Starting phenix.real_space_refine on Fri Mar 14 07:38:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgp_34745/03_2025/8hgp_34745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgp_34745/03_2025/8hgp_34745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hgp_34745/03_2025/8hgp_34745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgp_34745/03_2025/8hgp_34745.map" model { file = "/net/cci-nas-00/data/ceres_data/8hgp_34745/03_2025/8hgp_34745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgp_34745/03_2025/8hgp_34745.cif" } resolution = 4.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 315 atoms to isotropic. 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 110 5.16 5 C 5672 2.51 5 N 1629 2.21 5 O 1758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9169 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4345 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 35, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 4391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4391 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 26, 'TRANS': 541} Chain: "C" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 327 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ASN A 182 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 182 " occ=0.00 residue: pdb=" N HIS A 183 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS A 183 " occ=0.00 residue: pdb=" N LEU A 184 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 184 " occ=0.00 residue: pdb=" N GLY A 203 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 203 " occ=0.00 residue: pdb=" N CYS A 329 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 329 " occ=0.00 residue: pdb=" N GLU A 330 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 330 " occ=0.00 residue: pdb=" N GLY A 331 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 331 " occ=0.00 residue: pdb=" N PRO A 332 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 332 " occ=0.00 residue: pdb=" N CYS A 333 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 333 " occ=0.00 Time building chain proxies: 6.87, per 1000 atoms: 0.75 Number of scatterers: 9169 At special positions: 0 Unit cell: (78.11, 131.61, 127.33, 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 110 16.00 O 1758 8.00 N 1629 7.00 C 5672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 504 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 260 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 337 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 499 " distance=2.04 Simple disulfide: pdb=" SG CYS A 506 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 523 " distance=2.04 Simple disulfide: pdb=" SG CYS A 526 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 539 " - pdb=" SG CYS A 555 " distance=2.04 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 19 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 41 " 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 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-3 " NAG D 2 " - " BMA D 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A 801 " - " ASN A 56 " " NAG A 802 " - " ASN A 175 " " NAG D 1 " - " ASN A 352 " " NAG E 1 " - " ASN B 259 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 19 sheets defined 11.2% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.849A pdb=" N GLN B 75 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.964A pdb=" N ILE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.905A pdb=" N PHE B 381 " --> pdb=" O PRO B 378 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 382 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.726A pdb=" N GLN B 398 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL B 399 " --> pdb=" O GLN B 396 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE B 400 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 401 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR B 402 " --> pdb=" O VAL B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 395 through 402' Processing helix chain 'B' and resid 422 through 426 removed outlier: 3.568A pdb=" N GLN B 426 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.128A pdb=" N GLY B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.977A pdb=" N GLY B 518 " --> pdb=" O CYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 removed outlier: 3.577A pdb=" N GLN B 583 " --> pdb=" O GLU B 580 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS B 584 " --> pdb=" O ALA B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 580 through 584' Processing helix chain 'A' and resid 43 through 55 Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.620A pdb=" N LYS A 80 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 81 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.871A pdb=" N GLY A 197 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 198' Processing helix chain 'A' and resid 354 through 360 removed outlier: 4.334A pdb=" N LYS A 357 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A 358 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS A 360 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.604A pdb=" N LEU A 392 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 393 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 394 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 395 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 397 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.854A pdb=" N PHE A 420 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 434 Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 519 through 523 removed outlier: 4.462A pdb=" N CYS A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.588A pdb=" N MET C 10 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN C 11 " --> pdb=" O SER C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 11' Processing sheet with id=AA1, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AA3, first strand: chain 'B' and resid 272 through 274 Processing sheet with id=AA4, first strand: chain 'B' and resid 289 through 291 removed outlier: 3.604A pdb=" N TYR B 289 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 296 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 319 through 320 removed outlier: 3.573A pdb=" N GLU B 332 " --> pdb=" O GLN B 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 342 through 343 removed outlier: 6.665A pdb=" N CYS B 342 " --> pdb=" O PHE B 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 374 through 376 removed outlier: 5.179A pdb=" N TYR B 441 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU B 467 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 443 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N HIS B 469 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 445 " --> pdb=" O HIS B 469 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 553 through 555 removed outlier: 3.588A pdb=" N LEU B 561 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.632A pdb=" N ILE A 107 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.270A pdb=" N GLN A 40 " --> pdb=" O CYS C 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.354A pdb=" N ILE A 67 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASN A 94 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N TYR A 69 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL A 89 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU A 122 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 91 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 119 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N SER A 151 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 121 " --> pdb=" O SER A 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 236 through 240 removed outlier: 3.509A pdb=" N ALA A 237 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL A 250 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N GLY A 239 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS A 248 " --> pdb=" O GLY A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 254 through 255 removed outlier: 4.560A pdb=" N PHE A 254 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS A 261 " --> pdb=" O PHE A 254 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 307 through 308 removed outlier: 3.940A pdb=" N CYS A 326 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AB7, first strand: chain 'A' and resid 369 through 371 removed outlier: 7.330A pdb=" N ILE A 462 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ALA A 439 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 489 " --> pdb=" O VAL A 461 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 548 through 549 removed outlier: 3.730A pdb=" N PHE A 549 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 556 " --> pdb=" O PHE A 549 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 585 through 587 removed outlier: 3.737A pdb=" N TYR A 585 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 592 " --> pdb=" O TYR A 585 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 36 through 37 81 hydrogen bonds defined for protein. 