Starting phenix.real_space_refine on Fri Jun 5 17:39:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9va1_64896/06_2026/9va1_64896_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9va1_64896/06_2026/9va1_64896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9va1_64896/06_2026/9va1_64896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9va1_64896/06_2026/9va1_64896.map" model { file = "/net/cci-nas-00/data/ceres_data/9va1_64896/06_2026/9va1_64896_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9va1_64896/06_2026/9va1_64896_neut.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.055 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 14184 2.51 5 N 3530 2.21 5 O 3978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21820 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 6096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6096 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Chain: "D" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain: "A" Number of atoms: 6096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6096 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Chain: "B" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 5.65, per 1000 atoms: 0.26 Number of scatterers: 21820 At special positions: 0 Unit cell: (141.93, 135.945, 182.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3978 8.00 N 3530 7.00 C 14184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 383 " distance=2.03 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: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5088 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 67.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'C' and resid 20 through 53 removed outlier: 4.051A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 Processing helix chain 'C' and resid 94 through 100 removed outlier: 3.511A pdb=" N GLN C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 157 through 193 removed outlier: 3.592A pdb=" N ARG C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLN C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.778A pdb=" N VAL C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.737A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 252 removed outlier: 3.546A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 275 through 280 removed outlier: 3.810A pdb=" N SER C 280 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 300 Processing helix chain 'C' and resid 305 through 318 Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.540A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.874A pdb=" N ARG C 393 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.927A pdb=" N ALA C 403 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 404 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 412 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 431 through 465 removed outlier: 3.639A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR C 449 " --> pdb=" O THR C 445 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU C 450 " --> pdb=" O ILE C 446 " (cutoff:3.500A) Proline residue: C 451 - end of helix removed outlier: 3.703A pdb=" N LYS C 465 " --> pdb=" O TRP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 513 through 533 removed outlier: 3.604A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N CYS C 530 " --> pdb=" O GLN C 526 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 547 through 559 removed outlier: 4.014A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 removed outlier: 3.621A pdb=" N VAL C 573 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 588 through 599 Processing helix chain 'C' and resid 623 through 628 removed outlier: 3.548A pdb=" N ALA C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 658 removed outlier: 3.638A pdb=" N MET C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 696 through 715 removed outlier: 5.402A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 714 " --> pdb=" O ARG C 710 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 767 removed outlier: 3.736A pdb=" N ILE C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 37 through 48 Processing helix chain 'D' and resid 56 through 65 removed outlier: 4.090A pdb=" N TYR D 60 " --> pdb=" O TRP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 97 removed outlier: 5.060A pdb=" N ILE D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix removed outlier: 3.626A pdb=" N ARG D 97 " --> pdb=" O GLY D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 108 through 111 Processing helix chain 'D' and resid 112 through 142 removed outlier: 3.982A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR D 128 " --> pdb=" O MET D 124 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 152 removed outlier: 4.160A pdb=" N ASP D 152 " --> pdb=" O PRO D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 169 Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 194 through 212 removed outlier: 3.840A pdb=" N LEU D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS D 200 " --> pdb=" O TRP D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 227 removed outlier: 3.891A pdb=" N ALA D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 243 removed outlier: 3.962A pdb=" N THR D 235 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.879A pdb=" N PHE D 255 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 279 removed outlier: 3.567A pdb=" N TRP D 268 " --> pdb=" O GLN D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 290 removed outlier: 3.943A pdb=" N ILE D 287 " --> pdb=" O PHE D 283 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 298 through 349 removed outlier: 4.229A pdb=" N ASP D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 4.160A pdb=" N ASN D 354 " --> pdb=" O PRO D 351 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL D 355 " --> pdb=" O GLU D 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 355' Processing helix chain 'D' and resid 359 through 371 Processing helix chain 'D' and resid 371 through 377 Processing helix chain 'D' and resid 401 through 408 Processing helix chain 'D' and resid 412 through 430 removed outlier: 3.540A pdb=" N TRP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 445 Proline residue: D 442 - end of helix removed outlier: 3.541A pdb=" N ASP D 445 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 470 removed outlier: 4.127A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 475 Processing helix chain 'D' and resid 477 through 490 removed outlier: 3.533A pdb=" N TRP D 481 " --> pdb=" O SER D 477 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY D 490 " --> pdb=" O ASP D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 508 removed outlier: 4.196A pdb=" N ALA D 498 " --> pdb=" O LEU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 523 Processing helix chain 'D' and resid 527 through 536 removed outlier: 3.502A pdb=" N GLN D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.835A pdb=" N LEU D 540 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE D 550 " --> pdb=" O PHE D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 583 Processing helix chain 'D' and resid 584 through 608 removed outlier: 4.574A pdb=" N VAL D 592 " --> pdb=" O ILE D 588 " (cutoff:3.500A) Proline residue: D 593 - end of helix removed outlier: 4.463A pdb=" N ILE D 597 " --> pdb=" O PRO D 593 " (cutoff:3.500A) Proline residue: D 598 - end of helix Processing helix chain 'A' and resid 21 through 53 removed outlier: 4.051A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.511A pdb=" N GLN A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 193 removed outlier: 