERT: L 153 ARG cc_start: 0.4201 (ttm170) cc_final: 0.3625 (ttm-80) outliers start: 90 outliers final: 62 residues processed: 469 average time/residue: 0.5040 time to fit residues: 353.6825 Evaluate side-chains 467 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 395 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain J residue 65 GLU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 50 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 336 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 343 optimal weight: 8.9990 chunk 264 optimal weight: 7.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN G 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.154896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.132881 restraints weight = 34629.951| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 0.88 r_work: 0.3115 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30052 Z= 0.151 Angle : 0.535 6.948 40716 Z= 0.277 Chirality : 0.044 0.250 4564 Planarity : 0.005 0.048 5331 Dihedral : 5.144 80.909 4214 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.69 % Allowed : 14.43 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3764 helix: 1.41 (0.13), residues: 1577 sheet: -0.86 (0.20), residues: 611 loop : -0.16 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 119 HIS 0.004 0.001 HIS D 375 PHE 0.020 0.002 PHE E 130 TYR 0.012 0.001 TYR C 562 ARG 0.008 0.000 ARG G 159 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 1303) hydrogen bonds : angle 4.56218 ( 3738) covalent geometry : bond 0.00366 (30052) covalent geometry : angle 0.53537 (40716) *********************** 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 491 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 408 time to evaluate : 3.290 Fit side-chains REVERT: A 53 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: A 95 ARG cc_start: 0.7086 (tpt-90) cc_final: 0.6685 (tmt170) REVERT: A 156 ARG cc_start: 0.6308 (mtp-110) cc_final: 0.5854 (ttp-170) REVERT: A 169 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7122 (mt-10) REVERT: A 354 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7845 (tp) REVERT: A 374 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7095 (tt0) REVERT: A 416 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7112 (mtp85) REVERT: A 481 ARG cc_start: 0.7571 (mtm-85) cc_final: 0.7295 (mtp-110) REVERT: A 541 GLN cc_start: 0.6560 (mt0) cc_final: 0.6074 (pt0) REVERT: A 546 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6844 (mm-30) REVERT: A 547 ARG cc_start: 0.7284 (ttm110) cc_final: 0.6841 (ttm110) REVERT: B 85 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7364 (m-30) REVERT: B 166 TYR cc_start: 0.7248 (m-80) cc_final: 0.6469 (m-80) REVERT: B 197 ARG cc_start: 0.7448 (ttp80) cc_final: 0.7079 (ttp-110) REVERT: B 340 ARG cc_start: 0.7437 (tpp-160) cc_final: 0.7072 (tpt-90) REVERT: B 449 GLU cc_start: 0.6372 (mm-30) cc_final: 0.6147 (mp0) REVERT: B 477 GLN cc_start: 0.6799 (pm20) cc_final: 0.6578 (mp10) REVERT: B 480 GLU cc_start: 0.6791 (mp0) cc_final: 0.6040 (mt-10) REVERT: B 481 ARG cc_start: 0.7064 (mmm-85) cc_final: 0.6391 (ttt-90) REVERT: B 547 ARG cc_start: 0.6507 (ttm-80) cc_final: 0.5616 (mmm160) REVERT: C 1 MET cc_start: 0.5950 (mmm) cc_final: 0.5234 (mmp) REVERT: C 3 GLN cc_start: 0.7465 (mt0) cc_final: 0.7214 (mm-40) REVERT: C 125 PRO cc_start: 0.7559 (Cg_exo) cc_final: 0.7075 (Cg_endo) REVERT: C 183 MET cc_start: 0.8624 (mtp) cc_final: 0.8363 (mtt) REVERT: C 416 ARG cc_start: 0.7759 (mtm110) cc_final: 0.7324 (mtm180) REVERT: C 525 GLU cc_start: 0.6232 (mt-10) cc_final: 0.6025 (mt-10) REVERT: C 547 ARG cc_start: 0.6527 (mtp85) cc_final: 0.6272 (mtp180) REVERT: C 550 ARG cc_start: 0.7444 (ttm-80) cc_final: 0.6886 (mtm110) REVERT: C 574 PHE cc_start: 0.6203 (m-80) cc_final: 0.5692 (m-80) REVERT: D 34 ASP cc_start: 0.7289 (m-30) cc_final: 0.6774 (t0) REVERT: D 42 VAL