174 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: 2.62 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3115 1.35 - 1.46: 1988 1.46 - 1.58: 4129 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 9358 Sorted by residual: bond pdb=" C5 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.418 1.475 -0.057 2.00e-02 2.50e+03 8.22e+00 bond pdb=" C PRO B 593 " pdb=" N PRO B 594 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.32e+00 bond pdb=" C LYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.28e+00 bond pdb=" C1 NAG A 801 " pdb=" O5 NAG A 801 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.32e+00 bond pdb=" C1 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.399 1.442 -0.043 2.00e-02 2.50e+03 4.62e+00 ... (remaining 9353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 12358 1.88 - 3.76: 273 3.76 - 5.64: 36 5.64 - 7.52: 9 7.52 - 9.40: 4 Bond angle restraints: 12680 Sorted by residual: angle pdb=" C ALA B 324 " pdb=" N GLU B 325 " pdb=" CA GLU B 325 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C GLU A 204 " pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" CA PRO B 593 " pdb=" C PRO B 593 " pdb=" N PRO B 594 " ideal model delta sigma weight residual 117.93 122.18 -4.25 1.20e+00 6.94e-01 1.25e+01 angle pdb=" N LEU A 509 " pdb=" CA LEU A 509 " pdb=" C LEU A 509 " ideal model delta sigma weight residual 111.74 116.29 -4.55 1.35e+00 5.49e-01 1.14e+01 angle pdb=" N PRO B 593 " pdb=" CA PRO B 593 " pdb=" C PRO B 593 " ideal model delta sigma weight residual 110.70 114.75 -4.05 1.22e+00 6.72e-01 1.10e+01 ... (remaining 12675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.72: 5691 22.72 - 45.43: 153 45.43 - 68.15: 33 68.15 - 90.86: 19 90.86 - 113.58: 7 Dihedral angle restraints: 5903 sinusoidal: 2540 harmonic: 3363 Sorted by residual: dihedral pdb=" CB CYS B 299 " pdb=" SG CYS B 299 " pdb=" SG CYS B 311 " pdb=" CB CYS B 311 " ideal model delta sinusoidal sigma weight residual -86.00 -175.48 89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS B 544 " pdb=" SG CYS B 544 " pdb=" SG CYS B 560 " pdb=" CB CYS B 560 " ideal model delta sinusoidal sigma weight residual 93.00 -179.23 -87.77 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS A 215 " pdb=" SG CYS A 215 " pdb=" SG CYS A 223 " pdb=" CB CYS A 223 " ideal model delta sinusoidal sigma weight residual -86.00 -172.55 86.55 1 1.00e+01 1.00e-02 9.02e+01 ... (remaining 5900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1233 0.078 - 0.155: 178 0.155 - 0.233: 3 0.233 - 0.311: 2 0.311 - 0.388: 1 Chirality restraints: 1417 Sorted by residual: chirality pdb=" C2 NAG A 802 " pdb=" C1 NAG A 802 " pdb=" C3 NAG A 802 " pdb=" N2 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 352 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1414 not shown) Planarity restraints: 1673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 511 " 0.040 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO A 512 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 519 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO A 520 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 520 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 550 " -0.034 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO B 551 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 551 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 551 " -0.028 5.00e-02 4.00e+02 ... (remaining 1670 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2178 2.80 - 3.32: 7398 3.32 - 3.85: 14321 3.85 - 4.37: 16134 4.37 - 4.90: 27582 Nonbonded interactions: 67613 Sorted by model distance: nonbonded pdb=" OH TYR B 163 " pdb=" O HIS B 193 " model vdw 2.270 3.040 nonbonded pdb=" O VAL B 356 " pdb=" OG SER B 380 " model vdw 2.328 3.040 nonbonded pdb=" NH1 ARG B 103 " pdb=" O LEU B 256 " model vdw 2.392 3.120 nonbonded pdb=" OG SER B 373 " pdb=" O TYR B 409 " model vdw 2.396 3.040 nonbonded pdb=" NH2 ARG B 34 " pdb=" OD1 ASN B 438 " model vdw 2.398 3.120 ... (remaining 67608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.600 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9358 Z= 0.231 Angle : 0.680 9.403 12680 Z= 0.377 Chirality : 0.052 0.388 1417 Planarity : 0.007 0.061 1669 Dihedral : 10.200 113.578 3600 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.20 % Allowed : 0.78 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.19), residues: 1164 helix: -3.84 (0.43), residues: 41 sheet: -2.91 (0.57), residues: 67 loop : -2.85 (0.15), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 452 HIS 0.011 0.001 HIS B 48 PHE 0.017 0.001 PHE A 404 TYR 0.012 0.001 TYR B 554 ARG 0.004 0.000 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 394 time to evaluate : 0.954 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: 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: B 24 GLN cc_start: 0.5362 (pp30) cc_final: 0.4620 (mm-40) REVERT: B 31 MET cc_start: 0.7681 (mtp) cc_final: 0.7319 (ptp) REVERT: B 46 LEU cc_start: 0.8532 (mt) cc_final: 0.8168 (mt) REVERT: B 54 GLN cc_start: 0.6707 (mt0) cc_final: 0.6494 (tp-100) REVERT: B 56 VAL cc_start: 0.7921 (t) cc_final: 0.7391 (t) REVERT: B 59 ASN cc_start: 0.6879 (m-40) cc_final: 0.6397 (m-40) REVERT: B 64 TYR cc_start: 0.7601 (m-80) cc_final: 0.7142 (m-80) REVERT: B 65 LEU cc_start: 0.8315 (mt) cc_final: 0.8109 (mt) REVERT: B 74 LEU cc_start: 0.8494 (mt) cc_final: 0.8247 (mt) REVERT: B 75 GLN cc_start: 0.7729 (pt0) cc_final: 0.7504 (pt0) REVERT: B 79 GLU cc_start: 0.6741 (tt0) cc_final: 0.6199 (tt0) REVERT: B 81 GLN cc_start: 0.6821 (mt0) cc_final: 0.6445 (mt0) REVERT: B 85 LEU cc_start: 0.8257 (tp) cc_final: 0.7186 (mt) REVERT: B 91 VAL cc_start: 0.7907 (m) cc_final: 0.7347 (p) REVERT: B 92 ARG cc_start: 0.7556 (mtt90) cc_final: 0.7145 (mmm-85) REVERT: B 93 GLN cc_start: 0.8562 (pp30) cc_final: 0.8131 (pp30) REVERT: B 100 ARG cc_start: 0.7709 (tpp80) cc_final: 0.7472 (mmm-85) REVERT: B 103 ARG cc_start: 0.7084 (mtt-85) cc_final: 0.6672 (tpp80) REVERT: B 105 THR cc_start: 0.7413 (p) cc_final: 0.6406 (t) REVERT: B 106 GLN cc_start: 0.7453 (mt0) cc_final: 0.6879 (mp-120) REVERT: B 160 GLN cc_start: 0.7577 (mm-40) cc_final: 0.6707 (tp-100) REVERT: B 167 ILE cc_start: 0.8461 (mm) cc_final: 0.8205 (mm) REVERT: B 185 ASP cc_start: 0.6906 (t0) cc_final: 0.6446 (t0) REVERT: B 193 HIS cc_start: 0.7972 (m90) cc_final: 0.7337 (m90) REVERT: B 248 LYS cc_start: 0.8559 (mmtt) cc_final: 0.7936 (mmtt) REVERT: B 251 ASP cc_start: 0.7697 (p0) cc_final: 0.7359 (p0) REVERT: B 265 GLU cc_start: 0.6626 (pm20) cc_final: 0.6276 (pm20) REVERT: B 271 LEU cc_start: 0.8310 (mp) cc_final: 0.7992 (mm) REVERT: B 275 ASN cc_start: 0.8240 (t0) cc_final: 0.7631 (t0) REVERT: B 288 ARG cc_start: 0.7796 (mmt180) cc_final: 0.7407 (mmp80) REVERT: B 300 PRO cc_start: 0.7941 (Cg_exo) cc_final: 0.7456 (Cg_endo) REVERT: B 303 TYR cc_start: 0.7536 (m-80) cc_final: 0.7052 (m-80) REVERT: B 320 GLN cc_start: 0.6366 (mt0) cc_final: 0.6080 (mt0) REVERT: B 323 THR cc_start: 0.7139 (m) cc_final: 0.6647 (t) REVERT: B 332 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6486 (mp0) REVERT: B 374 LEU cc_start: 0.7242 (mt) cc_final: 0.7001 (mt) REVERT: B 407 THR cc_start: 0.8040 (p) cc_final: 0.7597 (m) REVERT: B 409 TYR cc_start: 0.7101 (p90) cc_final: 0.6872 (p90) REVERT: B 411 TYR cc_start: 0.6729 (t80) cc_final: 0.6439 (t80) REVERT: B 420 PRO cc_start: 0.8345 (Cg_endo) cc_final: 0.8057 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7769 (p0) cc_final: 0.7394 (p0) REVERT: B 426 GLN cc_start: 0.7495 (pt0) cc_final: 0.6460 (pp30) REVERT: B 429 GLN cc_start: 0.6604 (mt0) cc_final: 0.6299 (mt0) REVERT: B 432 ARG cc_start: 0.7486 (mmt180) cc_final: 0.6526 (tpp-160) REVERT: B 434 ARG cc_start: 0.7237 (mtt90) cc_final: 0.6018 (mtt90) REVERT: B 443 LEU cc_start: 0.7593 (tp) cc_final: 0.7246 (mm) REVERT: B 444 THR cc_start: 0.7127 (m) cc_final: 0.6618 (m) REVERT: B 452 TRP cc_start: 0.7786 (p90) cc_final: 0.7220 (p90) REVERT: B 481 PRO cc_start: 0.8311 (Cg_endo) cc_final: 0.7750 (Cg_exo) REVERT: B 483 ASP cc_start: 0.8442 (m-30) cc_final: 0.7763 (t70) REVERT: B 487 ARG cc_start: 0.7826 (mmt-90) cc_final: 0.7358 (tpp80) REVERT: B 517 ARG cc_start: 0.8311 (mtt180) cc_final: 0.8108 (mtt180) REVERT: B 556 ASN cc_start: 0.7970 (t0) cc_final: 0.7349 (t0) REVERT: B 566 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6484 (tm-30) REVERT: B 577 PHE cc_start: 0.8115 (m-80) cc_final: 0.7860 (m-80) REVERT: B 580 GLU cc_start: 0.8487 (tp30) cc_final: 0.8148 (tp30) REVERT: A 36 ASN cc_start: 0.8103 (p0) cc_final: 0.7592 (p0) REVERT: A 37 LYS cc_start: 0.7941 (ptpt) cc_final: 0.7718 (ptpp) REVERT: A 46 ASP cc_start: 0.7385 (t70) cc_final: 0.6643 (t70) REVERT: A 47 HIS cc_start: 0.7807 (t-90) cc_final: 0.6617 (t70) REVERT: A 61 VAL cc_start: 0.8276 (t) cc_final: 0.8031 (t) REVERT: A 65 LEU cc_start: 0.7749 (tp) cc_final: 0.7477 (tt) REVERT: A 74 TYR cc_start: 0.7696 (m-80) cc_final: 0.6862 (m-80) REVERT: A 85 VAL cc_start: 0.8529 (t) cc_final: 0.8298 (p) REVERT: A 122 LEU cc_start: 0.7460 (mt) cc_final: 0.7113 (mm) REVERT: A 137 MET cc_start: 0.7960 (mtm) cc_final: 0.7582 (mtm) REVERT: A 143 ILE cc_start: 0.8856 (mt) cc_final: 0.8535 (mm) REVERT: A 144 LEU cc_start: 0.8089 (mt) cc_final: 0.7832 (mt) REVERT: A 156 LEU cc_start: 0.7413 (tp) cc_final: 0.7075 (tt) REVERT: A 162 ILE cc_start: 0.8768 (mm) cc_final: 0.8425 (mm) REVERT: A 163 GLN cc_start: 0.8701 (pt0) cc_final: 0.8048 (tt0) REVERT: A 172 PHE cc_start: 0.7404 (m-10) cc_final: 0.7014 (m-10) REVERT: A 209 LYS cc_start: 0.8044 (mttt) cc_final: 0.7431 (mtmm) REVERT: A 226 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7390 (mtpt) REVERT: A 227 SER cc_start: 0.8152 (t) cc_final: 0.7879 (p) REVERT: A 230 ASP cc_start: 0.8359 (m-30) cc_final: 0.8076 (m-30) REVERT: A 233 HIS cc_start: 0.7507 (t-90) cc_final: 0.6877 (t-90) REVERT: A 253 LYS cc_start: 0.8022 (tptm) cc_final: 0.7335 (tptm) REVERT: A 257 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7953 (mm-30) REVERT: A 261 LYS cc_start: 0.7161 (mttm) cc_final: 0.6884 (mttm) REVERT: A 268 MET cc_start: 0.6175 (mtm) cc_final: 0.4995 (mtm) REVERT: A 277 MET cc_start: 0.6327 (mtt) cc_final: 0.5339 (mtt) REVERT: A 293 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7468 (mmmt) REVERT: A 316 TYR cc_start: 0.7526 (t80) cc_final: 0.7063 (t80) REVERT: A 318 MET cc_start: 0.7687 (tpp) cc_final: 0.6812 (tpp) REVERT: A 358 HIS cc_start: 0.7969 (m90) cc_final: 0.7545 (m90) REVERT: A 360 LYS cc_start: 0.8702 (tttt) cc_final: 0.8472 (tttt) REVERT: A 365 ILE cc_start: 0.8183 (mm) cc_final: 0.7890 (mm) REVERT: A 368 ASP cc_start: 0.5199 (m-30) cc_final: 0.4276 (m-30) REVERT: A 369 LEU cc_start: 0.7330 (mt) cc_final: 0.7083 (mm) REVERT: A 372 LEU cc_start: 0.8657 (mt) cc_final: 0.8391 (mt) REVERT: A 396 LYS cc_start: 0.8131 (tppp) cc_final: 0.7686 (tppp) REVERT: A 399 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7854 (mmtt) REVERT: A 401 ILE cc_start: 0.7884 (mt) cc_final: 0.7512 (mt) REVERT: A 404 PHE cc_start: 0.7548 (p90) cc_final: 0.6203 (p90) REVERT: A 421 GLU cc_start: 0.8651 (tt0) cc_final: 0.8039 (tt0) REVERT: A 429 ARG cc_start: 0.7201 (mtt180) cc_final: 0.6876 (mtt-85) REVERT: A 430 THR cc_start: 0.7427 (m) cc_final: 0.6067 (t) REVERT: A 431 LYS cc_start: 0.8218 (mtmm) cc_final: 0.7929 (mtmt) REVERT: A 432 GLN cc_start: 0.8489 (tp-100) cc_final: 0.8255 (tp-100) REVERT: A 433 HIS cc_start: 0.8295 (m-70) cc_final: 0.8060 (m-70) REVERT: A 455 GLU cc_start: 0.6230 (tt0) cc_final: 0.5953 (tt0) REVERT: A 489 LYS cc_start: 0.7830 (ttmp) cc_final: 0.7570 (mtpp) REVERT: A 534 GLU cc_start: 0.6860 (pt0) cc_final: 0.6269 (pt0) REVERT: C 5 LYS cc_start: 0.8063 (mttt) cc_final: 0.7821 (tppp) REVERT: C 18 GLN cc_start: 0.7594 (tt0) cc_final: 0.7259 (pm20) REVERT: C 22 LEU cc_start: 0.7549 (mt) cc_final: 0.7276 (mt) REVERT: C 25 MET cc_start: 0.7937 (mmp) cc_final: 0.7163 (mmp) REVERT: C 29 TYR cc_start: 0.5004 (t80) cc_final: 0.3865 (t80) outliers start: 2 outliers final: 1 residues processed: 396 average time/residue: 0.2448 time to fit residues: 127.0515 Evaluate side-chains 347 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.0770 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 105 optimal weight: 0.0870 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 260 HIS B 302 ASN ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 47 HIS A 57 ASN A 64 ASN A 158 ASN A 408 GLN A 432 GLN A 433 HIS A 486 GLN A 493 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.143950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.118315 restraints weight = 16635.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.123782 restraints weight = 9317.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.127654 restraints weight = 5903.308| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9358 Z= 0.200 Angle : 0.607 9.704 12680 Z= 0.308 Chirality : 0.047 0.268 1417 Planarity : 0.005 0.052 1669 Dihedral : 9.351 93.579 1426 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.10 % Allowed : 1.86 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.21), residues: 1164 helix: -2.73 (0.63), residues: 57 sheet: -2.80 (0.54), residues: 71 loop : -2.48 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.004 0.001 HIS A 507 PHE 0.019 0.001 PHE A 180 TYR 0.012 0.001 TYR B 301 ARG 0.008 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 376 time to evaluate : 0.965 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.5948 (pp30) cc_final: 0.4683 (mm-40) REVERT: B 31 MET cc_start: 0.7814 (mtp) cc_final: 0.7256 (ptp) REVERT: B 32 LYS cc_start: 0.8013 (mptt) cc_final: 0.7598 (mmtt) REVERT: B 46 LEU cc_start: 0.8723 (mt) cc_final: 0.8440 (mt) REVERT: B 54 GLN cc_start: 0.6898 (mt0) cc_final: 0.6610 (tp-100) REVERT: B 56 VAL cc_start: 0.8126 (t) cc_final: 0.7708 (t) REVERT: B 59 ASN cc_start: 0.6751 (m-40) cc_final: 0.6286 (m-40) REVERT: B 65 LEU cc_start: 0.8412 (mt) cc_final: 0.8211 (mt) REVERT: B 73 PHE cc_start: 0.8080 (p90) cc_final: 0.7822 (p90) REVERT: B 74 LEU cc_start: 0.8381 (mt) cc_final: 0.8119 (mt) REVERT: B 75 GLN cc_start: 0.7777 (pt0) cc_final: 0.7460 (pt0) REVERT: B 79 GLU cc_start: 0.7232 (tt0) cc_final: 0.6637 (tt0) REVERT: B 81 GLN cc_start: 0.6720 (mt0) cc_final: 0.6252 (mt0) REVERT: B 92 ARG cc_start: 0.7477 (mtt90) cc_final: 0.7150 (mmm-85) REVERT: B 93 GLN cc_start: 0.8477 (pp30) cc_final: 0.7713 (tm-30) REVERT: B 94 VAL cc_start: 0.8911 (t) cc_final: 0.8585 (t) REVERT: B 105 THR cc_start: 0.7728 (p) cc_final: 0.6772 (t) REVERT: B 106 GLN cc_start: 0.7668 (mt0) cc_final: 0.7107 (mp-120) REVERT: B 116 VAL cc_start: 0.6974 (t) cc_final: 0.6544 (p) REVERT: B 160 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7214 (tp40) REVERT: B 171 ASP cc_start: 0.7937 (t70) cc_final: 0.6650 (t70) REVERT: B 173 PHE cc_start: 0.6696 (m-10) cc_final: 0.6337 (m-10) REVERT: B 185 ASP cc_start: 0.7070 (t0) cc_final: 0.6820 (t0) REVERT: B 193 HIS cc_start: 0.7903 (m90) cc_final: 0.7269 (m90) REVERT: B 211 ASP cc_start: 0.8045 (m-30) cc_final: 0.7694 (m-30) REVERT: B 213 GLN cc_start: 0.7566 (tm-30) cc_final: 0.7250 (tm-30) REVERT: B 248 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8031 (mmtt) REVERT: B 251 ASP cc_start: 0.7634 (p0) cc_final: 0.7383 (p0) REVERT: B 253 LEU cc_start: 0.7451 (mt) cc_final: 0.6956 (mt) REVERT: B 265 GLU cc_start: 0.6921 (pm20) cc_final: 0.6598 (pm20) REVERT: B 271 LEU cc_start: 0.8543 (mp) cc_final: 0.8285 (mt) REVERT: B 275 ASN cc_start: 0.8266 (t0) cc_final: 0.7556 (t0) REVERT: B 282 MET cc_start: 0.8105 (mtp) cc_final: 0.7763 (mtp) REVERT: B 300 PRO cc_start: 0.7982 (Cg_exo) cc_final: 0.7587 (Cg_endo) REVERT: B 303 TYR cc_start: 0.7886 (m-80) cc_final: 0.7265 (m-80) REVERT: B 332 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6504 (mp0) REVERT: B 376 PHE cc_start: 0.8109 (m-10) cc_final: 0.7515 (m-10) REVERT: B 377 LEU cc_start: 0.8420 (tp) cc_final: 0.8157 (tt) REVERT: B 407 THR cc_start: 0.7745 (p) cc_final: 0.7442 (m) REVERT: B 411 TYR cc_start: 0.7150 (t80) cc_final: 0.6671 (t80) REVERT: B 420 PRO cc_start: 0.8414 (Cg_endo) cc_final: 0.8033 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7732 (p0) cc_final: 0.7412 (p0) REVERT: B 422 LEU cc_start: 0.8599 (tp) cc_final: 0.7706 (pp) REVERT: B 426 GLN cc_start: 0.7737 (pt0) cc_final: 0.6928 (pp30) REVERT: B 430 VAL cc_start: 0.7417 (p) cc_final: 0.7057 (t) REVERT: B 436 LEU cc_start: 0.7952 (mt) cc_final: 0.7417 (mt) REVERT: B 443 LEU cc_start: 0.7926 (tp) cc_final: 0.7444 (mm) REVERT: B 444 THR cc_start: 0.7448 (m) cc_final: 0.6843 (m) REVERT: B 452 TRP cc_start: 0.7703 (p90) cc_final: 0.7188 (p90) REVERT: B 463 SER cc_start: 0.7460 (t) cc_final: 0.7017 (m) REVERT: B 481 PRO cc_start: 0.8294 (Cg_endo) cc_final: 0.7683 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8513 (m100) cc_final: 0.8311 (m100) REVERT: B 488 ASN cc_start: 0.8022 (t0) cc_final: 0.7810 (t0) REVERT: B 494 LEU cc_start: 0.8491 (mt) cc_final: 0.8251 (mm) REVERT: B 517 ARG cc_start: 0.8278 (mtt180) cc_final: 0.7978 (mtm110) REVERT: B 556 ASN cc_start: 0.8071 (t0) cc_final: 0.7447 (t0) REVERT: B 566 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6593 (tm-30) REVERT: B 577 PHE cc_start: 0.8091 (m-80) cc_final: 0.7869 (m-80) REVERT: B 580 GLU cc_start: 0.8455 (tp30) cc_final: 0.8084 (tp30) REVERT: A 29 LYS cc_start: 0.7925 (pttm) cc_final: 0.7572 (pttm) REVERT: A 36 ASN cc_start: 0.8267 (p0) cc_final: 0.7806 (p0) REVERT: A 46 ASP cc_start: 0.7360 (t70) cc_final: 0.6576 (t70) REVERT: A 47 HIS cc_start: 0.7889 (t70) cc_final: 0.6681 (t70) REVERT: A 51 LEU cc_start: 0.8705 (tp) cc_final: 0.8478 (tp) REVERT: A 55 PHE cc_start: 0.7831 (m-10) cc_final: 0.7414 (m-10) REVERT: A 62 LEU cc_start: 0.8471 (mt) cc_final: 0.8230 (mm) REVERT: A 74 TYR cc_start: 0.7759 (m-80) cc_final: 0.6911 (m-80) REVERT: A 80 LYS cc_start: 0.8269 (mttm) cc_final: 0.7865 (mttm) REVERT: A 83 GLN cc_start: 0.7949 (mm110) cc_final: 0.7422 (mm110) REVERT: A 93 LEU cc_start: 0.8223 (mp) cc_final: 0.7990 (mt) REVERT: A 114 GLU cc_start: 0.7427 (tt0) cc_final: 0.6948 (tt0) REVERT: A 132 LEU cc_start: 0.7865 (tp) cc_final: 0.7627 (mm) REVERT: A 143 ILE cc_start: 0.8965 (mt) cc_final: 0.8689 (mm) REVERT: A 163 GLN cc_start: 0.8637 (pt0) cc_final: 0.7982 (tt0) REVERT: A 176 MET cc_start: 0.7917 (ptp) cc_final: 0.7517 (ptt) REVERT: A 209 LYS cc_start: 0.8096 (mttt) cc_final: 0.7505 (mtmm) REVERT: A 226 LYS cc_start: 0.7827 (mtpt) cc_final: 0.7252 (mtpt) REVERT: A 227 SER cc_start: 0.8116 (t) cc_final: 0.7885 (p) REVERT: A 233 HIS cc_start: 0.7580 (t-90) cc_final: 0.7003 (t-90) REVERT: A 253 LYS cc_start: 0.8143 (tptm) cc_final: 0.7424 (tptm) REVERT: A 256 ASP cc_start: 0.6923 (t70) cc_final: 0.6542 (t0) REVERT: A 261 LYS cc_start: 0.7336 (mttm) cc_final: 0.6856 (mttm) REVERT: A 262 ASP cc_start: 0.7560 (t0) cc_final: 0.7191 (t0) REVERT: A 268 MET cc_start: 0.6211 (mtm) cc_final: 0.5074 (mtm) REVERT: A 277 MET cc_start: 0.6382 (mtt) cc_final: 0.5335 (mtt) REVERT: A 285 TYR cc_start: 0.5895 (m-10) cc_final: 0.5694 (m-10) REVERT: A 293 LYS cc_start: 0.7894 (mtpp) cc_final: 0.7021 (mmmt) REVERT: A 316 TYR cc_start: 0.7469 (t80) cc_final: 0.7048 (t80) REVERT: A 318 MET cc_start: 0.7738 (tpp) cc_final: 0.6919 (tpp) REVERT: A 338 ASN cc_start: 0.6920 (p0) cc_final: 0.6196 (p0) REVERT: A 345 PHE cc_start: 0.8146 (m-80) cc_final: 0.7765 (m-80) REVERT: A 358 HIS cc_start: 0.8186 (m90) cc_final: 0.7670 (m90) REVERT: A 360 LYS cc_start: 0.8696 (tttt) cc_final: 0.8331 (tttt) REVERT: A 368 ASP cc_start: 0.5222 (m-30) cc_final: 0.4072 (m-30) REVERT: A 369 LEU cc_start: 0.7250 (mt) cc_final: 0.7002 (mm) REVERT: A 396 LYS cc_start: 0.8228 (tppp) cc_final: 0.7803 (tppp) REVERT: A 404 PHE cc_start: 0.7470 (p90) cc_final: 0.6113 (p90) REVERT: A 421 GLU cc_start: 0.8675 (tt0) cc_final: 0.7999 (tt0) REVERT: A 430 THR cc_start: 0.7759 (m) cc_final: 0.6417 (t) REVERT: A 432 GLN cc_start: 0.8624 (tp40) cc_final: 0.8090 (tp-100) REVERT: A 433 HIS cc_start: 0.8287 (m90) cc_final: 0.8071 (m90) REVERT: A 476 ASN cc_start: 0.7692 (t0) cc_final: 0.7337 (t0) REVERT: A 489 LYS cc_start: 0.7924 (ttmm) cc_final: 0.7659 (mtpp) REVERT: A 496 GLU cc_start: 0.7583 (mp0) cc_final: 0.7309 (mp0) REVERT: A 521 ARG cc_start: 0.7840 (ptt180) cc_final: 0.7556 (tmm-80) REVERT: A 551 GLU cc_start: 0.8568 (pt0) cc_final: 0.8056 (pm20) REVERT: C 5 LYS cc_start: 0.8041 (mttt) cc_final: 0.7838 (tppp) REVERT: C 18 GLN cc_start: 0.7727 (tt0) cc_final: 0.7271 (pm20) REVERT: C 22 LEU cc_start: 0.7579 (mt) cc_final: 0.7244 (mt) REVERT: C 25 MET cc_start: 0.7925 (mmp) cc_final: 0.7244 (mmp) outliers start: 1 outliers final: 1 residues processed: 377 average time/residue: 0.2514 time to fit residues: 124.4462 Evaluate side-chains 346 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 345 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 77 optimal weight: 0.0670 chunk 47 optimal weight: 0.8980 chunk 24 optimal weight: 0.0040 chunk 86 optimal weight: 0.0670 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.1668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 267 HIS B 302 ASN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 145 HIS A 435 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.139300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.113256 restraints weight = 16459.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.118858 restraints weight = 9212.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.122790 restraints weight = 5832.982| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9358 Z= 0.154 Angle : 0.581 9.538 12680 Z= 0.293 Chirality : 0.046 0.259 1417 Planarity : 0.004 0.043 1669 Dihedral : 8.218 84.897 1426 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.22), residues: 1164 helix: -2.15 (0.73), residues: 51 sheet: -2.22 (0.63), residues: 61 loop : -2.30 (0.17), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 415 HIS 0.006 0.001 HIS A 145 PHE 0.022 0.001 PHE B 486 TYR 0.016 0.001 TYR B 301 ARG 0.006 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.001 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6069 (pp30) cc_final: 0.4807 (mm-40) REVERT: B 31 MET cc_start: 0.7894 (mtp) cc_final: 0.7299 (ptp) REVERT: B 34 ARG cc_start: 0.7753 (ptp90) cc_final: 0.7487 (mtm110) REVERT: B 44 ASP cc_start: 0.7361 (t0) cc_final: 0.6632 (t0) REVERT: B 46 LEU cc_start: 0.8737 (mt) cc_final: 0.8491 (mt) REVERT: B 47 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7388 (ttp80) REVERT: B 54 GLN cc_start: 0.6860 (mt0) cc_final: 0.6587 (tp-100) REVERT: B 56 VAL cc_start: 0.8124 (t) cc_final: 0.7798 (m) REVERT: B 59 ASN cc_start: 0.6681 (m-40) cc_final: 0.6359 (m-40) REVERT: B 73 PHE cc_start: 0.8067 (p90) cc_final: 0.7713 (p90) REVERT: B 74 LEU cc_start: 0.8389 (mt) cc_final: 0.8174 (mt) REVERT: B 75 GLN cc_start: 0.7775 (pt0) cc_final: 0.7476 (pt0) REVERT: B 79 GLU cc_start: 0.7214 (tt0) cc_final: 0.6403 (tt0) REVERT: B 81 GLN cc_start: 0.6804 (mt0) cc_final: 0.6236 (mt0) REVERT: B 93 GLN cc_start: 0.8501 (pp30) cc_final: 0.8185 (tm-30) REVERT: B 100 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7370 (mmm-85) REVERT: B 103 ARG cc_start: 0.7330 (ttm110) cc_final: 0.6979 (ttm110) REVERT: B 105 THR cc_start: 0.7883 (p) cc_final: 0.6866 (t) REVERT: B 106 GLN cc_start: 0.7732 (mt0) cc_final: 0.7141 (mp-120) REVERT: B 143 ARG cc_start: 0.7657 (mtt180) cc_final: 0.7292 (mtt180) REVERT: B 155 ILE cc_start: 0.8016 (mt) cc_final: 0.7744 (mm) REVERT: B 158 ASN cc_start: 0.7634 (m-40) cc_final: 0.7418 (m110) REVERT: B 173 PHE cc_start: 0.6833 (m-10) cc_final: 0.6508 (m-10) REVERT: B 184 ILE cc_start: 0.8285 (mm) cc_final: 0.8047 (mm) REVERT: B 185 ASP cc_start: 0.7089 (t0) cc_final: 0.6507 (t0) REVERT: B 193 HIS cc_start: 0.7867 (m90) cc_final: 0.7276 (m90) REVERT: B 211 ASP cc_start: 0.7927 (m-30) cc_final: 0.7356 (m-30) REVERT: B 213 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7283 (tm-30) REVERT: B 226 ARG cc_start: 0.7912 (tpp-160) cc_final: 0.7424 (mmm160) REVERT: B 248 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8017 (mmtt) REVERT: B 251 ASP cc_start: 0.7602 (p0) cc_final: 0.7318 (p0) REVERT: B 265 GLU cc_start: 0.6970 (pm20) cc_final: 0.6392 (pm20) REVERT: B 266 LEU cc_start: 0.8298 (tp) cc_final: 0.8097 (tp) REVERT: B 267 HIS cc_start: 0.7500 (m170) cc_final: 0.7100 (m170) REVERT: B 271 LEU cc_start: 0.8608 (mp) cc_final: 0.8356 (mt) REVERT: B 274 TYR cc_start: 0.6881 (t80) cc_final: 0.5984 (t80) REVERT: B 275 ASN cc_start: 0.7892 (t0) cc_final: 0.7623 (t0) REVERT: B 282 MET cc_start: 0.8315 (mtp) cc_final: 0.7800 (mtp) REVERT: B 291 PHE cc_start: 0.7591 (t80) cc_final: 0.7373 (t80) REVERT: B 300 PRO cc_start: 0.8185 (Cg_exo) cc_final: 0.7778 (Cg_endo) REVERT: B 303 TYR cc_start: 0.7950 (m-80) cc_final: 0.7250 (m-80) REVERT: B 313 LEU cc_start: 0.8213 (mt) cc_final: 0.7886 (pt) REVERT: B 332 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6537 (mp0) REVERT: B 377 LEU cc_start: 0.8423 (tp) cc_final: 0.8152 (tt) REVERT: B 398 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7802 (mm-40) REVERT: B 407 THR cc_start: 0.7738 (p) cc_final: 0.7240 (m) REVERT: B 411 TYR cc_start: 0.7210 (t80) cc_final: 0.6368 (t80) REVERT: B 420 PRO cc_start: 0.8474 (Cg_endo) cc_final: 0.8201 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7707 (p0) cc_final: 0.7435 (p0) REVERT: B 422 LEU cc_start: 0.8537 (tp) cc_final: 0.8211 (mt) REVERT: B 426 GLN cc_start: 0.7843 (pt0) cc_final: 0.7085 (pp30) REVERT: B 436 LEU cc_start: 0.8062 (mt) cc_final: 0.7502 (mt) REVERT: B 443 LEU cc_start: 0.7930 (tp) cc_final: 0.7381 (mm) REVERT: B 444 THR cc_start: 0.7292 (m) cc_final: 0.6735 (m) REVERT: B 451 SER cc_start: 0.8060 (p) cc_final: 0.7631 (m) REVERT: B 452 TRP cc_start: 0.7697 (p90) cc_final: 0.7478 (p90) REVERT: B 481 PRO cc_start: 0.8237 (Cg_endo) cc_final: 0.7660 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8636 (m100) cc_final: 0.8388 (m100) REVERT: B 494 LEU cc_start: 0.8539 (mt) cc_final: 0.8277 (mt) REVERT: B 556 ASN cc_start: 0.8021 (t0) cc_final: 0.7406 (t0) REVERT: B 566 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6554 (tm-30) REVERT: B 577 PHE cc_start: 0.8091 (m-80) cc_final: 0.7859 (m-80) REVERT: B 580 GLU cc_start: 0.8454 (tp30) cc_final: 0.8140 (tp30) REVERT: A 29 LYS cc_start: 0.7764 (pttm) cc_final: 0.7391 (pttt) REVERT: A 36 ASN cc_start: 0.8272 (p0) cc_final: 0.7882 (p0) REVERT: A 46 ASP cc_start: 0.7201 (t70) cc_final: 0.6560 (t70) REVERT: A 47 HIS cc_start: 0.7799 (t70) cc_final: 0.6715 (t70) REVERT: A 51 LEU cc_start: 0.8697 (tp) cc_final: 0.8469 (tp) REVERT: A 55 PHE cc_start: 0.7743 (m-10) cc_final: 0.7400 (m-10) REVERT: A 61 VAL cc_start: 0.8158 (m) cc_final: 0.7915 (p) REVERT: A 65 LEU cc_start: 0.7949 (tp) cc_final: 0.7516 (tt) REVERT: A 74 TYR cc_start: 0.7800 (m-80) cc_final: 0.6905 (m-80) REVERT: A 80 LYS cc_start: 0.8259 (mttm) cc_final: 0.8040 (mttm) REVERT: A 83 GLN cc_start: 0.7872 (mm110) cc_final: 0.7068 (mm110) REVERT: A 85 VAL cc_start: 0.8153 (t) cc_final: 0.7932 (p) REVERT: A 98 ARG cc_start: 0.7644 (ttt90) cc_final: 0.7315 (tpp80) REVERT: A 102 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6910 (mt-10) REVERT: A 103 ASN cc_start: 0.7307 (m-40) cc_final: 0.6378 (m-40) REVERT: A 110 ASN cc_start: 0.7895 (m-40) cc_final: 0.7573 (p0) REVERT: A 132 LEU cc_start: 0.7677 (tp) cc_final: 0.7318 (mm) REVERT: A 143 ILE cc_start: 0.8929 (mt) cc_final: 0.8594 (mm) REVERT: A 163 GLN cc_start: 0.8538 (pt0) cc_final: 0.8180 (tt0) REVERT: A 167 ILE cc_start: 0.8492 (mp) cc_final: 0.8283 (mp) REVERT: A 176 MET cc_start: 0.7992 (ptp) cc_final: 0.7652 (ptt) REVERT: A 209 LYS cc_start: 0.8110 (mttt) cc_final: 0.7536 (mtmm) REVERT: A 226 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7274 (mtpt) REVERT: A 227 SER cc_start: 0.8121 (t) cc_final: 0.7874 (p) REVERT: A 229 SER cc_start: 0.8271 (p) cc_final: 0.7899 (t) REVERT: A 230 ASP cc_start: 0.8325 (m-30) cc_final: 0.8118 (m-30) REVERT: A 233 HIS cc_start: 0.7308 (t-90) cc_final: 0.6965 (t-90) REVERT: A 253 LYS cc_start: 0.8124 (tptm) cc_final: 0.7502 (tptm) REVERT: A 254 PHE cc_start: 0.7252 (m-10) cc_final: 0.5957 (m-80) REVERT: A 255 ARG cc_start: 0.6796 (ttt-90) cc_final: 0.6563 (ttp80) REVERT: A 262 ASP cc_start: 0.7572 (t0) cc_final: 0.7126 (t0) REVERT: A 268 MET cc_start: 0.6173 (mtm) cc_final: 0.4962 (mtm) REVERT: A 277 MET cc_start: 0.6191 (mtt) cc_final: 0.5146 (mtt) REVERT: A 290 THR cc_start: 0.6891 (t) cc_final: 0.6678 (t) REVERT: A 293 LYS cc_start: 0.7636 (mtpp) cc_final: 0.7219 (tppt) REVERT: A 298 ASN cc_start: 0.7834 (p0) cc_final: 0.6541 (p0) REVERT: A 316 TYR cc_start: 0.7325 (t80) cc_final: 0.6952 (t80) REVERT: A 318 MET cc_start: 0.7624 (tpp) cc_final: 0.6802 (tpp) REVERT: A 338 ASN cc_start: 0.7084 (p0) cc_final: 0.6836 (p0) REVERT: A 358 HIS cc_start: 0.8292 (m90) cc_final: 0.7774 (m90) REVERT: A 360 LYS cc_start: 0.8705 (tttt) cc_final: 0.8355 (tttt) REVERT: A 368 ASP cc_start: 0.5064 (m-30) cc_final: 0.4031 (m-30) REVERT: A 396 LYS cc_start: 0.8251 (tppp) cc_final: 0.7807 (tppp) REVERT: A 404 PHE cc_start: 0.7436 (p90) cc_final: 0.6038 (p90) REVERT: A 421 GLU cc_start: 0.8684 (tt0) cc_final: 0.8064 (tt0) REVERT: A 429 ARG cc_start: 0.7741 (mtt180) cc_final: 0.6876 (mmm-85) REVERT: A 430 THR cc_start: 0.7754 (m) cc_final: 0.6327 (t) REVERT: A 431 LYS cc_start: 0.8241 (mtmm) cc_final: 0.7888 (mtmt) REVERT: A 432 GLN cc_start: 0.8628 (tp40) cc_final: 0.8238 (tp-100) REVERT: A 476 ASN cc_start: 0.7660 (t0) cc_final: 0.7260 (t0) REVERT: A 489 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7585 (mmmm) REVERT: A 496 GLU cc_start: 0.7548 (mp0) cc_final: 0.7317 (mp0) REVERT: A 551 GLU cc_start: 0.8625 (pt0) cc_final: 0.8166 (pm20) REVERT: C 5 LYS cc_start: 0.8057 (mttt) cc_final: 0.7855 (tppp) REVERT: C 22 LEU cc_start: 0.7449 (mt) cc_final: 0.7179 (mt) REVERT: C 25 MET cc_start: 0.7893 (mmp) cc_final: 0.7330 (mmp) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.2580 time to fit residues: 125.3594 Evaluate side-chains 342 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 96 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 98 optimal weight: 0.0370 chunk 55 optimal weight: 0.0980 chunk 15 optimal weight: 4.9990 chunk 113 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.133061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.106997 restraints weight = 16619.