3.592A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.777A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 232 removed outlier: 3.737A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.545A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.810A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.540A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.874A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.927A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 431 through 465 removed outlier: 3.638A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.703A pdb=" N LYS A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.604A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N CYS A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.014A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.621A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.548A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 658 removed outlier: 3.637A pdb=" N MET A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 696 through 715 removed outlier: 5.402A pdb=" N SER A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 767 removed outlier: 3.737A pdb=" N ILE A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 37 through 48 Processing helix chain 'B' and resid 56 through 65 removed outlier: 4.090A pdb=" N TYR B 60 " --> pdb=" O TRP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 97 removed outlier: 5.060A pdb=" N ILE B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix removed outlier: 3.626A pdb=" N ARG B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 108 through 111 Processing helix chain 'B' and resid 112 through 142 removed outlier: 3.982A pdb=" N LEU B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 132 " --> pdb=" O TYR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 152 removed outlier: 4.161A pdb=" N ASP B 152 " --> pdb=" O PRO B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 169 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.840A pdb=" N LEU B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS B 200 " --> pdb=" O TRP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 227 removed outlier: 3.890A pdb=" N ALA B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 243 removed outlier: 3.961A pdb=" N THR B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.879A pdb=" N PHE B 255 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 279 removed outlier: 3.568A pdb=" N TRP B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 290 removed outlier: 3.943A pdb=" N ILE B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 298 through 349 removed outlier: 4.228A pdb=" N ASP B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 removed outlier: 4.159A pdb=" N ASN B 354 " --> pdb=" O PRO B 351 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL B 355 " --> pdb=" O GLU B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 355' Processing helix chain 'B' and resid 359 through 371 Processing helix chain 'B' and resid 371 through 377 Processing helix chain 'B' and resid 401 through 408 Processing helix chain 'B' and resid 412 through 430 removed outlier: 3.540A pdb=" N TRP B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 445 Proline residue: B 442 - end of helix removed outlier: 3.541A pdb=" N ASP B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 470 removed outlier: 4.127A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 Processing helix chain 'B' and resid 477 through 490 removed outlier: 3.694A pdb=" N TYR B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY B 490 " --> pdb=" O ASP B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 508 removed outlier: 4.197A pdb=" N ALA B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 523 Processing helix chain 'B' and resid 527 through 536 removed outlier: 3.501A pdb=" N GLN B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 552 removed outlier: 3.834A pdb=" N LEU B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 550 " --> pdb=" O PHE B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 583 Processing helix chain 'B' and resid 584 through 608 removed outlier: 4.575A pdb=" N VAL B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Proline residue: B 593 - end of helix removed outlier: 4.463A pdb=" N ILE B 597 " --> pdb=" O PRO B 593 " (cutoff:3.500A) Proline residue: B 598 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'C' and resid 262 through 263 removed outlier: 5.780A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 670 through 673 Processing sheet with id=AA4, first strand: chain 'D' and resid 559 through 562 removed outlier: 3.903A pdb=" N GLN D 574 " --> pdb=" O ILE D 562 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.779A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 670 through 673 Processing sheet with id=AA8, first strand: chain 'B' and resid 559 through 562 removed outlier: 3.902A pdb=" N GLN B 574 " --> pdb=" O ILE B 562 " (cutoff:3.500A) 1150 hydrogen bonds defined for protein. 3372 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: 3.80 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5536 1.33 - 1.45: 4601 1.45 - 1.57: 12083 1.57 - 1.69: 0 1.69 - 1.81: 210 Bond restraints: 22430 Sorted by residual: bond pdb=" CA THR D 160 " pdb=" C THR D 160 " ideal model delta sigma weight residual 1.523 1.501 0.022 8.20e-03 1.49e+04 7.33e+00 bond pdb=" CA THR B 160 " pdb=" C THR B 160 " ideal model delta sigma weight residual 1.523 1.501 0.022 8.20e-03 1.49e+04 7.12e+00 bond pdb=" N GLN A 89 " pdb=" CA GLN A 89 " ideal model delta sigma weight residual 1.458 1.485 -0.026 1.23e-02 6.61e+03 4.47e+00 bond pdb=" N GLN C 89 " pdb=" CA GLN C 89 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.23e-02 6.61e+03 4.37e+00 bond pdb=" CB TRP D 56 " pdb=" CG TRP D 56 " ideal model delta sigma weight residual 1.498 1.437 0.061 3.10e-02 1.04e+03 3.91e+00 ... (remaining 22425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 29758 1.84 - 3.67: 631 3.67 - 5.51: 118 5.51 - 7.35: 21 7.35 - 9.18: 8 Bond angle restraints: 30536 Sorted by residual: angle pdb=" N THR B 160 " pdb=" CA THR B 160 " pdb=" C THR B 160 " ideal model delta sigma weight residual 111.34 104.21 7.13 1.49e+00 4.50e-01 2.29e+01 angle pdb=" N THR D 160 " pdb=" CA THR D 160 " pdb=" C THR D 160 " ideal model delta sigma weight residual 111.34 104.22 7.12 1.49e+00 4.50e-01 2.28e+01 angle pdb=" C GLU A 171 " pdb=" N VAL A 172 " pdb=" CA VAL A 172 " ideal model delta sigma weight residual 122.66 118.46 4.20 9.70e-01 1.06e+00 1.88e+01 angle pdb=" C GLU C 171 " pdb=" N VAL C 172 " pdb=" CA VAL C 172 " ideal model delta sigma weight residual 122.66 118.47 4.19 9.70e-01 1.06e+00 1.86e+01 angle pdb=" N ILE A 259 " pdb=" CA ILE A 259 " pdb=" C ILE A 259 " ideal model delta sigma weight residual 113.10 109.09 4.01 9.70e-01 1.06e+00 1.71e+01 ... (remaining 30531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 11810 17.91 - 35.82: 1096 35.82 - 53.72: 161 53.72 - 71.63: 54 71.63 - 89.54: 27 Dihedral angle restraints: 13148 sinusoidal: 5238 harmonic: 7910 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -135.07 49.07 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS C 530 " pdb=" SG CYS C 530 " pdb=" SG CYS C 542 " pdb=" CB CYS C 542 " ideal model delta sinusoidal sigma weight residual -86.00 -135.07 49.07 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CA CYS C 530 " pdb=" C CYS C 530 " pdb=" N GLN C 531 " pdb=" CA GLN C 531 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 13145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2418 0.044 - 0.088: 754 0.088 - 0.132: 154 0.132 - 0.176: 8 0.176 - 