cc_start: 0.7611 (t) cc_final: 0.7320 (m) REVERT: D 52 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7216 (mt-10) REVERT: D 305 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.6861 (mtpt) REVERT: D 420 ARG cc_start: 0.7482 (mtp-110) cc_final: 0.7117 (mtp-110) REVERT: D 444 SER cc_start: 0.8363 (p) cc_final: 0.8151 (m) REVERT: D 463 TYR cc_start: 0.7944 (t80) cc_final: 0.7380 (t80) REVERT: E 88 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7535 (mtt) REVERT: E 110 LYS cc_start: 0.7306 (ttmm) cc_final: 0.6961 (mtpp) REVERT: E 259 ASP cc_start: 0.6864 (m-30) cc_final: 0.6457 (m-30) REVERT: E 278 PRO cc_start: 0.8593 (Cg_endo) cc_final: 0.8222 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7302 (tt0) cc_final: 0.6702 (tp30) REVERT: E 410 ARG cc_start: 0.5956 (mtm-85) cc_final: 0.4779 (mmp80) REVERT: E 445 MET cc_start: 0.7411 (mtp) cc_final: 0.6956 (mtt) REVERT: F 6 LYS cc_start: 0.6476 (tptm) cc_final: 0.6195 (mtpp) REVERT: F 7 GLU cc_start: 0.7579 (mt-10) cc_final: 0.6865 (mt-10) REVERT: F 109 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6342 (mm-30) REVERT: F 302 GLU cc_start: 0.7955 (tt0) cc_final: 0.7723 (tt0) REVERT: G 9 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.7084 (ptm) REVERT: G 47 MET cc_start: 0.5618 (mmm) cc_final: 0.5054 (ttm) REVERT: G 59 GLU cc_start: 0.5602 (OUTLIER) cc_final: 0.4327 (tp30) REVERT: G 200 LYS cc_start: 0.5834 (OUTLIER) cc_final: 0.5210 (mttt) REVERT: H 63 MET cc_start: 0.4068 (mmm) cc_final: 0.2428 (ttp) REVERT: H 77 LEU cc_start: 0.4214 (mm) cc_final: 0.3686 (mt) REVERT: J 173 ARG cc_start: 0.3825 (ttt180) cc_final: 0.3432 (mtp85) REVERT: K 102 LYS cc_start: 0.5742 (tptp) cc_final: 0.4086 (mmtt) REVERT: L 86 ARG cc_start: 0.5731 (mtt180) cc_final: 0.5385 (mtp180) REVERT: L 102 GLU cc_start: 0.5537 (mp0) cc_final: 0.4620 (tp30) REVERT: L 138 ARG cc_start: 0.4583 (mtt180) cc_final: 0.3950 (mtt90) REVERT: L 141 GLU cc_start: 0.5074 (OUTLIER) cc_final: 0.4448 (mm-30) REVERT: L 164 GLU cc_start: 0.5796 (tp30) cc_final: 0.5286 (mt-10) outliers start: 83 outliers final: 58 residues processed: 464 average time/residue: 0.5427 time to fit residues: 374.8135 Evaluate side-chains 461 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 394 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 367 optimal weight: 20.0000 chunk 366 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 131 optimal weight: 0.4980 chunk 84 optimal weight: 7.9990 chunk 300 optimal weight: 7.9990 chunk 279 optimal weight: 0.9980 chunk 237 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 171 optimal weight: 0.0980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN F 388 ASN F 413 GLN G 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.155734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.131402 restraints weight = 34380.200| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 0.97 r_work: 0.3099 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30052 Z= 0.133 Angle : 0.515 7.714 40716 Z= 0.266 Chirality : 0.043 0.237 4564 Planarity : 0.005 0.048 5331 Dihedral : 4.998 82.242 4214 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.37 % Allowed : 14.79 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3764 helix: 1.53 (0.13), residues: 1598 sheet: -0.78 (0.20), residues: 606 loop : -0.16 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 119 HIS 0.003 0.001 HIS D 375 PHE 0.020 0.001 PHE E 130 TYR 0.011 0.001 TYR C 562 ARG 0.010 0.000 ARG L 153 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 1303) hydrogen bonds : angle 4.46256 ( 3738) covalent geometry : bond 0.00318 (30052) covalent geometry : angle 0.51512 (40716) *********************** 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 478 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 405 time to evaluate : 3.949 Fit side-chains REVERT: A 53 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: A 95 ARG cc_start: 0.7076 (tpt-90) cc_final: 0.6632 (tmt170) REVERT: A 156 ARG cc_start: 0.6284 (mtp-110) cc_final: 0.5800 (ttp-170) REVERT: A 169 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7091 (mt-10) REVERT: A 354 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7780 (tp) REVERT: A 374 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7061 (tt0) REVERT: A 416 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7095 (mtp85) REVERT: A 481 ARG cc_start: 0.7489 (mtm-85) cc_final: 0.7148 (mtp-110) REVERT: A 541 GLN cc_start: 0.6549 (mt0) cc_final: 0.6003 (pt0) REVERT: A 542 LEU cc_start: 0.7518 (mm) cc_final: 0.7312 (mp) REVERT: A 547 ARG cc_start: 0.7224 (ttm110) cc_final: 0.6744 (ttm110) REVERT: B 166 TYR cc_start: 0.7265 (m-80) cc_final: 0.6463 (m-80) REVERT: B 197 ARG cc_start: 0.7375 (ttp80) cc_final: 0.7007 (ttp-110) REVERT: B 340 ARG cc_start: 0.7461 (tpp-160) cc_final: 0.7083 (tpt-90) REVERT: B 449 GLU cc_start: 0.6380 (mm-30) cc_final: 0.6126 (mp0) REVERT: B 477 GLN cc_start: 0.6725 (pm20) cc_final: 0.6503 (mp10) REVERT: B 480 GLU cc_start: 0.6734 (mp0) cc_final: 0.5940 (mt-10) REVERT: B 481 ARG cc_start: 0.6957 (mmm-85) cc_final: 0.6318 (ttt-90) REVERT: B 547 ARG cc_start: 0.6471 (ttm-80) cc_final: 0.5500 (mmm160) REVERT: C 3 GLN cc_start: 0.7494 (mt0) cc_final: 0.7209 (mm-40) REVERT: C 125 PRO cc_start: 0.7491 (Cg_exo) cc_final: 0.7056 (Cg_endo) REVERT: C 183 MET cc_start: 0.8599 (mtp) cc_final: 0.8309 (mtt) REVERT: C 312 TYR cc_start: 0.8886 (t80) cc_final: 0.8648 (t80) REVERT: C 391 MET cc_start: 0.8812 (mmt) cc_final: 0.8395 (mmt) REVERT: C 416 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7258 (mtm180) REVERT: C 525 GLU cc_start: 0.6237 (mt-10) cc_final: 0.6017 (mt-10) REVERT: C 547 ARG cc_start: 0.6501 (mtp85) cc_final: 0.6216 (mtp180) REVERT: C 550 ARG cc_start: 0.7347 (ttm-80) cc_final: 0.6775 (mtm110) REVERT: C 574 PHE cc_start: 0.6281 (m-80) cc_final: 0.5746 (m-80) REVERT: D 34 ASP cc_start: 0.7280 (m-30) cc_final: 0.6778 (t0) REVERT: D 42 VAL cc_start: 0.7623 (t) cc_final: 0.7316 (m) REVERT: D 52 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7205 (mt-10) REVERT: D 305 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6813 (mtpt) REVERT: D 420 ARG cc_start: 0.7412 (mtp-110) cc_final: 0.7054 (mtp-110) REVERT: D 463 TYR cc_start: 0.7958 (t80) cc_final: 0.7382 (t80) REVERT: E 88 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7571 (mtt) REVERT: E 110 LYS cc_start: 0.7227 (ttmm) cc_final: 0.6890 (mtpp) REVERT: E 259 ASP cc_start: 0.6885 (m-30) cc_final: 0.6475 (m-30) REVERT: E 278 PRO cc_start: 0.8527 (Cg_endo) cc_final: 0.8204 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7378 (tt0) cc_final: 0.6731 (tp30) REVERT: E 410 ARG cc_start: 0.5902 (mtm-85) cc_final: 0.4698 (mmp80) REVERT: E 445 MET cc_start: 0.7444 (mtp) cc_final: 0.6959 (mtt) REVERT: F 6 LYS cc_start: 0.6450 (tptm) cc_final: 0.6172 (mtpp) REVERT: F 7 GLU cc_start: 0.7619 (mt-10) cc_final: 0.6820 (mt-10) REVERT: F 109 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6273 (mm-30) REVERT: F 210 ARG cc_start: 0.6629 (ttp80) cc_final: 0.6382 (mtm110) REVERT: F 302 GLU cc_start: 0.7935 (tt0) cc_final: 0.7687 (tt0) REVERT: G 9 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7062 (ptm) REVERT: G 47 MET cc_start: 0.5514 (mmm) cc_final: 0.4943 (ttm) REVERT: G 59 GLU cc_start: 0.5506 (OUTLIER) cc_final: 0.4267 (tp30) REVERT: G 200 LYS cc_start: 0.5712 (OUTLIER) cc_final: 0.5165 (mttt) REVERT: H 63 MET cc_start: 0.3974 (mmm) cc_final: 0.2427 (ttp) REVERT: H 77 LEU cc_start: 0.4104 (mm) cc_final: 0.3635 (mt) REVERT: J 112 LEU cc_start: 0.4485 (OUTLIER) cc_final: 0.4249 (mp) REVERT: J 173 ARG cc_start: 0.3757 (ttt180) cc_final: 0.3383 (mtp85) REVERT: K 102 LYS cc_start: 0.5694 (tptp) cc_final: 0.4047 (mmtt) REVERT: L 86 ARG cc_start: 0.5736 (mtt180) cc_final: 0.5361 (mtp180) REVERT: L 102 GLU cc_start: 0.5586 (mp0) cc_final: 0.4684 (tp30) REVERT: L 138 ARG cc_start: 0.4470 (mtt180) cc_final: 0.3843 (mtt90) REVERT: L 141 GLU cc_start: 0.5017 (OUTLIER) cc_final: 0.4468 (mm-30) REVERT: L 153 ARG cc_start: 0.5940 (mtp-110) cc_final: 0.3826 (mtt180) REVERT: L 164 GLU cc_start: 0.5845 (tp30) cc_final: 0.4884 (mt-10) outliers start: 73 outliers final: 59 residues processed: 454 average time/residue: 0.5513 time to fit residues: 377.3016 Evaluate side-chains 472 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 404 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 265 optimal weight: 0.0770 chunk 302 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 chunk 371 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 271 optimal weight: 5.9990 overall best weight: 1.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN G 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.156544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.135557 restraints weight = 34217.095| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 0.85 r_work: 0.3164 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30052 Z= 0.114 Angle : 0.495 7.512 40716 Z= 0.256 Chirality : 0.043 0.227 4564 Planarity : 0.004 0.048 5331 Dihedral : 4.887 83.706 4214 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.08 % Allowed : 15.28 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3764 helix: 1.62 (0.13), residues: 1598 sheet: -0.71 (0.20), residues: 607 loop : -0.10 (0.16), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 119 HIS 0.003 0.001 HIS D 375 PHE 0.019 0.001 PHE E 130 TYR 0.010 0.001 TYR C 312 ARG 0.010 0.000 ARG G 159 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 1303) hydrogen bonds : angle 4.39722 ( 3738) covalent geometry : bond 0.00267 (30052) covalent geometry : angle 0.49520 (40716) ********************** 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 471 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 407 time to evaluate : 3.286 Fit side-chains REVERT: A 53 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: A 95 ARG cc_start: 0.7139 (tpt-90) cc_final: 0.6792 (tmt170) REVERT: A 156 ARG cc_start: 0.6341 (mtp-110) cc_final: 0.5885 (ttp-170) REVERT: A 169 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7213 (mt-10) REVERT: A 354 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7816 (tp) REVERT: A 374 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7186 (tt0) REVERT: A 416 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7203 (mtp85) REVERT: A 513 TYR cc_start: 0.8492 (t80) cc_final: 0.8289 (t80) REVERT: A 541 GLN cc_start: 0.6577 (mt0) cc_final: 0.6108 (pt0) REVERT: A 547 ARG cc_start: 0.7256 (ttm110) cc_final: 0.6869 (ttm110) REVERT: B 166 TYR cc_start: 0.7230 (m-80) cc_final: 0.6532 (m-80) REVERT: B 197 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7212 (ttp-110) REVERT: B 340 ARG cc_start: 0.7486 (tpp-160) cc_final: 0.7118 (tpt-90) REVERT: B 481 ARG cc_start: 0.7164 (mmm-85) cc_final: 0.6617 (ttt-90) REVERT: B 547 ARG cc_start: 0.6576 (ttm-80) cc_final: 0.5660 (mmm160) REVERT: C 3 GLN cc_start: 0.7509 (mt0) cc_final: 0.7293 (mm-40) REVERT: C 106 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8229 (t) REVERT: C 125 PRO cc_start: 0.7651 (Cg_exo) cc_final: 0.7216 (Cg_endo) REVERT: C 183 MET cc_start: 0.8555 (mtp) cc_final: 0.8251 (mtt) REVERT: C 312 TYR cc_start: 0.8812 (t80) cc_final: 0.8577 (t80) REVERT: C 391 MET cc_start: 0.8772 (mmt) cc_final: 0.8406 (mmt) REVERT: C 416 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7431 (mtm180) REVERT: C 547 ARG cc_start: 0.6484 (mtp85) cc_final: 0.6260 (mtp180) REVERT: C 550 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7004 (mtm110) REVERT: C 574 PHE cc_start: 0.6388 (m-80) cc_final: 0.5838 (m-80) REVERT: D 34 ASP cc_start: 0.7413 (m-30) cc_final: 0.6884 (t0) REVERT: D 42 VAL cc_start: 0.7593 (t) cc_final: 0.7318 (m) REVERT: D 52 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7279 (mt-10) REVERT: D 209 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7452 (mt-10) REVERT: D 305 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.6929 (mtpt) REVERT: D 420 ARG cc_start: 0.7491 (mtp-110) cc_final: 0.7177 (mtp-110) REVERT: D 463 TYR cc_start: 0.7981 (t80) cc_final: 0.7459 (t80) REVERT: E 88 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7690 (mtt) REVERT: E 110 LYS cc_start: 0.7242 (ttmm) cc_final: 0.6928 (mtpp) REVERT: E 259 ASP cc_start: 0.6932 (m-30) cc_final: 0.6552 (m-30) REVERT: E 278 PRO cc_start: 0.8526 (Cg_endo) cc_final: 0.8187 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7379 (tt0) cc_final: 0.6895 (tp30) REVERT: E 410 ARG cc_start: 0.5960 (mtm-85) cc_final: 0.4774 (mmp80) REVERT: E 445 MET cc_start: 0.7446 (mtp) cc_final: 0.7025 (mtt) REVERT: F 6 LYS cc_start: 0.6517 (tptm) cc_final: 0.6247 (mtpp) REVERT: F 7 GLU cc_start: 0.7729 (mt-10) cc_final: 0.6955 (mt-10) REVERT: F 109 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6321 (mm-30) REVERT: F 210 ARG cc_start: 0.6797 (ttp80) cc_final: 0.5935 (mtm110) REVERT: G 9 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7103 (ptm) REVERT: G 47 MET cc_start: 0.5746 (mmm) cc_final: 0.5148 (ttm) REVERT: G 58 LYS cc_start: 0.6252 (tmmt) cc_final: 0.5397 (tptt) REVERT: G 59 GLU cc_start: 0.5569 (OUTLIER) cc_final: 0.4370 (tp30) REVERT: G 200 LYS cc_start: 0.5811 (OUTLIER) cc_final: 0.5210 (mttt) REVERT: H 63 MET cc_start: 0.4084 (mmm) cc_final: 0.2433 (ttp) REVERT: H 77 LEU cc_start: 0.4345 (mm) cc_final: 0.3821 (mt) REVERT: J 112 LEU cc_start: 0.4580 (OUTLIER) cc_final: 0.4343 (mp) REVERT: J 173 ARG cc_start: 0.3896 (ttt180) cc_final: 0.3467 (mtp85) REVERT: K 102 LYS cc_start: 0.5902 (tptp) cc_final: 0.4173 (mmtt) REVERT: L 86 ARG cc_start: 0.5838 (mtt180) cc_final: 0.5477 (mtp180) REVERT: L 102 GLU cc_start: 0.5570 (mp0) cc_final: 0.4698 (tp30) REVERT: L 138 ARG cc_start: 0.4514 (mtt180) cc_final: 0.3976 (mtt90) REVERT: L 141 GLU cc_start: 0.5129 (OUTLIER) cc_final: 0.4516 (mm-30) REVERT: L 153 ARG cc_start: 0.6082 (mtp-110) cc_final: 0.4084 (mtt180) REVERT: L 164 GLU cc_start: 0.5814 (tp30) cc_final: 0.5071 (mt-10) outliers start: 64 outliers final: 53 residues processed: 451 average time/residue: 0.5113 time to fit residues: 344.5861 Evaluate side-chains 456 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 393 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 367 optimal weight: 20.0000 chunk 194 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 313 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 265 optimal weight: 0.6980 chunk 294 optimal weight: 6.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN F 413 GLN G 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.153534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.120260 restraints weight = 34520.689| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.36 r_work: 0.3041 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30052 Z= 0.140 Angle : 0.522 6.787 40716 Z= 0.270 Chirality : 0.044 0.218 4564 Planarity : 0.005 0.048 5331 Dihedral : 4.963 83.291 4214 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.21 % Allowed : 15.15 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 3764 helix: 1.54 (0.13), residues: 1583 sheet: -0.72 (0.20), residues: 602 loop : -0.11 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 119 HIS 0.004 0.001 HIS D 375 PHE 0.021 0.002 PHE A 522 TYR 0.012 0.001 TYR C 562 ARG 0.010 0.000 ARG G 159 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 1303) hydrogen bonds : angle 4.42959 ( 3738) covalent geometry : bond 0.00339 (30052) covalent geometry : angle 0.52155 (40716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20239.82 seconds wall clock time: 354 minutes 24.67 seconds (21264.67 seconds total)