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.112627 restraints weight = 9362.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.116560 restraints weight = 5928.203| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9358 Z= 0.204 Angle : 0.604 9.491 12680 Z= 0.308 Chirality : 0.046 0.276 1417 Planarity : 0.004 0.045 1669 Dihedral : 7.397 78.215 1426 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.23), residues: 1164 helix: -1.41 (0.79), residues: 48 sheet: -1.56 (0.58), residues: 84 loop : -2.06 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 477 HIS 0.006 0.001 HIS A 507 PHE 0.013 0.001 PHE A 172 TYR 0.015 0.001 TYR A 113 ARG 0.007 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 1.102 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: 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: symmetry clash REVERT: B 24 GLN cc_start: 0.6602 (pp30) cc_final: 0.5383 (mm-40) REVERT: B 31 MET cc_start: 0.7783 (mtp) cc_final: 0.7193 (ptp) REVERT: B 44 ASP cc_start: 0.7532 (t0) cc_final: 0.6587 (t0) REVERT: B 46 LEU cc_start: 0.8824 (mt) cc_final: 0.8404 (mt) REVERT: B 47 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7434 (ttp80) REVERT: B 54 GLN cc_start: 0.7038 (mt0) cc_final: 0.6679 (tp40) REVERT: B 55 VAL cc_start: 0.7409 (t) cc_final: 0.6681 (t) REVERT: B 56 VAL cc_start: 0.8003 (t) cc_final: 0.7789 (m) REVERT: B 65 LEU cc_start: 0.8325 (mt) cc_final: 0.8015 (mt) REVERT: B 75 GLN cc_start: 0.7838 (pt0) cc_final: 0.7476 (pt0) REVERT: B 79 GLU cc_start: 0.7197 (tt0) cc_final: 0.6484 (tt0) REVERT: B 81 GLN cc_start: 0.6885 (mt0) cc_final: 0.6310 (mt0) REVERT: B 85 LEU cc_start: 0.8372 (tp) cc_final: 0.8096 (tp) REVERT: B 100 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7491 (mmm-85) REVERT: B 105 THR cc_start: 0.8013 (p) cc_final: 0.7071 (t) REVERT: B 106 GLN cc_start: 0.7783 (mt0) cc_final: 0.7389 (mp-120) REVERT: B 109 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7508 (mt-10) REVERT: B 112 TYR cc_start: 0.7155 (m-80) cc_final: 0.6803 (m-80) REVERT: B 143 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7298 (mtt180) REVERT: B 153 VAL cc_start: 0.7664 (t) cc_final: 0.7420 (t) REVERT: B 160 GLN cc_start: 0.6990 (tp40) cc_final: 0.6752 (tp40) REVERT: B 169 TRP cc_start: 0.8553 (m100) cc_final: 0.7394 (m100) REVERT: B 173 PHE cc_start: 0.7056 (m-10) cc_final: 0.6471 (m-10) REVERT: B 181 LEU cc_start: 0.8115 (mp) cc_final: 0.7909 (mm) REVERT: B 193 HIS cc_start: 0.7855 (m90) cc_final: 0.7251 (m90) REVERT: B 208 SER cc_start: 0.7615 (m) cc_final: 0.7250 (p) REVERT: B 211 ASP cc_start: 0.7935 (m-30) cc_final: 0.6983 (m-30) REVERT: B 217 ARG cc_start: 0.7027 (mtp-110) cc_final: 0.6423 (mtt-85) REVERT: B 248 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8027 (mmtt) REVERT: B 251 ASP cc_start: 0.7640 (p0) cc_final: 0.7422 (p0) REVERT: B 265 GLU cc_start: 0.7075 (pm20) cc_final: 0.6521 (pm20) REVERT: B 267 HIS cc_start: 0.7537 (m170) cc_final: 0.7252 (m170) REVERT: B 271 LEU cc_start: 0.8560 (mp) cc_final: 0.8321 (mt) REVERT: B 274 TYR cc_start: 0.6903 (t80) cc_final: 0.6502 (t80) REVERT: B 275 ASN cc_start: 0.8124 (t0) cc_final: 0.7718 (t0) REVERT: B 282 MET cc_start: 0.8378 (mtp) cc_final: 0.7837 (mtp) REVERT: B 303 TYR cc_start: 0.8047 (m-80) cc_final: 0.7624 (m-80) REVERT: B 311 CYS cc_start: 0.4221 (p) cc_final: 0.3258 (m) REVERT: B 332 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7075 (mt-10) REVERT: B 364 PHE cc_start: 0.8519 (m-80) cc_final: 0.7799 (m-80) REVERT: B 398 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7876 (mm-40) REVERT: B 407 THR cc_start: 0.7881 (p) cc_final: 0.6810 (m) REVERT: B 409 TYR cc_start: 0.7166 (p90) cc_final: 0.6911 (p90) REVERT: B 411 TYR cc_start: 0.7309 (t80) cc_final: 0.6560 (t80) REVERT: B 420 PRO cc_start: 0.8488 (Cg_endo) cc_final: 0.8106 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7679 (p0) cc_final: 0.7290 (p0) REVERT: B 422 LEU cc_start: 0.8618 (tp) cc_final: 0.8365 (tp) REVERT: B 426 GLN cc_start: 0.7930 (pt0) cc_final: 0.7239 (pp30) REVERT: B 430 VAL cc_start: 0.7843 (p) cc_final: 0.7614 (t) REVERT: B 436 LEU cc_start: 0.8081 (mt) cc_final: 0.7382 (mt) REVERT: B 444 THR cc_start: 0.7423 (m) cc_final: 0.7050 (m) REVERT: B 451 SER cc_start: 0.8082 (p) cc_final: 0.7604 (m) REVERT: B 452 TRP cc_start: 0.7905 (p90) cc_final: 0.7598 (p90) REVERT: B 467 LEU cc_start: 0.7182 (tp) cc_final: 0.6959 (tp) REVERT: B 481 PRO cc_start: 0.8168 (Cg_endo) cc_final: 0.7536 (Cg_exo) REVERT: B 487 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7329 (mtt90) REVERT: B 488 ASN cc_start: 0.8023 (t0) cc_final: 0.7633 (t0) REVERT: B 494 LEU cc_start: 0.8697 (mt) cc_final: 0.8343 (mt) REVERT: B 556 ASN cc_start: 0.8160 (t0) cc_final: 0.7494 (t0) REVERT: B 566 GLU cc_start: 0.7667 (mm-30) cc_final: 0.6575 (tm-30) REVERT: B 577 PHE cc_start: 0.8194 (m-80) cc_final: 0.7930 (m-80) REVERT: B 580 GLU cc_start: 0.8473 (tp30) cc_final: 0.8155 (tp30) REVERT: A 29 LYS cc_start: 0.7922 (pttm) cc_final: 0.7385 (pttm) REVERT: A 35 SER cc_start: 0.8209 (t) cc_final: 0.7999 (p) REVERT: A 36 ASN cc_start: 0.8354 (p0) cc_final: 0.7891 (p0) REVERT: A 46 ASP cc_start: 0.7287 (t70) cc_final: 0.6687 (t70) REVERT: A 47 HIS cc_start: 0.7896 (t70) cc_final: 0.6846 (t70) REVERT: A 51 LEU cc_start: 0.8834 (tp) cc_final: 0.8568 (tp) REVERT: A 55 PHE cc_start: 0.7856 (m-10) cc_final: 0.7549 (m-10) REVERT: A 61 VAL cc_start: 0.8242 (m) cc_final: 0.8034 (p) REVERT: A 71 GLN cc_start: 0.7092 (mm110) cc_final: 0.6650 (mm-40) REVERT: A 74 TYR cc_start: 0.7947 (m-80) cc_final: 0.7015 (m-80) REVERT: A 80 LYS cc_start: 0.8398 (mttm) cc_final: 0.8150 (mttm) REVERT: A 83 GLN cc_start: 0.7792 (mm110) cc_final: 0.7010 (mm110) REVERT: A 85 VAL cc_start: 0.8118 (t) cc_final: 0.7854 (p) REVERT: A 98 ARG cc_start: 0.7557 (ttt90) cc_final: 0.7206 (tpp80) REVERT: A 102 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6992 (mt-10) REVERT: A 103 ASN cc_start: 0.7378 (m-40) cc_final: 0.6481 (m-40) REVERT: A 114 GLU cc_start: 0.7606 (tt0) cc_final: 0.7036 (tt0) REVERT: A 143 ILE cc_start: 0.8991 (mt) cc_final: 0.8623 (mm) REVERT: A 163 GLN cc_start: 0.8575 (pt0) cc_final: 0.8053 (tt0) REVERT: A 176 MET cc_start: 0.8243 (ptp) cc_final: 0.7884 (ptt) REVERT: A 209 LYS cc_start: 0.8245 (mttt) cc_final: 0.7641 (mtmm) REVERT: A 227 SER cc_start: 0.8077 (t) cc_final: 0.7858 (p) REVERT: A 229 SER cc_start: 0.8256 (p) cc_final: 0.7997 (t) REVERT: A 230 ASP cc_start: 0.8308 (m-30) cc_final: 0.8065 (m-30) REVERT: A 233 HIS cc_start: 0.7554 (t-90) cc_final: 0.7312 (t-90) REVERT: A 257 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7989 (mm-30) REVERT: A 261 LYS cc_start: 0.7219 (ptmt) cc_final: 0.6750 (ptmt) REVERT: A 268 MET cc_start: 0.6182 (mtm) cc_final: 0.5030 (mtm) REVERT: A 277 MET cc_start: 0.6271 (mtt) cc_final: 0.5173 (mtt) REVERT: A 293 LYS cc_start: 0.7767 (mtpp) cc_final: 0.6855 (mtpp) REVERT: A 338 ASN cc_start: 0.7264 (p0) cc_final: 0.6254 (p0) REVERT: A 345 PHE cc_start: 0.8259 (m-80) cc_final: 0.7572 (m-80) REVERT: A 358 HIS cc_start: 0.8336 (m90) cc_final: 0.8090 (m90) REVERT: A 360 LYS cc_start: 0.8734 (tttt) cc_final: 0.8401 (tttt) REVERT: A 368 ASP cc_start: 0.5082 (m-30) cc_final: 0.3753 (m-30) REVERT: A 396 LYS cc_start: 0.8337 (tppp) cc_final: 0.7850 (tppp) REVERT: A 404 PHE cc_start: 0.7471 (p90) cc_final: 0.6169 (p90) REVERT: A 421 GLU cc_start: 0.8680 (tt0) cc_final: 0.7034 (tt0) REVERT: A 429 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7513 (mtt-85) REVERT: A 430 THR cc_start: 0.7701 (m) cc_final: 0.6398 (p) REVERT: A 432 GLN cc_start: 0.8624 (tp40) cc_final: 0.7932 (tm-30) REVERT: A 433 HIS cc_start: 0.8220 (m90) cc_final: 0.7868 (m90) REVERT: A 451 ARG cc_start: 0.7071 (mtt90) cc_final: 0.5564 (ptp-110) REVERT: A 456 ILE cc_start: 0.8380 (mm) cc_final: 0.7722 (pt) REVERT: A 457 SER cc_start: 0.7903 (m) cc_final: 0.7491 (m) REVERT: A 460 ASP cc_start: 0.6903 (t70) cc_final: 0.6471 (t70) REVERT: A 476 ASN cc_start: 0.7768 (t0) cc_final: 0.7352 (t0) REVERT: A 487 LYS cc_start: 0.7666 (mtmm) cc_final: 0.7334 (mtmm) REVERT: A 496 GLU cc_start: 0.7581 (mp0) cc_final: 0.7225 (mp0) REVERT: A 521 ARG cc_start: 0.7804 (ptt180) cc_final: 0.6697 (ptt180) REVERT: A 551 GLU cc_start: 0.8647 (pt0) cc_final: 0.8236 (pm20) REVERT: C 22 LEU cc_start: 0.7720 (mt) cc_final: 0.7395 (mt) REVERT: C 25 MET cc_start: 0.7907 (mmp) cc_final: 0.7317 (mmp) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.2586 time to fit residues: 127.1795 Evaluate side-chains 357 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 44 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 7 optimal weight: 0.0870 chunk 14 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 80 optimal weight: 0.0020 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 280 ASN A 435 GLN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.130507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104805 restraints weight = 16525.