0.220: 4 Chirality restraints: 3338 Sorted by residual: chirality pdb=" CB ILE B 597 " pdb=" CA ILE B 597 " pdb=" CG1 ILE B 597 " pdb=" CG2 ILE B 597 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE D 597 " pdb=" CA ILE D 597 " pdb=" CG1 ILE D 597 " pdb=" CG2 ILE D 597 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB VAL A 59 " pdb=" CA VAL A 59 " pdb=" CG1 VAL A 59 " pdb=" CG2 VAL A 59 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 3335 not shown) Planarity restraints: 3876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 701 " 0.017 2.00e-02 2.50e+03 1.03e-02 2.66e+00 pdb=" CG TRP B 701 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP B 701 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 701 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 701 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 701 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 701 " -0.022 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 701 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 701 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 701 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 701 " -0.017 2.00e-02 2.50e+03 1.03e-02 2.64e+00 pdb=" CG TRP D 701 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP D 701 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP D 701 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 701 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 701 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 701 " 0.022 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 701 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 701 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 701 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 732 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 733 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 733 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 733 " -0.021 5.00e-02 4.00e+02 ... (remaining 3873 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2230 2.74 - 3.28: 24962 3.28 - 3.82: 38289 3.82 - 4.36: 44513 4.36 - 4.90: 72528 Nonbonded interactions: 182522 Sorted by model distance: nonbonded pdb=" O ASN D 182 " pdb=" ND2 ASN D 476 " model vdw 2.195 3.120 nonbonded pdb=" NH1 ARG A 678 " pdb=" OD1 ASN B 346 " model vdw 2.215 3.120 nonbonded pdb=" NH1 ARG C 678 " pdb=" OD1 ASN D 346 " model vdw 2.216 3.120 nonbonded pdb=" O THR C 125 " pdb=" OG1 THR C 129 " model vdw 2.217 3.040 nonbonded pdb=" O THR A 125 " pdb=" OG1 THR A 129 " model vdw 2.217 3.040 ... (remaining 182517 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' } ncs_group { reference = chain 'D' selection = chain 'B' } 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: 0.010 Normalize map: mean=0, sd=1: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.520 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 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 : 0.004 0.061 22440 Z= 0.217 Angle : 0.707 9.184 30556 Z= 0.416 Chirality : 0.043 0.220 3338 Planarity : 0.004 0.037 3876 Dihedral : 14.612 89.541 8030 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.88 % Allowed : 6.99 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.14), residues: 2700 helix: -1.20 (0.11), residues: 1630 sheet: -3.06 (0.60), residues: 44 loop : -2.90 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 169 TYR 0.013 0.001 TYR A 41 PHE 0.015 0.001 PHE B 548 TRP 0.022 0.001 TRP B 701 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.22 (22430) covalent geometry : angle 0.70638 / 0.42 (30536) SS BOND : bond 0.00267 / 0.16 ( 10) SS BOND : angle 1.21660 / 0.70 ( 20) hydrogen bonds : bond 0.13671 / 9.14 ( 1150) hydrogen bonds : angle 5.81526 / 4.26 ( 3372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 597 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 PHE cc_start: 0.8747 (t80) cc_final: 0.8205 (t80) REVERT: C 157 ASP cc_start: 0.7037 (t0) cc_final: 0.6619 (t70) REVERT: C 312 GLU cc_start: 0.7629 (tt0) cc_final: 0.7215 (tt0) REVERT: C 323 MET cc_start: 0.6646 (mmp) cc_final: 0.6282 (mmm) REVERT: C 465 LYS cc_start: 0.7436 (ptpt) cc_final: 0.7132 (ptmt) REVERT: C 470 LYS cc_start: 0.8368 (mtpp) cc_final: 0.8036 (mttt) REVERT: C 483 GLU cc_start: 0.7070 (tt0) cc_final: 0.6856 (tt0) REVERT: C 578 ASN cc_start: 0.8191 (p0) cc_final: 0.7979 (p0) REVERT: C 607 SER cc_start: 0.8734 (m) cc_final: 0.8286 (p) REVERT: C 625 LYS cc_start: 0.8348 (mtpp) cc_final: 0.8050 (ttmm) REVERT: C 706 MET cc_start: 0.8058 (ttm) cc_final: 0.7854 (ttt) REVERT: C 723 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7575 (mt-10) REVERT: C 740 SER cc_start: 0.3846 (OUTLIER) cc_final: 0.3582 (p) REVERT: D 28 GLU cc_start: 0.5839 (OUTLIER) cc_final: 0.4758 (pm20) REVERT: D 92 ILE cc_start: 0.7599 (tt) cc_final: 0.7399 (tt) REVERT: D 107 ILE cc_start: 0.8350 (mm) cc_final: 0.8129 (tt) REVERT: D 217 GLU cc_start: 0.5310 (tm-30) cc_final: 0.5023 (tm-30) REVERT: D 218 THR cc_start: 0.7275 (m) cc_final: 0.6772 (p) REVERT: D 221 LYS cc_start: 0.6683 (mptt) cc_final: 0.6455 (mmtp) REVERT: D 266 ASP cc_start: 0.8069 (p0) cc_final: 0.7572 (t70) REVERT: D 391 GLU cc_start: 0.7205 (pp20) cc_final: 0.6998 (tt0) REVERT: D 401 ILE cc_start: 0.6344 (mm) cc_final: 0.6068 (mt) REVERT: D 405 GLU cc_start: 0.7579 (tt0) cc_final: 0.7258 (tt0) REVERT: D 415 LEU cc_start: 0.7129 (pp) cc_final: 0.6579 (mt) REVERT: D 430 SER cc_start: 0.7290 (t) cc_final: 0.6908 (p) REVERT: D 525 LYS cc_start: 0.8408 (mttt) cc_final: 0.8039 (ptpt) REVERT: D 542 MET cc_start: 0.8057 (mmp) cc_final: 0.7459 (mtt) REVERT: D 562 ILE cc_start: 0.8639 (pt) cc_final: 0.8429 (pt) REVERT: A 152 MET cc_start: 0.6395 (mmm) cc_final: 0.5412 (mmt) REVERT: A 312 GLU cc_start: 0.7517 (tt0) cc_final: 0.6963 (mt-10) REVERT: A 323 MET cc_start: 0.6174 (mmp) cc_final: 0.5153 (mmp) REVERT: A 383 MET cc_start: 0.7382 (mtp) cc_final: 0.7176 (mtt) REVERT: A 514 ARG cc_start: 0.6826 (ptp-170) cc_final: 0.6567 (ptp90) REVERT: A 657 LYS cc_start: 0.7882 (mttt) cc_final: 0.7259 (mtmt) REVERT: B 28 GLU cc_start: 0.5964 (OUTLIER) cc_final: 0.4692 (pm20) REVERT: B 60 TYR cc_start: 0.6621 (p90) cc_final: 0.6213 (p90) REVERT: B 71 MET cc_start: 0.4837 (mpp) cc_final: 0.4500 (ttm) REVERT: B 108 HIS cc_start: 0.7555 (t70) cc_final: 0.7335 (t-170) REVERT: B 114 LEU cc_start: 0.5596 (pp) cc_final: 0.5041 (pp) REVERT: B 365 GLN cc_start: 0.6668 (pp30) cc_final: 0.6108 (mm110) REVERT: B 415 LEU cc_start: 0.7036 (pp) cc_final: 0.6395 (mt) REVERT: B 469 ILE cc_start: 0.7321 (tt) cc_final: 0.7087 (pt) REVERT: B 534 TRP cc_start: 0.6227 (m-10) cc_final: 0.5952 (m-10) REVERT: B 535 ARG cc_start: 0.6884 (mtm180) cc_final: 0.6390 (mmm-85) outliers start: 45 outliers final: 10 residues processed: 631 average time/residue: 0.1492 time to fit residues: 148.4389 Evaluate side-chains 371 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 358 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.0670 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 51 ASN C 58 ASN C 86 GLN C 98 GLN C 149 ASN C 277 ASN C 340 GLN C 505 HIS C 526 GLN C 660 ASN C 674 ASN D 63 GLN D 158 ASN D 194 GLN D 264 GLN D 297 ASN D 608 ASN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN A 51 ASN A 58 ASN A 86 GLN ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 149 ASN A 277 ASN A 340 GLN A 345 HIS A 505 HIS A 674 ASN B 40 GLN B 63 GLN ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 194 GLN B 264 GLN B 354 ASN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.200768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136672 restraints weight = 33407.720| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.50 r_work: 0.3408 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22440 Z= 0.134 Angle : 0.663 9.014 30556 Z= 0.328 Chirality : 0.043 0.300 3338 Planarity : 0.004 0.036 3876 Dihedral : 5.746 85.515 2936 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.85 % Allowed : 13.68 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.16), residues: 2700 helix: 0.34 (0.13), residues: 1612 sheet: -1.96 (0.69), residues: 44 loop : -2.35 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 57 TYR 0.024 0.001 TYR A 516 PHE 0.025 0.002 PHE C 555 TRP 0.016 0.001 TRP B 196 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (22430) covalent geometry : angle 0.66231 / 0.33 (30536) SS BOND : bond 0.00287 / 0.18 ( 10) SS BOND : angle 1.26070 / 0.72 ( 20) hydrogen bonds : bond 0.04779 / 3.17 ( 1150) hydrogen bonds : angle 4.38574 / 3.17 ( 3372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 410 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 PHE cc_start: 0.8904 (t80) cc_final: 0.8647 (t80) REVERT: C 91 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.5901 (pt) REVERT: C 202 TYR cc_start: 0.8742 (t80) cc_final: 0.8464 (t80) REVERT: C 332 MET cc_start: 0.6487 (tpt) cc_final: 0.6267 (mmm) REVERT: C 408 MET cc_start: 0.8671 (mmm) cc_final: 0.8001 (mmm) REVERT: C 416 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8181 (tttt) REVERT: C 468 ILE cc_start: 0.8633 (mt) cc_final: 0.8331 (mt) REVERT: C 470 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8583 (mttt) REVERT: C 515 TYR cc_start: 0.8379 (m-80) cc_final: 0.8177 (m-80) REVERT: C 558 LEU cc_start: 0.8460 (mp) cc_final: 0.8066 (mp) REVERT: C 625 LYS cc_start: 0.8851 (mtpp) cc_final: 0.8647 (ttmm) REVERT: D 18 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.6163 (pp) REVERT: D 28 GLU cc_start: 0.5395 (OUTLIER) cc_final: 0.4545 (pm20) REVERT: D 56 TRP cc_start: 0.5971 (m-10) cc_final: 0.5302 (m-10) REVERT: D 170 SER cc_start: 0.7393 (t) cc_final: 0.7064 (m) REVERT: D 266 ASP cc_start: 0.8210 (p0) cc_final: 0.7361 (t70) REVERT: D 331 GLN cc_start: 0.7654 (tp40) cc_final: 0.7017 (tm-30) REVERT: D 415 LEU cc_start: 0.7390 (pp) cc_final: 0.7019 (mt) REVERT: D 419 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7291 (tp) REVERT: D 505 VAL cc_start: 0.7010 (OUTLIER) cc_final: 0.6755 (p) REVERT: D 509 TYR cc_start: 0.7403 (t80) cc_final: 0.6416 (t80) REVERT: D 513 ARG cc_start: 0.8493 (mtt90) cc_final: 0.8148 (mmm160) REVERT: D 525 LYS cc_start: 0.8310 (mttt) cc_final: 0.7935 (ptpt) REVERT: D 542 MET cc_start: 0.8037 (mmp) cc_final: 0.7685 (mtt) REVERT: D 583 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.6660 (t80) REVERT: A 152 MET cc_start: 0.8520 (mmm) cc_final: 0.8166 (mmt) REVERT: A 227 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8227 (tm-30) REVERT: A 312 GLU cc_start: 0.7865 (tt0) cc_final: 0.7639 (tt0) REVERT: A 323 MET cc_start: 0.6932 (mmp) cc_final: 0.6417 (mmm) REVERT: A 381 TYR cc_start: 0.7698 (t80) cc_final: 0.7483 (t80) REVERT: A 416 LYS cc_start: 0.8766 (tttt) cc_final: 0.8560 (tttt) REVERT: A 527 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8401 (tm-30) REVERT: A 558 LEU cc_start: 0.8736 (mp) cc_final: 0.8530 (mp) REVERT: A 657 LYS cc_start: 0.8259 (mttt) cc_final: 0.7840 (mtmt) REVERT: B 28 GLU cc_start: 0.5398 (OUTLIER) cc_final: 0.4429 (pm20) REVERT: B 80 LEU cc_start: 0.8026 (mt) cc_final: 0.7782 (tt) REVERT: B 108 HIS cc_start: 0.7729 (t70) cc_final: 0.7398 (t-170) REVERT: B 210 MET cc_start: 0.7507 (tmm) cc_final: 0.7269 (tmm) REVERT: B 238 LEU cc_start: 0.6814 (tt) cc_final: 0.6506 (tp) REVERT: B 245 LYS cc_start: 0.8261 (mppt) cc_final: 0.7454 (mtpp) REVERT: B 365 GLN cc_start: 0.7079 (pp30) cc_final: 0.6701 (mm110) REVERT: B 398 LEU cc_start: 0.7511 (tp) cc_final: 0.7205 (tt) REVERT: B 415 LEU cc_start: 0.7321 (pp) cc_final: 0.6715 (mt) REVERT: B 469 ILE cc_start: 0.7435 (tt) cc_final: 0.7194 (pt) REVERT: B 480 TYR cc_start: 0.6479 (m-80) cc_final: 0.6048 (m-80) REVERT: B 535 ARG cc_start: 0.7002 (mtm180) cc_final: 0.6431 (mmm-85) REVERT: B 548 PHE cc_start: 0.7889 (m-10) cc_final: 0.7607 (m-10) REVERT: B 569 GLU cc_start: 0.8279 (mp0) cc_final: 0.7754 (mp0) outliers start: 68 outliers final: 33 residues processed: 457 average time/residue: 0.1460 time to fit residues: 107.1030 Evaluate side-chains 369 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 329 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 576 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 261 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 chunk 126 optimal weight: 0.0870 chunk 30 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN C 378 HIS C 417 HIS C 586 ASN C 690 ASN D 40 GLN D 145 GLN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN A 101 GLN A 139 GLN A 373 HIS A 378 HIS A 586 ASN B 145 GLN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.196542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130243 restraints weight = 32956.263| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.94 r_work: 0.3312 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22440 Z= 0.143 Angle : 0.637 8.549 30556 Z= 0.318 Chirality : 0.044 0.291 3338 Planarity : 0.004 0.048 3876 Dihedral : 5.307 84.466 2929 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.64 % Allowed : 15.56 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.16), residues: 2700 helix: 0.67 (0.13), residues: 1614 sheet: -2.00 (0.74), residues: 42 loop : -2.00 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 97 TYR 0.020 0.001 TYR A 50 PHE 0.024 0.002 PHE B 546 TRP 0.031 0.002 TRP B 138 HIS 0.006 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (22430) covalent geometry : angle 0.63661 / 0.32 (30536) SS BOND : bond 0.00313 / 0.23 ( 10) SS BOND : angle 1.42277 / 0.90 ( 20) hydrogen bonds : bond 0.04770 / 3.20 ( 1150) hydrogen bonds : angle 4.23936 / 3.06 ( 3372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 351 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8705 (tptp) REVERT: C 91 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6105 (pt) REVERT: C 408 MET cc_start: 0.8690 (mmm) cc_final: 0.7845 (mmm) REVERT: C 416 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8235 (tttt) REVERT: C 470 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8629 (mttt) REVERT: C 557 MET cc_start: 0.8987 (tmm) cc_final: 0.8721 (tmm) REVERT: C 744 ILE cc_start: 0.8011 (mt) cc_final: 0.7796 (mt) REVERT: D 28 GLU cc_start: 0.5353 (OUTLIER) cc_final: 0.4562 (pm20) REVERT: D 159 GLN cc_start: 0.6428 (pp30) cc_final: 0.5777 (tt0) REVERT: D 170 SER cc_start: 0.7500 (t) cc_final: 0.7241 (m) REVERT: D 210 MET cc_start: 0.7542 (tmm) cc_final: 0.7319 (tmm) REVERT: D 266 ASP cc_start: 0.8387 (p0) cc_final: 0.7667 (t70) REVERT: D 415 LEU cc_start: 0.7399 (pp) cc_final: 0.7031 (mt) REVERT: D 419 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7241 (tp) REVERT: D 432 MET cc_start: 0.8031 (mmm) cc_final: 0.7711 (mmt) REVERT: D 437 GLU cc_start: 0.7498 (tp30) cc_final: 0.6744 (mm-30) REVERT: D 452 LYS cc_start: 0.7769 (tptp) cc_final: 0.7040 (ptmt) REVERT: D 505 VAL cc_start: 0.6956 (OUTLIER) cc_final: 0.6735 (p) REVERT: D 509 TYR cc_start: 0.7578 (t80) cc_final: 0.6758 (t80) REVERT: D 525 LYS cc_start: 0.8271 (mttt) cc_final: 0.7942 (ttpt) REVERT: D 542 MET cc_start: 0.8083 (mmp) cc_final: 0.7598 (mtt) REVERT: A 62 MET cc_start: 0.8029 (ptm) cc_final: 0.7760 (ptm) REVERT: A 227 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8394 (tm-30) REVERT: A 312 GLU cc_start: 0.8073 (tt0) cc_final: 0.7795 (tt0) REVERT: A 381 TYR cc_start: 0.7839 (t80) cc_final: 0.7381 (t80) REVERT: A 385 TYR cc_start: 0.6796 (p90) cc_final: 0.6258 (p90) REVERT: A 527 