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.110298 restraints weight = 9335.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.114234 restraints weight = 5906.218| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9358 Z= 0.191 Angle : 0.615 10.435 12680 Z= 0.309 Chirality : 0.046 0.267 1417 Planarity : 0.004 0.047 1669 Dihedral : 7.001 76.108 1426 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.10 % Allowed : 1.18 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.23), residues: 1164 helix: -1.39 (0.82), residues: 42 sheet: -1.06 (0.63), residues: 79 loop : -1.92 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.005 0.001 HIS A 507 PHE 0.019 0.001 PHE B 73 TYR 0.043 0.002 TYR A 117 ARG 0.005 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 0.958 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6834 (pp30) cc_final: 0.5039 (mm-40) REVERT: B 31 MET cc_start: 0.7569 (mtp) cc_final: 0.6550 (ptp) REVERT: B 44 ASP cc_start: 0.7499 (t0) cc_final: 0.6601 (t0) REVERT: B 46 LEU cc_start: 0.8681 (mt) cc_final: 0.8300 (mt) REVERT: B 47 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7436 (ttp80) REVERT: B 55 VAL cc_start: 0.7405 (t) cc_final: 0.6614 (t) REVERT: B 59 ASN cc_start: 0.7256 (m-40) cc_final: 0.6819 (m-40) REVERT: B 61 GLU cc_start: 0.6867 (tm-30) cc_final: 0.3934 (tm-30) REVERT: B 64 TYR cc_start: 0.7704 (m-80) cc_final: 0.7228 (m-80) REVERT: B 65 LEU cc_start: 0.8246 (mt) cc_final: 0.7985 (mt) REVERT: B 75 GLN cc_start: 0.7860 (pt0) cc_final: 0.7473 (pt0) REVERT: B 79 GLU cc_start: 0.7017 (tt0) cc_final: 0.6443 (tt0) REVERT: B 81 GLN cc_start: 0.6714 (mt0) cc_final: 0.6277 (mt0) REVERT: B 100 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7710 (mmm-85) REVERT: B 105 THR cc_start: 0.8070 (p) cc_final: 0.7550 (t) REVERT: B 106 GLN cc_start: 0.7791 (mt0) cc_final: 0.7390 (mp10) REVERT: B 112 TYR cc_start: 0.7248 (m-80) cc_final: 0.6799 (m-80) REVERT: B 143 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7340 (mtt180) REVERT: B 156 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7034 (tm-30) REVERT: B 169 TRP cc_start: 0.8490 (m100) cc_final: 0.7352 (m100) REVERT: B 184 ILE cc_start: 0.8708 (mm) cc_final: 0.8498 (mm) REVERT: B 185 ASP cc_start: 0.7218 (t0) cc_final: 0.6824 (t0) REVERT: B 188 ARG cc_start: 0.6790 (mmt180) cc_final: 0.6505 (mmm-85) REVERT: B 193 HIS cc_start: 0.7870 (m90) cc_final: 0.7271 (m90) REVERT: B 208 SER cc_start: 0.7899 (m) cc_final: 0.7561 (t) REVERT: B 211 ASP cc_start: 0.7936 (m-30) cc_final: 0.7200 (m-30) REVERT: B 248 LYS cc_start: 0.8610 (mmtt) cc_final: 0.7992 (mmtt) REVERT: B 251 ASP cc_start: 0.7570 (p0) cc_final: 0.7319 (p0) REVERT: B 267 HIS cc_start: 0.7539 (m170) cc_final: 0.7233 (m170) REVERT: B 274 TYR cc_start: 0.6860 (t80) cc_final: 0.6282 (t80) REVERT: B 282 MET cc_start: 0.8360 (mtp) cc_final: 0.7896 (mtp) REVERT: B 288 ARG cc_start: 0.7944 (mpt-90) cc_final: 0.7622 (mmt-90) REVERT: B 303 TYR cc_start: 0.8079 (m-80) cc_final: 0.7611 (m-80) REVERT: B 311 CYS cc_start: 0.4198 (p) cc_final: 0.3362 (m) REVERT: B 313 LEU cc_start: 0.8332 (mt) cc_final: 0.7943 (pt) REVERT: B 332 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7089 (mt-10) REVERT: B 351 ARG cc_start: 0.7827 (mmp80) cc_final: 0.7586 (tpp-160) REVERT: B 364 PHE cc_start: 0.8551 (m-80) cc_final: 0.7831 (m-80) REVERT: B 398 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7943 (mm-40) REVERT: B 407 THR cc_start: 0.7896 (p) cc_final: 0.7406 (m) REVERT: B 411 TYR cc_start: 0.7234 (t80) cc_final: 0.6485 (t80) REVERT: B 420 PRO cc_start: 0.8511 (Cg_endo) cc_final: 0.8169 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7668 (p0) cc_final: 0.7335 (p0) REVERT: B 422 LEU cc_start: 0.8607 (tp) cc_final: 0.8362 (tp) REVERT: B 426 GLN cc_start: 0.7963 (pt0) cc_final: 0.7289 (pp30) REVERT: B 436 LEU cc_start: 0.8079 (mt) cc_final: 0.7786 (mp) REVERT: B 444 THR cc_start: 0.7452 (m) cc_final: 0.7016 (m) REVERT: B 451 SER cc_start: 0.8122 (p) cc_final: 0.7661 (m) REVERT: B 452 TRP cc_start: 0.7881 (p90) cc_final: 0.7589 (p90) REVERT: B 467 LEU cc_start: 0.7187 (tp) cc_final: 0.6985 (tp) REVERT: B 481 PRO cc_start: 0.8181 (Cg_endo) cc_final: 0.7627 (Cg_exo) REVERT: B 487 ARG cc_start: 0.7929 (mmt90) cc_final: 0.7319 (ttm-80) REVERT: B 488 ASN cc_start: 0.8033 (t0) cc_final: 0.7585 (t0) REVERT: B 494 LEU cc_start: 0.8686 (mt) cc_final: 0.8386 (mt) REVERT: B 556 ASN cc_start: 0.8180 (t0) cc_final: 0.7508 (t0) REVERT: B 566 GLU cc_start: 0.7650 (mm-30) cc_final: 0.6567 (tm-30) REVERT: B 577 PHE cc_start: 0.8285 (m-80) cc_final: 0.7975 (m-80) REVERT: B 580 GLU cc_start: 0.8465 (tp30) cc_final: 0.8050 (tp30) REVERT: A 29 LYS cc_start: 0.8012 (pttm) cc_final: 0.7459 (pttm) REVERT: A 46 ASP cc_start: 0.7276 (t70) cc_final: 0.6667 (t70) REVERT: A 47 HIS cc_start: 0.7909 (t70) cc_final: 0.6880 (t70) REVERT: A 51 LEU cc_start: 0.8842 (tp) cc_final: 0.8568 (tp) REVERT: A 55 PHE cc_start: 0.7854 (m-10) cc_final: 0.7617 (m-10) REVERT: A 61 VAL cc_start: 0.8185 (m) cc_final: 0.7924 (p) REVERT: A 71 GLN cc_start: 0.7110 (mm110) cc_final: 0.6874 (mm110) REVERT: A 74 TYR cc_start: 0.7991 (m-80) cc_final: 0.7032 (m-80) REVERT: A 80 LYS cc_start: 0.8409 (mttm) cc_final: 0.8033 (mttm) REVERT: A 85 VAL cc_start: 0.8105 (t) cc_final: 0.7834 (p) REVERT: A 98 ARG cc_start: 0.7512 (ttt90) cc_final: 0.7116 (tpp80) REVERT: A 112 TYR cc_start: 0.6566 (m-80) cc_final: 0.6328 (m-10) REVERT: A 119 LEU cc_start: 0.7657 (tp) cc_final: 0.7293 (tp) REVERT: A 143 ILE cc_start: 0.9072 (mt) cc_final: 0.8692 (mm) REVERT: A 163 GLN cc_start: 0.8436 (pt0) cc_final: 0.7913 (tt0) REVERT: A 209 LYS cc_start: 0.8257 (mttt) cc_final: 0.7704 (mtmt) REVERT: A 227 SER cc_start: 0.8152 (t) cc_final: 0.7946 (p) REVERT: A 230 ASP cc_start: 0.8322 (m-30) cc_final: 0.8084 (m-30) REVERT: A 233 HIS cc_start: 0.7482 (t-90) cc_final: 0.7097 (t-90) REVERT: A 252 ARG cc_start: 0.7476 (mtp85) cc_final: 0.6996 (mtp85) REVERT: A 257 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8010 (mm-30) REVERT: A 261 LYS cc_start: 0.7157 (ptmt) cc_final: 0.6764 (ptmt) REVERT: A 268 MET cc_start: 0.6140 (mtm) cc_final: 0.4878 (mtm) REVERT: A 277 MET cc_start: 0.6290 (mtt) cc_final: 0.5190 (mtt) REVERT: A 293 LYS cc_start: 0.7798 (mtpp) cc_final: 0.6909 (mtpp) REVERT: A 338 ASN cc_start: 0.7368 (p0) cc_final: 0.7043 (p0) REVERT: A 340 ILE cc_start: 0.7452 (mp) cc_final: 0.7245 (mp) REVERT: A 358 HIS cc_start: 0.8451 (m90) cc_final: 0.8183 (m-70) REVERT: A 360 LYS cc_start: 0.8694 (tttt) cc_final: 0.8381 (tttt) REVERT: A 368 ASP cc_start: 0.5128 (m-30) cc_final: 0.4672 (m-30) REVERT: A 396 LYS cc_start: 0.8423 (tppp) cc_final: 0.7899 (tppp) REVERT: A 404 PHE cc_start: 0.7590 (p90) cc_final: 0.6581 (p90) REVERT: A 421 GLU cc_start: 0.8665 (tt0) cc_final: 0.7665 (tt0) REVERT: A 429 ARG cc_start: 0.8088 (mtt180) cc_final: 0.7522 (mtt-85) REVERT: A 432 GLN cc_start: 0.8561 (tp40) cc_final: 0.7800 (tm-30) REVERT: A 433 HIS cc_start: 0.8266 (m90) cc_final: 0.7834 (m90) REVERT: A 451 ARG cc_start: 0.7116 (mtt90) cc_final: 0.6876 (ptp-170) REVERT: A 456 ILE cc_start: 0.8432 (mm) cc_final: 0.7830 (pt) REVERT: A 457 SER cc_start: 0.8063 (m) cc_final: 0.7656 (m) REVERT: A 476 ASN cc_start: 0.7733 (t0) cc_final: 0.7288 (t0) REVERT: A 496 GLU cc_start: 0.7537 (mp0) cc_final: 0.7201 (mp0) REVERT: A 551 GLU cc_start: 0.8670 (pt0) cc_final: 0.8237 (pm20) REVERT: A 559 HIS cc_start: 0.7599 (t70) cc_final: 0.7218 (t-170) REVERT: C 18 GLN cc_start: 0.8046 (tt0) cc_final: 0.6876 (tt0) REVERT: C 25 MET cc_start: 0.7886 (mmp) cc_final: 0.7414 (mmp) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.2624 time to fit residues: 128.6587 Evaluate side-chains 349 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 57 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 257 HIS ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 280 ASN A 468 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.125059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.099354 restraints weight = 16533.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.104919 restraints weight = 9320.