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 657 LYS cc_start: 0.8405 (mttt) cc_final: 0.7982 (mtmt) REVERT: B 28 GLU cc_start: 0.5356 (OUTLIER) cc_final: 0.4370 (pm20) REVERT: B 162 TYR cc_start: 0.7260 (m-80) cc_final: 0.6978 (m-80) REVERT: B 210 MET cc_start: 0.7560 (tmm) cc_final: 0.7289 (tmm) REVERT: B 245 LYS cc_start: 0.8331 (mppt) cc_final: 0.7681 (mtpp) REVERT: B 365 GLN cc_start: 0.7308 (pp30) cc_final: 0.6969 (mm110) REVERT: B 415 LEU cc_start: 0.7393 (pp) cc_final: 0.6762 (mt) REVERT: B 469 ILE cc_start: 0.7738 (tt) cc_final: 0.7496 (pt) REVERT: B 480 TYR cc_start: 0.7168 (m-80) cc_final: 0.6780 (m-80) REVERT: B 535 ARG cc_start: 0.7051 (mtm180) cc_final: 0.6575 (mmm-85) outliers start: 87 outliers final: 52 residues processed: 408 average time/residue: 0.1437 time to fit residues: 94.5763 Evaluate side-chains 365 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 308 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 592 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 205 optimal weight: 0.0010 chunk 96 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 216 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 181 optimal weight: 0.0670 chunk 222 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.7926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN C 556 ASN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN B 435 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.196130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126414 restraints weight = 32941.154| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.96 r_work: 0.3311 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22440 Z= 0.127 Angle : 0.614 9.016 30556 Z= 0.304 Chirality : 0.042 0.237 3338 Planarity : 0.004 0.040 3876 Dihedral : 4.995 83.925 2929 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.51 % Allowed : 17.28 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 2700 helix: 0.80 (0.13), residues: 1622 sheet: -1.87 (0.77), residues: 42 loop : -1.87 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 97 TYR 0.026 0.001 TYR C 50 PHE 0.028 0.001 PHE B 546 TRP 0.037 0.001 TRP B 530 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (22430) covalent geometry : angle 0.61269 / 0.30 (30536) SS BOND : bond 0.00280 / 0.17 ( 10) SS BOND : angle 1.39806 / 0.86 ( 20) hydrogen bonds : bond 0.04308 / 2.88 ( 1150) hydrogen bonds : angle 4.10448 / 2.96 ( 3372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 334 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 LYS cc_start: 0.8982 (mtpp) cc_final: 0.8695 (mtpp) REVERT: C 51 ASN cc_start: 0.7021 (m110) cc_final: 0.6813 (m110) REVERT: C 73 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8703 (mm) REVERT: C 202 TYR cc_start: 0.8955 (t80) cc_final: 0.8726 (t80) REVERT: C 408 MET cc_start: 0.8653 (mmm) cc_final: 0.7834 (mmm) REVERT: C 416 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8167 (tttt) REVERT: C 470 LYS cc_start: 0.8882 (mtpp) cc_final: 0.8618 (mttt) REVERT: C 556 ASN cc_start: 0.8537 (m-40) cc_final: 0.7920 (t0) REVERT: C 693 ASP cc_start: 0.8276 (t0) cc_final: 0.7878 (t0) REVERT: C 744 ILE cc_start: 0.7992 (mt) cc_final: 0.7780 (mt) REVERT: D 28 GLU cc_start: 0.5470 (OUTLIER) cc_final: 0.4697 (pm20) REVERT: D 159 GLN cc_start: 0.6396 (pp30) cc_final: 0.5811 (tt0) REVERT: D 266 ASP cc_start: 0.8380 (p0) cc_final: 0.7627 (t70) REVERT: D 415 LEU cc_start: 0.7394 (pp) cc_final: 0.7043 (mt) REVERT: D 419 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7203 (tp) REVERT: D 432 MET cc_start: 0.7939 (mmm) cc_final: 0.7608 (mmt) REVERT: D 452 LYS cc_start: 0.7828 (tptp) cc_final: 0.7036 (ptmt) REVERT: D 509 TYR cc_start: 0.7342 (t80) cc_final: 0.6969 (t80) REVERT: D 525 LYS cc_start: 0.8189 (mttt) cc_final: 0.7851 (ttpt) REVERT: D 542 MET cc_start: 0.8084 (mmp) cc_final: 0.7446 (mtt) REVERT: D 583 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6683 (t80) REVERT: A 41 TYR cc_start: 0.8544 (t80) cc_final: 0.8204 (t80) REVERT: A 73 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8873 (mm) REVERT: A 227 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8341 (tm-30) REVERT: A 312 GLU cc_start: 0.8056 (tt0) cc_final: 0.7827 (mt-10) REVERT: A 332 MET cc_start: 0.7281 (tpt) cc_final: 0.7050 (tpt) REVERT: A 381 TYR cc_start: 0.7891 (t80) cc_final: 0.7444 (t80) REVERT: A 385 TYR cc_start: 0.6768 (p90) cc_final: 0.6174 (p90) REVERT: A 527 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8416 (tm-30) REVERT: A 598 GLN cc_start: 0.8073 (tp40) cc_final: 0.7840 (tp40) REVERT: A 657 LYS cc_start: 0.8320 (mttt) cc_final: 0.7892 (mtmt) REVERT: B 28 GLU cc_start: 0.5287 (OUTLIER) cc_final: 0.4483 (pm20) REVERT: B 92 ILE cc_start: 0.7441 (tt) cc_final: 0.7221 (tt) REVERT: B 162 TYR cc_start: 0.7344 (m-80) cc_final: 0.7120 (m-80) REVERT: B 245 LYS cc_start: 0.8346 (mppt) cc_final: 0.7841 (mtpp) REVERT: B 365 GLN cc_start: 0.7355 (pp30) cc_final: 0.7035 (mm110) REVERT: B 405 GLU cc_start: 0.7942 (tt0) cc_final: 0.7438 (pt0) REVERT: B 415 LEU cc_start: 0.7226 (pp) cc_final: 0.6792 (mt) REVERT: B 469 ILE cc_start: 0.7942 (tt) cc_final: 0.7702 (pt) REVERT: B 480 TYR cc_start: 0.7255 (m-80) cc_final: 0.6893 (m-80) REVERT: B 535 ARG cc_start: 0.7033 (mtm180) cc_final: 0.6451 (mmm-85) outliers start: 84 outliers final: 58 residues processed: 395 average time/residue: 0.1396 time to fit residues: 89.6433 Evaluate side-chains 378 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 314 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 592 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 209 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 190 optimal weight: 0.8980 chunk 47 optimal weight: 0.0040 chunk 109 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 76 GLN C 139 GLN D 435 ASN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.196351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126556 restraints weight = 32598.441| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.10 r_work: 0.3320 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22440 Z= 0.119 Angle : 0.606 9.420 30556 Z= 0.299 Chirality : 0.042 0.253 3338 Planarity : 0.004 0.038 3876 Dihedral : 4.750 83.037 2926 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.89 % Allowed : 17.78 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2700 helix: 0.90 (0.13), residues: 1618 sheet: -1.87 (0.77), residues: 42 loop : -1.79 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 513 TYR 0.031 0.001 TYR C 50 PHE 0.043 0.001 PHE C 72 TRP 0.020 0.001 TRP B 530 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (22430) covalent geometry : angle 0.60554 / 0.30 (30536) SS BOND : bond 0.00159 / 0.10 ( 10) SS BOND : angle 1.13113 / 0.68 ( 20) hydrogen bonds : bond 0.04069 / 2.74 ( 1150) hydrogen bonds : angle 4.03692 / 2.91 ( 3372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 323 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 ASN cc_start: 0.6830 (m110) cc_final: 0.6623 (m110) REVERT: C 73 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8810 (mm) REVERT: C 202 TYR cc_start: 0.8994 (t80) cc_final: 0.8763 (t80) REVERT: C 297 MET cc_start: 0.7534 (mtp) cc_final: 0.7322 (mmm) REVERT: C 416 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8193 (tttt) REVERT: C 556 ASN cc_start: 0.8545 (m-40) cc_final: 0.7928 (t0) REVERT: C 693 ASP cc_start: 0.8260 (t0) cc_final: 0.7952 (t0) REVERT: C 744 ILE cc_start: 0.7982 (mt) cc_final: 0.7777 (mt) REVERT: D 28 GLU cc_start: 0.5476 (OUTLIER) cc_final: 0.4744 (pm20) REVERT: D 159 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.5913 (tt0) REVERT: D 261 GLU cc_start: 0.5633 (mm-30) cc_final: 0.5405 (mm-30) REVERT: D 266 ASP cc_start: 0.8365 (p0) cc_final: 0.7683 (t70) REVERT: D 331 GLN cc_start: 0.7609 (tp40) cc_final: 0.7050 (tm-30) REVERT: D 415 LEU cc_start: 0.7361 (pp) cc_final: 0.7021 (mt) REVERT: D 419 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7213 (tp) REVERT: D 432 MET cc_start: 0.7880 (mmm) cc_final: 0.7561 (mmt) REVERT: D 494 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7520 (tt) REVERT: D 513 ARG cc_start: 0.8471 (mmm160) cc_final: 0.7989 (tpt-90) REVERT: D 521 MET cc_start: 0.6734 (tpp) cc_final: 0.6483 (tpp) REVERT: D 525 LYS cc_start: 0.8134 (mttt) cc_final: 0.7795 (ttpt) REVERT: D 583 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6710 (t80) REVERT: A 41 TYR cc_start: 0.8608 (t80) cc_final: 0.8283 (t80) REVERT: A 73 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8892 (mm) REVERT: A 227 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 312 GLU cc_start: 0.8039 (tt0) cc_final: 0.7782 (mt-10) REVERT: A 360 MET cc_start: 0.6805 (tmm) cc_final: 0.6593 (tmm) REVERT: A 416 LYS cc_start: 0.8565 (tttt) cc_final: 0.8253 (pttt) REVERT: A 527 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8371 (tm-30) REVERT: A 598 GLN cc_start: 0.8071 (tp40) cc_final: 0.7844 (tp40) REVERT: A 657 LYS cc_start: 0.8265 (mttt) cc_final: 0.7858 (mtmt) REVERT: B 28 GLU cc_start: 0.5254 (OUTLIER) cc_final: 0.4483 (pm20) REVERT: B 42 MET cc_start: 0.7540 (ttp) cc_final: 0.7057 (tpp) REVERT: B 162 TYR cc_start: 0.7278 (m-80) cc_final: 0.7003 (m-80) REVERT: B 245 LYS cc_start: 0.8311 (mppt) cc_final: 0.7869 (mtpp) REVERT: B 365 GLN cc_start: 0.7349 (pp30) cc_final: 0.7026 (mm-40) REVERT: B 405 GLU cc_start: 0.7952 (tt0) cc_final: 0.7507 (pt0) REVERT: B 415 LEU cc_start: 0.7250 (pp) cc_final: 0.6779 (mt) REVERT: B 469 ILE cc_start: 0.7985 (tt) cc_final: 0.7732 (pt) REVERT: B 480 TYR cc_start: 0.7416 (m-80) cc_final: 0.7139 (m-80) outliers start: 93 outliers final: 65 residues processed: 386 average time/residue: 0.1402 time to fit residues: 88.2308 Evaluate side-chains 381 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 308 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 592 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 29 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 354 ASN D 479 GLN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.193543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.123751 restraints weight = 32381.514| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.19 r_work: 0.3258 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22440 Z= 0.137 Angle : 0.626 9.341 30556 Z= 0.309 Chirality : 0.043 0.271 3338 Planarity : 0.004 0.073 3876 Dihedral : 4.760 81.642 2924 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.85 % Allowed : 19.25 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.16), residues: 2700 helix: 0.97 (0.13), residues: 1604 sheet: -1.60 (0.79), residues: 42 loop : -1.74 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 513 TYR 0.034 0.001 TYR A 50 PHE 0.030 0.002 PHE C 72 TRP 0.016 0.001 TRP D 268 HIS 0.018 0.001 HIS B 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (22430) covalent geometry : angle 0.62537 / 0.31 (30536) SS BOND : bond 0.00161 / 0.10 ( 10) SS BOND : angle 1.07263 / 0.65 ( 20) hydrogen bonds : bond 0.04424 / 2.98 ( 1150) hydrogen bonds : angle 4.02231 / 2.89 ( 3372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 324 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 ASN cc_start: 0.6631 (m110) cc_final: 0.6325 (m110) REVERT: C 73 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8782 (mm) REVERT: C 416 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8280 (tttt) REVERT: C 556 ASN cc_start: 0.8665 (m-40) cc_final: 0.8138 (t0) REVERT: C 557 MET cc_start: 0.8959 (tmm) cc_final: 0.8744 (tmm) REVERT: C 744 ILE cc_start: 0.8045 (mt) cc_final: 0.7836 (mt) REVERT: D 28 GLU cc_start: 0.5361 (OUTLIER) cc_final: 0.4616 (pm20) REVERT: D 159 GLN cc_start: 0.6514 (OUTLIER) cc_final: 0.6026 (tt0) REVERT: D 266 ASP cc_start: 0.8524 (p0) cc_final: 0.7708 (t70) REVERT: D 415 LEU cc_start: 0.7401 (pp) cc_final: 0.7088 (mt) REVERT: D 419 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7256 (tp) REVERT: D 494 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7576 (tt) REVERT: D 513 ARG cc_start: 0.8466 (mmm160) cc_final: 0.7886 (tpt-90) REVERT: D 525 LYS cc_start: 0.8120 (mttt) cc_final: 0.7799 (ttpt) REVERT: D 542 MET cc_start: 0.7950 (mmp) cc_final: 0.7685 (mpp) REVERT: D 583 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.6738 (t80) REVERT: A 41 TYR cc_start: 0.8623 (t80) cc_final: 0.8274 (t80) REVERT: A 73 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8926 (mm) REVERT: A 227 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8275 (tm-30) REVERT: A 360 MET cc_start: 0.6920 (tmm) cc_final: 0.6588 (tmm) REVERT: A 416 LYS cc_start: 0.8655 (tttt) cc_final: 0.8372 (pttt) REVERT: A 527 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8420 (tm-30) REVERT: A 598 GLN cc_start: 0.8114 (tp40) cc_final: 0.7880 (tp40) REVERT: A 657 LYS cc_start: 0.8401 (mttt) cc_final: 0.7963 (mtmt) REVERT: A 693 ASP cc_start: 0.8355 (t0) cc_final: 0.7974 (t0) REVERT: B 28 GLU cc_start: 0.5259 (OUTLIER) cc_final: 0.4512 (pm20) REVERT: B 42 MET cc_start: 0.7692 (ttp) cc_final: 0.7203 (tpp) REVERT: B 46 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6472 (tp) REVERT: B 56 TRP cc_start: 0.6171 (m100) cc_final: 0.5908 (m100) REVERT: B 162 TYR cc_start: 0.7328 (m-80) cc_final: 0.7080 (m-10) REVERT: B 245 LYS cc_start: 0.8202 (mppt) cc_final: 0.7840 (mtpp) REVERT: B 365 GLN cc_start: 0.7371 (pp30) cc_final: 0.7156 (mm-40) REVERT: B 415 LEU cc_start: 0.7245 (pp) cc_final: 0.6777 (mt) REVERT: B 432 MET cc_start: 0.7814 (mmm) cc_final: 0.7224 (mmt) REVERT: B 535 ARG cc_start: 0.6920 (mtm180) cc_final: 0.6471 (mmm-85) outliers start: 92 outliers final: 65 residues processed: 386 average time/residue: 0.1380 time to fit residues: 87.4044 Evaluate side-chains 376 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 302 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 592 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 57 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 chunk 175 optimal weight: 3.9990 chunk 219 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 183 optimal weight: 0.0070 chunk 228 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN ** D 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.193391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122864 restraints weight = 32925.157| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.15 r_work: 0.3284 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22440 Z= 0.117 Angle : 0.609 9.927 30556 Z= 0.298 Chirality : 0.042 0.287 3338 Planarity : 0.004 0.069 3876 Dihedral : 4.655 81.135 2924 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.43 % Allowed : 20.29 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.16), residues: 2700 helix: 1.02 (0.13), residues: 1628 sheet: -1.52 (0.80), residues: 42 loop : -1.69 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.031 0.001 TYR A 50 PHE 0.025 0.001 PHE C 72 TRP 0.018 0.001 TRP B 205 HIS 0.006 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (22430) covalent geometry : angle 0.60848 / 0.30 (30536) SS BOND : bond 0.00105 / 0.07 ( 10) SS BOND : angle 0.87694 / 0.53 ( 20) hydrogen bonds : bond 0.03960 / 2.66 ( 1150) hydrogen bonds : angle 3.97863 / 2.86 ( 3372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 321 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 ASN cc_start: 0.6532 (m110) cc_final: 0.6280 (m110) REVERT: C 73 