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.108851 restraints weight = 5896.112| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9358 Z= 0.246 Angle : 0.650 9.281 12680 Z= 0.330 Chirality : 0.047 0.274 1417 Planarity : 0.005 0.073 1669 Dihedral : 7.098 76.096 1426 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 0.10 % Allowed : 1.08 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.24), residues: 1164 helix: -1.74 (0.72), residues: 48 sheet: -1.04 (0.72), residues: 62 loop : -1.84 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 477 HIS 0.007 0.001 HIS A 507 PHE 0.021 0.002 PHE B 73 TYR 0.033 0.002 TYR A 117 ARG 0.013 0.001 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 0.990 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6725 (pp30) cc_final: 0.5500 (mm-40) REVERT: B 31 MET cc_start: 0.7545 (mtp) cc_final: 0.6465 (ptp) REVERT: B 44 ASP cc_start: 0.7502 (t0) cc_final: 0.6749 (t0) REVERT: B 46 LEU cc_start: 0.8670 (mt) cc_final: 0.8277 (mt) REVERT: B 47 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7421 (ttp80) REVERT: B 59 ASN cc_start: 0.7308 (m-40) cc_final: 0.6785 (m-40) REVERT: B 61 GLU cc_start: 0.7012 (tm-30) cc_final: 0.5212 (tm-30) REVERT: B 75 GLN cc_start: 0.7911 (pt0) cc_final: 0.7632 (pt0) REVERT: B 78 GLN cc_start: 0.7827 (pm20) cc_final: 0.7535 (pm20) REVERT: B 79 GLU cc_start: 0.6953 (tt0) cc_final: 0.6433 (tt0) REVERT: B 81 GLN cc_start: 0.6640 (mt0) cc_final: 0.6144 (mt0) REVERT: B 100 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7670 (mmm-85) REVERT: B 105 THR cc_start: 0.8079 (p) cc_final: 0.7644 (t) REVERT: B 106 GLN cc_start: 0.7854 (mt0) cc_final: 0.7439 (mp10) REVERT: B 112 TYR cc_start: 0.7451 (m-80) cc_final: 0.6929 (m-80) REVERT: B 143 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7457 (mtt180) REVERT: B 169 TRP cc_start: 0.8492 (m100) cc_final: 0.7515 (m100) REVERT: B 173 PHE cc_start: 0.7187 (m-10) cc_final: 0.6898 (m-10) REVERT: B 182 THR cc_start: 0.7707 (p) cc_final: 0.7299 (p) REVERT: B 184 ILE cc_start: 0.8770 (mm) cc_final: 0.8509 (mm) REVERT: B 185 ASP cc_start: 0.7181 (t0) cc_final: 0.6745 (t0) REVERT: B 208 SER cc_start: 0.7833 (m) cc_final: 0.7498 (t) REVERT: B 211 ASP cc_start: 0.7919 (m-30) cc_final: 0.7381 (m-30) REVERT: B 213 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7312 (tm-30) REVERT: B 217 ARG cc_start: 0.7035 (mtp-110) cc_final: 0.6389 (mtt-85) REVERT: B 248 LYS cc_start: 0.8644 (mmtt) cc_final: 0.7975 (mmtt) REVERT: B 251 ASP cc_start: 0.7608 (p0) cc_final: 0.7350 (p0) REVERT: B 267 HIS cc_start: 0.7534 (m170) cc_final: 0.7178 (m170) REVERT: B 274 TYR cc_start: 0.6772 (t80) cc_final: 0.6286 (t80) REVERT: B 275 ASN cc_start: 0.8034 (t0) cc_final: 0.7746 (t0) REVERT: B 282 MET cc_start: 0.8420 (mtp) cc_final: 0.7893 (mtp) REVERT: B 303 TYR cc_start: 0.8182 (m-80) cc_final: 0.7669 (m-80) REVERT: B 311 CYS cc_start: 0.4285 (p) cc_final: 0.3506 (m) REVERT: B 313 LEU cc_start: 0.8293 (mt) cc_final: 0.7982 (pt) REVERT: B 332 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7048 (mt-10) REVERT: B 364 PHE cc_start: 0.8666 (m-80) cc_final: 0.7956 (m-80) REVERT: B 398 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7925 (mm-40) REVERT: B 407 THR cc_start: 0.7939 (p) cc_final: 0.7470 (m) REVERT: B 411 TYR cc_start: 0.7268 (t80) cc_final: 0.6508 (t80) REVERT: B 426 GLN cc_start: 0.7952 (pt0) cc_final: 0.7172 (pp30) REVERT: B 436 LEU cc_start: 0.8040 (mt) cc_final: 0.7704 (mp) REVERT: B 444 THR cc_start: 0.7477 (m) cc_final: 0.7021 (m) REVERT: B 451 SER cc_start: 0.8136 (p) cc_final: 0.7699 (m) REVERT: B 452 TRP cc_start: 0.7954 (p90) cc_final: 0.7591 (p90) REVERT: B 481 PRO cc_start: 0.8146 (Cg_endo) cc_final: 0.7670 (Cg_exo) REVERT: B 483 ASP cc_start: 0.8460 (m-30) cc_final: 0.7715 (t0) REVERT: B 486 PHE cc_start: 0.8274 (m-10) cc_final: 0.7936 (m-10) REVERT: B 487 ARG cc_start: 0.7917 (mmt90) cc_final: 0.7324 (ttm-80) REVERT: B 488 ASN cc_start: 0.7970 (t0) cc_final: 0.7714 (t0) REVERT: B 491 GLN cc_start: 0.6220 (mt0) cc_final: 0.5750 (mt0) REVERT: B 493 LEU cc_start: 0.7985 (tp) cc_final: 0.7662 (tp) REVERT: B 494 LEU cc_start: 0.8687 (mt) cc_final: 0.8440 (mt) REVERT: B 556 ASN cc_start: 0.8252 (t0) cc_final: 0.7603 (t0) REVERT: B 566 GLU cc_start: 0.7744 (mm-30) cc_final: 0.6505 (tm-30) REVERT: B 577 PHE cc_start: 0.8310 (m-80) cc_final: 0.7975 (m-80) REVERT: B 580 GLU cc_start: 0.8465 (tp30) cc_final: 0.8057 (tp30) REVERT: A 28 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7392 (ptpp) REVERT: A 36 ASN cc_start: 0.8513 (p0) cc_final: 0.8124 (p0) REVERT: A 46 ASP cc_start: 0.7271 (t70) cc_final: 0.6658 (t70) REVERT: A 47 HIS cc_start: 0.8030 (t70) cc_final: 0.7026 (t70) REVERT: A 51 LEU cc_start: 0.8934 (tp) cc_final: 0.8606 (tp) REVERT: A 74 TYR cc_start: 0.8073 (m-80) cc_final: 0.7077 (m-80) REVERT: A 77 SER cc_start: 0.8060 (m) cc_final: 0.6967 (p) REVERT: A 80 LYS cc_start: 0.8392 (mttm) cc_final: 0.8070 (mttm) REVERT: A 83 GLN cc_start: 0.7802 (mm110) cc_final: 0.7592 (mm110) REVERT: A 85 VAL cc_start: 0.8141 (t) cc_final: 0.7860 (p) REVERT: A 102 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7259 (mt-10) REVERT: A 112 TYR cc_start: 0.7196 (m-10) cc_final: 0.6909 (m-80) REVERT: A 119 LEU cc_start: 0.7826 (tp) cc_final: 0.7559 (tp) REVERT: A 143 ILE cc_start: 0.9089 (mt) cc_final: 0.8678 (mm) REVERT: A 163 GLN cc_start: 0.8330 (pt0) cc_final: 0.7760 (pp30) REVERT: A 167 ILE cc_start: 0.8403 (mp) cc_final: 0.8094 (mp) REVERT: A 176 MET cc_start: 0.8549 (ptp) cc_final: 0.8156 (ptt) REVERT: A 209 LYS cc_start: 0.8300 (mttt) cc_final: 0.7777 (mtmm) REVERT: A 212 LYS cc_start: 0.7490 (ttmm) cc_final: 0.7288 (ttmm) REVERT: A 227 SER cc_start: 0.8342 (t) cc_final: 0.7957 (p) REVERT: A 230 ASP cc_start: 0.8376 (m-30) cc_final: 0.7889 (m-30) REVERT: A 257 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 261 LYS cc_start: 0.7291 (ptmt) cc_final: 0.6848 (ptmt) REVERT: A 268 MET cc_start: 0.6234 (mtm) cc_final: 0.4987 (mtm) REVERT: A 277 MET cc_start: 0.6432 (mtt) cc_final: 0.5243 (mtt) REVERT: A 293 LYS cc_start: 0.7888 (mtpp) cc_final: 0.7345 (tppt) REVERT: A 338 ASN cc_start: 0.7414 (p0) cc_final: 0.7213 (p0) REVERT: A 358 HIS cc_start: 0.8523 (m90) cc_final: 0.8317 (m-70) REVERT: A 360 LYS cc_start: 0.8719 (tttt) cc_final: 0.8410 (tttt) REVERT: A 368 ASP cc_start: 0.5178 (m-30) cc_final: 0.4963 (m-30) REVERT: A 396 LYS cc_start: 0.8498 (tppp) cc_final: 0.7935 (tppp) REVERT: A 404 PHE cc_start: 0.7649 (p90) cc_final: 0.6468 (p90) REVERT: A 416 ASP cc_start: 0.7203 (p0) cc_final: 0.6902 (p0) REVERT: A 417 LEU cc_start: 0.7613 (mt) cc_final: 0.7393 (mp) REVERT: A 421 GLU cc_start: 0.8697 (tt0) cc_final: 0.7639 (tt0) REVERT: A 429 ARG cc_start: 0.8201 (mtt180) cc_final: 0.7630 (mtt-85) REVERT: A 432 GLN cc_start: 0.8467 (tp40) cc_final: 0.8005 (tp-100) REVERT: A 433 HIS cc_start: 0.8234 (m90) cc_final: 0.7922 (m-70) REVERT: A 436 PHE cc_start: 0.7968 (m-80) cc_final: 0.7595 (m-80) REVERT: A 445 ILE cc_start: 0.7918 (pt) cc_final: 0.7626 (pt) REVERT: A 454 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8129 (mmtt) REVERT: A 456 ILE cc_start: 0.8585 (mm) cc_final: 0.8016 (pt) REVERT: A 457 SER cc_start: 0.8118 (m) cc_final: 0.7755 (m) REVERT: A 476 ASN cc_start: 0.7770 (t0) cc_final: 0.7354 (t0) REVERT: A 489 LYS cc_start: 0.7781 (mmmm) cc_final: 0.7444 (mtpp) REVERT: A 496 GLU cc_start: 0.7523 (mp0) cc_final: 0.7241 (mp0) REVERT: A 551 GLU cc_start: 0.8667 (pt0) cc_final: 0.8246 (pm20) REVERT: A 559 HIS cc_start: 0.7659 (t70) cc_final: 0.7242 (t-170) REVERT: C 18 GLN cc_start: 0.7996 (tt0) cc_final: 0.7428 (tt0) REVERT: C 25 MET cc_start: 0.7886 (mmp) cc_final: 0.7428 (mmp) REVERT: C 31 ARG cc_start: 0.6759 (ttp-170) cc_final: 0.6292 (ttm170) outliers start: 1 outliers final: 0 residues processed: 385 average time/residue: 0.2490 time to fit residues: 125.1222 Evaluate side-chains 355 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 103 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 280 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100406 restraints weight = 16657.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105844 restraints weight = 9457.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.109741 restraints weight = 5977.948| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9358 Z= 0.226 Angle : 0.661 10.871 12680 Z= 0.335 Chirality : 0.048 0.267 1417 Planarity : 0.005 0.085 1669 Dihedral : 7.168 76.491 1426 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 0.10 % Allowed : 0.98 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.24), residues: 1164 helix: -1.66 (0.75), residues: 48 sheet: -1.07 (0.68), residues: 64 loop : -1.82 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 477 HIS 0.014 0.001 HIS A 183 PHE 0.019 0.001 PHE B 73 TYR 0.017 0.002 TYR A 117 ARG 0.010 0.001 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 0.945 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.7501 (mtp) cc_final: 0.6485 (ptp) REVERT: B 44 ASP cc_start: 0.7662 (t0) cc_final: 0.6776 (t0) REVERT: B 45 MET cc_start: 0.8329 (tmm) cc_final: 0.8120 (tmm) REVERT: B 46 LEU cc_start: 0.8626 (mt) cc_final: 0.8229 (mt) REVERT: B 47 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7344 (ttp80) REVERT: B 55 VAL cc_start: 0.7757 (t) cc_final: 0.7222 (p) REVERT: B 59 ASN cc_start: 0.7345 (m-40) cc_final: 0.6924 (m-40) REVERT: B 61 GLU cc_start: 0.6986 (tm-30) cc_final: 0.3777 (tm-30) REVERT: B 65 LEU cc_start: 0.8219 (mt) cc_final: 0.7796 (mt) REVERT: B 75 GLN cc_start: 0.7925 (pt0) cc_final: 0.7120 (pp30) REVERT: B 81 GLN cc_start: 0.6663 (mt0) cc_final: 0.6223 (mt0) REVERT: B 100 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7736 (mmm-85) REVERT: B 103 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.6804 (mtp85) REVERT: B 105 THR cc_start: 0.7965 (p) cc_final: 0.7603 (t) REVERT: B 106 GLN cc_start: 0.7818 (mt0) cc_final: 0.7392 (mp-120) REVERT: B 109 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7626 (mm-30) REVERT: B 143 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7470 (mtt180) REVERT: B 182 THR cc_start: 0.7696 (p) cc_final: 0.7313 (p) REVERT: B 185 ASP cc_start: 0.7194 (t0) cc_final: 0.6679 (t0) REVERT: B 208 SER cc_start: 0.7913 (m) cc_final: 0.7631 (t) REVERT: B 211 ASP cc_start: 0.7921 (m-30) cc_final: 0.7415 (m-30) REVERT: B 217 ARG cc_start: 0.7145 (mtp-110) cc_final: 0.6809 (mtp-110) REVERT: B 226 ARG cc_start: 0.7583 (tpp80) cc_final: 0.7269 (tpp80) REVERT: B 