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8806 (mm) REVERT: C 323 MET cc_start: 0.7783 (mmp) cc_final: 0.7476 (mmp) REVERT: C 416 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8227 (tttt) REVERT: C 556 ASN cc_start: 0.8647 (m-40) cc_final: 0.8101 (t0) REVERT: C 693 ASP cc_start: 0.8417 (t0) cc_final: 0.7991 (p0) REVERT: C 744 ILE cc_start: 0.8072 (mt) cc_final: 0.7870 (mt) REVERT: D 28 GLU cc_start: 0.5329 (OUTLIER) cc_final: 0.4623 (pm20) REVERT: D 159 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.6166 (tt0) REVERT: D 261 GLU cc_start: 0.5598 (mm-30) cc_final: 0.5340 (mm-30) REVERT: D 266 ASP cc_start: 0.8493 (p0) cc_final: 0.7774 (t70) REVERT: D 415 LEU cc_start: 0.7382 (pp) cc_final: 0.7078 (mt) REVERT: D 419 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7277 (tp) REVERT: D 452 LYS cc_start: 0.7332 (tptm) cc_final: 0.6559 (ptmt) REVERT: D 494 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7488 (tt) REVERT: D 513 ARG cc_start: 0.8511 (mmm160) cc_final: 0.7959 (tpt-90) REVERT: D 525 LYS cc_start: 0.8067 (mttt) cc_final: 0.7743 (ttpt) REVERT: A 41 TYR cc_start: 0.8605 (t80) cc_final: 0.8259 (t80) REVERT: A 73 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8929 (mm) REVERT: A 227 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 416 LYS cc_start: 0.8709 (tttt) cc_final: 0.8425 (pttt) REVERT: A 527 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8367 (tm-30) REVERT: A 598 GLN cc_start: 0.8078 (tp40) cc_final: 0.7853 (tp40) REVERT: A 693 ASP cc_start: 0.8284 (t0) cc_final: 0.7943 (t0) REVERT: B 28 GLU cc_start: 0.5139 (OUTLIER) cc_final: 0.4460 (pm20) REVERT: B 42 MET cc_start: 0.7753 (ttp) cc_final: 0.7534 (ttt) REVERT: B 56 TRP cc_start: 0.6133 (m100) cc_final: 0.5796 (m100) REVERT: B 162 TYR cc_start: 0.7369 (m-80) cc_final: 0.7106 (m-10) REVERT: B 209 TYR cc_start: 0.5950 (t80) cc_final: 0.5586 (t80) REVERT: B 245 LYS cc_start: 0.8192 (mppt) cc_final: 0.7908 (mtpp) REVERT: B 405 GLU cc_start: 0.7914 (tt0) cc_final: 0.7436 (pt0) REVERT: B 415 LEU cc_start: 0.7291 (pp) cc_final: 0.6820 (mt) REVERT: B 535 ARG cc_start: 0.6786 (mtm180) cc_final: 0.6287 (mmm-85) outliers start: 82 outliers final: 59 residues processed: 377 average time/residue: 0.1403 time to fit residues: 86.4504 Evaluate side-chains 371 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 305 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 586 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 125 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN ** D 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 574 GLN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.193248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123687 restraints weight = 32217.066| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.93 r_work: 0.3265 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22440 Z= 0.127 Angle : 0.623 10.655 30556 Z= 0.305 Chirality : 0.043 0.271 3338 Planarity : 0.004 0.059 3876 Dihedral : 4.661 80.348 2924 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.39 % Allowed : 20.71 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.16), residues: 2700 helix: 1.15 (0.13), residues: 1602 sheet: -1.37 (0.81), residues: 42 loop : -1.68 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 513 TYR 0.032 0.001 TYR C 41 PHE 0.034 0.002 PHE B 546 TRP 0.026 0.001 TRP B 205 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (22430) covalent geometry : angle 0.62295 / 0.31 (30536) SS BOND : bond 0.00117 / 0.08 ( 10) SS BOND : angle 0.92173 / 0.56 ( 20) hydrogen bonds : bond 0.04194 / 2.83 ( 1150) hydrogen bonds : angle 3.99454 / 2.87 ( 3372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 309 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 ASN cc_start: 0.6589 (m110) cc_final: 0.6301 (m110) REVERT: C 63 ASN cc_start: 0.8689 (t0) cc_final: 0.8159 (m110) REVERT: C 73 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8778 (mm) REVERT: C 108 LEU cc_start: 0.5769 (OUTLIER) cc_final: 0.5522 (pp) REVERT: C 323 MET cc_start: 0.7814 (mmp) cc_final: 0.7568 (mmp) REVERT: C 332 MET cc_start: 0.7358 (tpt) cc_final: 0.7115 (tpt) REVERT: C 408 MET cc_start: 0.8541 (mmm) cc_final: 0.7767 (mmm) REVERT: C 416 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8227 (tttt) REVERT: C 556 ASN cc_start: 0.8660 (m-40) cc_final: 0.8459 (m110) REVERT: C 693 ASP cc_start: 0.8525 (t0) cc_final: 0.7987 (t0) REVERT: D 28 GLU cc_start: 0.5370 (OUTLIER) cc_final: 0.4686 (pm20) REVERT: D 159 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6141 (tt0) REVERT: D 261 GLU cc_start: 0.5731 (mm-30) cc_final: 0.5179 (mm-30) REVERT: D 415 LEU cc_start: 0.7389 (pp) cc_final: 0.7101 (mt) REVERT: D 419 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7250 (tp) REVERT: D 513 ARG cc_start: 0.8478 (mmm160) cc_final: 0.7891 (tpt-90) REVERT: D 525 LYS cc_start: 0.8062 (mttt) cc_final: 0.7739 (ttmt) REVERT: D 542 MET cc_start: 0.7885 (mmm) cc_final: 0.7163 (mmm) REVERT: A 73 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8912 (mm) REVERT: A 227 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 359 LEU cc_start: 0.8228 (tp) cc_final: 0.7922 (tp) REVERT: A 416 LYS cc_start: 0.8735 (tttt) cc_final: 0.8458 (pttt) REVERT: A 527 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8377 (tm-30) REVERT: A 598 GLN cc_start: 0.8138 (tp40) cc_final: 0.7892 (tp40) REVERT: A 693 ASP cc_start: 0.8354 (t0) cc_final: 0.8044 (t0) REVERT: B 28 GLU cc_start: 0.5128 (OUTLIER) cc_final: 0.4477 (pm20) REVERT: B 42 MET cc_start: 0.7747 (ttp) cc_final: 0.7519 (ttt) REVERT: B 46 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6615 (tp) REVERT: B 162 TYR cc_start: 0.7390 (m-80) cc_final: 0.7141 (m-10) REVERT: B 209 TYR cc_start: 0.6040 (t80) cc_final: 0.5694 (t80) REVERT: B 415 LEU cc_start: 0.7304 (pp) cc_final: 0.6824 (mt) REVERT: B 535 ARG cc_start: 0.6740 (mtm180) cc_final: 0.6268 (mmm-85) outliers start: 81 outliers final: 60 residues processed: 365 average time/residue: 0.1359 time to fit residues: 81.7750 Evaluate side-chains 363 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 295 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 586 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 39 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.188575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116159 restraints weight = 32054.028| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.92 r_work: 0.3204 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22440 Z= 0.201 Angle : 0.701 11.341 30556 Z= 0.350 Chirality : 0.046 0.270 3338 Planarity : 0.005 0.061 3876 Dihedral : 5.047 81.181 2924 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.39 % Allowed : 20.88 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2700 helix: 0.79 (0.13), residues: 1634 sheet: -0.75 (1.09), residues: 22 loop : -1.63 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 652 TYR 0.031 0.002 TYR A 50 PHE 0.040 0.002 PHE D 546 TRP 0.034 0.002 TRP D 205 HIS 0.024 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (22430) covalent geometry : angle 0.70099 / 0.35 (30536) SS BOND : bond 0.00210 / 0.14 ( 10) SS BOND : angle 1.24732 / 0.79 ( 20) hydrogen bonds : bond 0.05309 / 3.57 ( 1150) hydrogen bonds : angle 4.17350 / 2.99 ( 3372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 302 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 ASN cc_start: 0.6609 (m110) cc_final: 0.6314 (m110) REVERT: C 63 ASN cc_start: 0.8659 (t0) cc_final: 0.8154 (m110) REVERT: C 73 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8830 (mm) REVERT: C 108 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5754 (pp) REVERT: C 215 TYR cc_start: 0.7775 (m-80) cc_final: 0.7442 (m-10) REVERT: C 300 GLN cc_start: 0.7303 (mt0) cc_final: 0.7049 (pt0) REVERT: C 332 MET cc_start: 0.7401 (tpt) cc_final: 0.7186 (tpt) REVERT: C 408 MET cc_start: 0.8687 (mmm) cc_final: 0.8201 (mmm) REVERT: C 416 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8243 (tttt) REVERT: C 527 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8414 (tm-30) REVERT: C 693 ASP cc_start: 0.8905 (t0) cc_final: 0.8495 (t0) REVERT: D 28 GLU cc_start: 0.5529 (OUTLIER) cc_final: 0.4750 (pm20) REVERT: D 224 TYR cc_start: 0.7512 (m-80) cc_final: 0.7220 (m-80) REVERT: D 419 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7464 (tp) REVERT: D 513 ARG cc_start: 0.8501 (mmm160) cc_final: 0.7930 (tpt-90) REVERT: D 525 LYS cc_start: 0.8213 (mttt) cc_final: 0.7645 (pptt) REVERT: D 542 MET cc_start: 0.7886 (mmm) cc_final: 0.7229 (mmm) REVERT: A 63 ASN cc_start: 0.8775 (t0) cc_final: 0.8295 (m110) REVERT: A 73 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8890 (mm) REVERT: A 227 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8412 (tm-30) REVERT: A 359 LEU cc_start: 0.8445 (tp) cc_final: 0.8171 (tp) REVERT: A 408 MET cc_start: 0.9000 (mmp) cc_final: 0.8607 (mmm) REVERT: A 416 LYS cc_start: 0.8704 (tttt) cc_final: 0.8438 (pttt) REVERT: A 527 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8523 (tm-30) REVERT: A 598 GLN cc_start: 0.8222 (tp40) cc_final: 0.7964 (tp40) REVERT: A 625 LYS cc_start: 0.8991 (mtpp) cc_final: 0.8643 (mttm) REVERT: A 693 ASP cc_start: 0.8601 (t0) cc_final: 0.8175 (t70) REVERT: B 28 GLU cc_start: 0.5337 (OUTLIER) cc_final: 0.4587 (pm20) REVERT: B 162 TYR cc_start: 0.7589 (m-80) cc_final: 0.7317 (m-10) REVERT: B 209 TYR cc_start: 0.6075 (t80) cc_final: 0.5788 (t80) REVERT: B 415 LEU cc_start: 0.7361 (pp) cc_final: 0.6981 (mt) REVERT: B 495 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7952 (pp) REVERT: B 535 ARG cc_start: 0.6770 (mtm180) cc_final: 0.6259 (mmm-85) outliers start: 81 outliers final: 66 residues processed: 363 average time/residue: 0.1370 time to fit residues: 81.4924 Evaluate side-chains 354 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 281 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 586 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 136 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 260 optimal weight: 10.0000 chunk 74 optimal weight: 0.0370 chunk 229 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 201 optimal weight: 0.6980 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.192205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.121695 restraints weight = 32219.129| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.91 r_work: 0.3268 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22440 Z= 0.125 Angle : 0.649 14.628 30556 Z= 0.317 Chirality : 0.043 0.264 3338 Planarity : 0.004 0.067 3876 Dihedral : 4.799 82.695 2924 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.80 % Allowed : 22.13 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2700 helix: 1.07 (0.13), residues: 1608 sheet: -0.85 (1.08), residues: 22 loop : -1.60 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 678 TYR 0.029 0.001 TYR A 50 PHE 0.033 0.001 PHE D 546 TRP 0.034 0.001 TRP D 205 HIS 0.016 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (22430) covalent geometry : angle 0.64932 / 0.32 (30536) SS BOND : bond 0.00105 / 0.07 ( 10) SS BOND : angle 0.85699 / 0.52 ( 20) hydrogen bonds : bond 0.04268 / 2.88 ( 1150) hydrogen bonds : angle 4.05869 / 2.92 ( 3372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 305 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 ASN cc_start: 0.6636 (m110) cc_final: 0.6339 (m110) REVERT: C 63 ASN cc_start: 0.8651 (t0) cc_final: 0.8157 (m110) REVERT: C 73 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8846 (mm) REVERT: C 101 GLN cc_start: 0.7184 (tp-100) cc_final: 0.6631 (mt0) REVERT: C 108 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5840 (pp) REVERT: C 215 TYR cc_start: 0.7626 (m-80) cc_final: 0.7145 (m-10) REVERT: C 300 GLN cc_start: 0.7282 (mt0) cc_final: 0.7047 (pt0) REVERT: C 408 MET cc_start: 0.8680 (mmm) cc_final: 0.8242 (mmm) REVERT: C 416 LYS cc_start: 0.8540 (ttpt) cc_final: 0.8213 (tttt) REVERT: C 462 MET cc_start: 0.8478 (mtp) cc_final: 0.8225 (mtp) REVERT: C 527 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8405 (tm-30) REVERT: C 693 ASP cc_start: 0.8727 (t0) cc_final: 0.8234 (t0) REVERT: D 28 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.4809 (pm20) REVERT: D 331 GLN cc_start: 0.7794 (tp40) cc_final: 0.7376 (tm-30) REVERT: D 419 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7448 (tp) REVERT: D 432 MET cc_start: 0.7837 (mmm) cc_final: 0.7141 (mmt) REVERT: D 437 GLU cc_start: 0.7877 (tp30) cc_final: 0.6994 (mm-30) REVERT: D 513 ARG cc_start: 0.8517 (mmm160) cc_final: 0.7941 (tpt-90) REVERT: D 525 LYS cc_start: 0.8123 (mttt) cc_final: 0.7752 (ttmt) REVERT: D 542 MET cc_start: 0.7793 (mmm) cc_final: 0.7129 (mmm) REVERT: A 41 TYR cc_start: 0.8567 (t80) cc_final: 0.8290 (t80) REVERT: A 63 ASN cc_start: 0.8743 (t0) cc_final: 0.8298 (m110) REVERT: A 73 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8910 (mm) REVERT: A 359 LEU cc_start: 0.8486 (tp) cc_final: 0.8147 (tp) REVERT: A 408 MET cc_start: 0.8979 (mmp) cc_final: 0.8594 (mmm) REVERT: A 598 GLN cc_start: 0.8172 (tp40) cc_final: 0.7930 (tp40) REVERT: A 693 ASP cc_start: 0.8465 (t0) cc_final: 0.8208 (t0) REVERT: B 28 GLU cc_start: 0.5297 (OUTLIER) cc_final: 0.4592 (pm20) REVERT: B 162 TYR cc_start: 0.7502 (m-80) cc_final: 0.7255 (m-10) REVERT: B 209 TYR cc_start: 0.6324 (t80) cc_final: 0.6035 (t80) REVERT: B 415 LEU cc_start: 0.7245 (pp) cc_final: 0.6933 (mt) REVERT: B 535 ARG cc_start: 0.6789 (mtm180) cc_final: 0.6240 (mmm-85) outliers start: 67 outliers final: 57 residues processed: 354 average time/residue: 0.1413 time to fit residues: 81.7785 Evaluate side-chains 352 residues out of total 2390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 289 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 530 CYS Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 583 TYR Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 586 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 260 optimal weight: 0.0470 chunk 19 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 125 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 74 optimal weight: 0.0040 chunk 157 optimal weight: 0.9980 overall best weight: 0.3468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.193950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125733 restraints weight = 32274.208| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.94 r_work: 0.3294 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22440 Z= 0.119 Angle : 0.641 15.308 30556 Z= 0.310 Chirality : 0.042 0.244 3338 Planarity : 0.004 0.061 3876 Dihedral : 4.614 82.842 2924 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.55 % Allowed : 22.30 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.16), residues: 2700 helix: 1.13 (0.13), residues: 1616 sheet: -1.22 (1.01), residues: 22 loop : -1.61 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 559 TYR 0.027 0.001 TYR A 50 PHE 0.026 0.001 PHE C 72 TRP 0.036 0.001 TRP D 534 HIS 0.012 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (22430) covalent geometry : angle 0.64085 / 0.31 (30536) SS BOND : bond 0.00077 / 0.05 ( 10) SS BOND : angle 0.77993 / 0.47 ( 20) hydrogen bonds : bond 0.03884 / 2.64 ( 1150) hydrogen bonds : angle 3.99278 / 2.88 ( 3372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7404.23 seconds wall clock time: 126 minutes 57.07 seconds (7617.07 seconds total)