237 HIS cc_start: 0.7516 (t-90) cc_final: 0.7301 (t-90) REVERT: B 248 LYS cc_start: 0.8636 (mmtt) cc_final: 0.7996 (mmtt) REVERT: B 251 ASP cc_start: 0.7552 (p0) cc_final: 0.7303 (p0) REVERT: B 267 HIS cc_start: 0.7553 (m170) cc_final: 0.7264 (m170) REVERT: B 274 TYR cc_start: 0.6825 (t80) cc_final: 0.6294 (t80) REVERT: B 275 ASN cc_start: 0.8095 (t0) cc_final: 0.7782 (t0) REVERT: B 282 MET cc_start: 0.8338 (mtp) cc_final: 0.7834 (mtp) REVERT: B 303 TYR cc_start: 0.8192 (m-80) cc_final: 0.7661 (m-80) REVERT: B 311 CYS cc_start: 0.4173 (p) cc_final: 0.3395 (m) REVERT: B 313 LEU cc_start: 0.8382 (mt) cc_final: 0.8030 (pt) REVERT: B 319 ASN cc_start: 0.7627 (m-40) cc_final: 0.7418 (m-40) REVERT: B 323 THR cc_start: 0.7420 (t) cc_final: 0.6958 (p) REVERT: B 332 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7073 (mt-10) REVERT: B 351 ARG cc_start: 0.7902 (mmp80) cc_final: 0.7685 (tpp-160) REVERT: B 364 PHE cc_start: 0.8687 (m-80) cc_final: 0.8047 (m-80) REVERT: B 398 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7836 (mp10) REVERT: B 407 THR cc_start: 0.7941 (p) cc_final: 0.7478 (m) REVERT: B 411 TYR cc_start: 0.7263 (t80) cc_final: 0.5793 (t80) REVERT: B 426 GLN cc_start: 0.8030 (pt0) cc_final: 0.7248 (pp30) REVERT: B 436 LEU cc_start: 0.8044 (mt) cc_final: 0.7659 (mp) REVERT: B 444 THR cc_start: 0.7461 (m) cc_final: 0.6716 (m) REVERT: B 446 GLN cc_start: 0.6811 (mt0) cc_final: 0.6253 (mt0) REVERT: B 451 SER cc_start: 0.8245 (p) cc_final: 0.7743 (m) REVERT: B 452 TRP cc_start: 0.7936 (p90) cc_final: 0.7553 (p90) REVERT: B 481 PRO cc_start: 0.8121 (Cg_endo) cc_final: 0.7730 (Cg_exo) REVERT: B 484 GLN cc_start: 0.8791 (mt0) cc_final: 0.8303 (mp10) REVERT: B 486 PHE cc_start: 0.8363 (m-10) cc_final: 0.7602 (m-10) REVERT: B 493 LEU cc_start: 0.8091 (tp) cc_final: 0.7735 (tp) REVERT: B 494 LEU cc_start: 0.8721 (mt) cc_final: 0.8466 (mt) REVERT: B 513 GLN cc_start: 0.8164 (pm20) cc_final: 0.7841 (mp10) REVERT: B 556 ASN cc_start: 0.8293 (t0) cc_final: 0.7643 (t0) REVERT: B 577 PHE cc_start: 0.8331 (m-80) cc_final: 0.7888 (m-80) REVERT: B 580 GLU cc_start: 0.8407 (tp30) cc_final: 0.8061 (tp30) REVERT: A 29 LYS cc_start: 0.8136 (pttm) cc_final: 0.7555 (pttm) REVERT: A 36 ASN cc_start: 0.8504 (p0) cc_final: 0.8082 (p0) REVERT: A 45 GLU cc_start: 0.8344 (mp0) cc_final: 0.7988 (mp0) REVERT: A 46 ASP cc_start: 0.7202 (t70) cc_final: 0.6717 (t70) REVERT: A 47 HIS cc_start: 0.7937 (t70) cc_final: 0.6864 (t70) REVERT: A 51 LEU cc_start: 0.8934 (tp) cc_final: 0.8610 (tp) REVERT: A 55 PHE cc_start: 0.7921 (m-10) cc_final: 0.7617 (m-10) REVERT: A 74 TYR cc_start: 0.8075 (m-80) cc_final: 0.7066 (m-80) REVERT: A 76 LEU cc_start: 0.8403 (mt) cc_final: 0.8119 (mt) REVERT: A 77 SER cc_start: 0.8076 (m) cc_final: 0.6977 (p) REVERT: A 80 LYS cc_start: 0.8422 (mttm) cc_final: 0.8040 (mttm) REVERT: A 85 VAL cc_start: 0.8162 (t) cc_final: 0.7917 (p) REVERT: A 98 ARG cc_start: 0.7477 (tpp80) cc_final: 0.7120 (tpp80) REVERT: A 112 TYR cc_start: 0.7247 (m-10) cc_final: 0.6916 (m-80) REVERT: A 114 GLU cc_start: 0.7376 (tt0) cc_final: 0.6521 (tt0) REVERT: A 119 LEU cc_start: 0.7611 (tp) cc_final: 0.7181 (tp) REVERT: A 143 ILE cc_start: 0.9129 (mt) cc_final: 0.8718 (mm) REVERT: A 163 GLN cc_start: 0.8198 (pt0) cc_final: 0.7869 (pt0) REVERT: A 176 MET cc_start: 0.8548 (ptp) cc_final: 0.7979 (ptp) REVERT: A 196 ASN cc_start: 0.8933 (m-40) cc_final: 0.8578 (m110) REVERT: A 209 LYS cc_start: 0.8297 (mttt) cc_final: 0.7748 (mtmm) REVERT: A 230 ASP cc_start: 0.8363 (m-30) cc_final: 0.6740 (t0) REVERT: A 236 CYS cc_start: 0.5609 (m) cc_final: 0.5235 (t) REVERT: A 257 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8014 (mm-30) REVERT: A 261 LYS cc_start: 0.7220 (ptmt) cc_final: 0.6824 (ptmt) REVERT: A 268 MET cc_start: 0.6305 (mtm) cc_final: 0.5007 (mtm) REVERT: A 277 MET cc_start: 0.6422 (mtt) cc_final: 0.5207 (mtt) REVERT: A 293 LYS cc_start: 0.7901 (mtpp) cc_final: 0.7002 (mtpp) REVERT: A 298 ASN cc_start: 0.8712 (p0) cc_final: 0.8369 (p0) REVERT: A 340 ILE cc_start: 0.7351 (mp) cc_final: 0.7104 (mp) REVERT: A 360 LYS cc_start: 0.8679 (tttt) cc_final: 0.8374 (tttt) REVERT: A 396 LYS cc_start: 0.8532 (tppp) cc_final: 0.7909 (tppp) REVERT: A 404 PHE cc_start: 0.7678 (p90) cc_final: 0.6813 (p90) REVERT: A 421 GLU cc_start: 0.8595 (tt0) cc_final: 0.8022 (tt0) REVERT: A 429 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7572 (mtt-85) REVERT: A 431 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7719 (mtmm) REVERT: A 432 GLN cc_start: 0.8556 (tp40) cc_final: 0.8101 (tp-100) REVERT: A 454 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8159 (mmtt) REVERT: A 456 ILE cc_start: 0.8600 (mm) cc_final: 0.8091 (pt) REVERT: A 457 SER cc_start: 0.8105 (m) cc_final: 0.7399 (t) REVERT: A 476 ASN cc_start: 0.7780 (t0) cc_final: 0.7343 (t0) REVERT: A 487 LYS cc_start: 0.7903 (ptpp) cc_final: 0.7687 (ptpp) REVERT: A 496 GLU cc_start: 0.7567 (mp0) cc_final: 0.7203 (mp0) REVERT: A 551 GLU cc_start: 0.8650 (pt0) cc_final: 0.8221 (pm20) REVERT: A 559 HIS cc_start: 0.7653 (t70) cc_final: 0.7246 (t-170) REVERT: A 569 ILE cc_start: 0.8415 (tp) cc_final: 0.8087 (tp) REVERT: C 18 GLN cc_start: 0.8009 (tt0) cc_final: 0.7588 (tt0) REVERT: C 25 MET cc_start: 0.7748 (mmp) cc_final: 0.7434 (mmp) REVERT: C 31 ARG cc_start: 0.6903 (ttp-170) cc_final: 0.6429 (ttm170) outliers start: 1 outliers final: 0 residues processed: 374 average time/residue: 0.2489 time to fit residues: 121.2095 Evaluate side-chains 347 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 280 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 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 = 0.3747 r_free = 0.3747 target = 0.125059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099540 restraints weight = 16875.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.104870 restraints weight = 9543.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.108726 restraints weight = 6061.329| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9358 Z= 0.225 Angle : 0.667 9.588 12680 Z= 0.339 Chirality : 0.048 0.266 1417 Planarity : 0.005 0.074 1669 Dihedral : 7.162 75.721 1426 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 0.10 % Allowed : 0.59 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.24), residues: 1164 helix: -1.88 (0.69), residues: 54 sheet: -1.19 (0.64), residues: 72 loop : -1.76 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 164 HIS 0.013 0.001 HIS A 183 PHE 0.018 0.002 PHE B 73 TYR 0.020 0.002 TYR A 117 ARG 0.010 0.001 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 0.973 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: 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: symmetry clash REVERT: B 31 MET cc_start: 0.7521 (mtp) cc_final: 0.6656 (ptp) REVERT: B 44 ASP cc_start: 0.7522 (t0) cc_final: 0.6781 (t0) REVERT: B 45 MET cc_start: 0.8372 (tmm) cc_final: 0.8149 (tmm) REVERT: B 46 LEU cc_start: 0.8617 (mt) cc_final: 0.8201 (mt) REVERT: B 47 ARG cc_start: 0.7867 (ttp80) cc_final: 0.7316 (ttp80) REVERT: B 55 VAL cc_start: 0.7782 (t) cc_final: 0.7281 (p) REVERT: B 59 ASN cc_start: 0.7500 (m-40) cc_final: 0.6965 (m-40) REVERT: B 61 GLU cc_start: 0.7025 (tm-30) cc_final: 0.3923 (tm-30) REVERT: B 75 GLN cc_start: 0.7995 (pt0) cc_final: 0.7194 (pp30) REVERT: B 81 GLN cc_start: 0.6661 (mt0) cc_final: 0.6220 (mt0) REVERT: B 100 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7829 (mmm-85) REVERT: B 103 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.7069 (ttm110) REVERT: B 106 GLN cc_start: 0.7792 (mt0) cc_final: 0.7458 (mp10) REVERT: B 109 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7599 (mm-30) REVERT: B 173 PHE cc_start: 0.7221 (m-10) cc_final: 0.6974 (m-10) REVERT: B 185 ASP cc_start: 0.7272 (t0) cc_final: 0.7056 (t0) REVERT: B 193 HIS cc_start: 0.7740 (m90) cc_final: 0.7271 (m90) REVERT: B 208 SER cc_start: 0.7906 (m) cc_final: 0.7670 (t) REVERT: B 211 ASP cc_start: 0.7948 (m-30) cc_final: 0.7630 (m-30) REVERT: B 217 ARG cc_start: 0.7204 (mtp-110) cc_final: 0.6425 (mtt-85) REVERT: B 248 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8025 (mmtt) REVERT: B 251 ASP cc_start: 0.7577 (p0) cc_final: 0.7353 (p0) REVERT: B 265 GLU cc_start: 0.7007 (pm20) cc_final: 0.6646 (pm20) REVERT: B 266 LEU cc_start: 0.8207 (tp) cc_final: 0.7718 (tp) REVERT: B 267 HIS cc_start: 0.7611 (m170) cc_final: 0.6694 (m170) REVERT: B 274 TYR cc_start: 0.7042 (t80) cc_final: 0.6266 (t80) REVERT: B 282 MET cc_start: 0.8414 (mtp) cc_final: 0.7893 (mtp) REVERT: B 303 TYR cc_start: 0.8099 (m-80) cc_final: 0.7600 (m-80) REVERT: B 313 LEU cc_start: 0.8353 (mt) cc_final: 0.8017 (pt) REVERT: B 319 ASN cc_start: 0.7629 (m-40) cc_final: 0.7386 (m-40) REVERT: B 323 THR cc_start: 0.7381 (t) cc_final: 0.6984 (p) REVERT: B 332 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7085 (mt-10) REVERT: B 364 PHE cc_start: 0.8719 (m-80) cc_final: 0.8083 (m-80) REVERT: B 398 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7833 (mp10) REVERT: B 405 GLU cc_start: 0.6540 (tp30) cc_final: 0.6320 (tp30) REVERT: B 407 THR cc_start: 0.7983 (p) cc_final: 0.7532 (m) REVERT: B 409 TYR cc_start: 0.7134 (p90) cc_final: 0.6914 (p90) REVERT: B 411 TYR cc_start: 0.7244 (t80) cc_final: 0.5841 (t80) REVERT: B 426 GLN cc_start: 0.8007 (pt0) cc_final: 0.7318 (pp30) REVERT: B 436 LEU cc_start: 0.8001 (mt) cc_final: 0.7747 (mt) REVERT: B 444 THR cc_start: 0.7476 (m) cc_final: 0.5668 (m) REVERT: B 446 GLN cc_start: 0.6789 (mt0) cc_final: 0.6316 (mt0) REVERT: B 451 SER cc_start: 0.8241 (p) cc_final: 0.7754 (m) REVERT: B 452 TRP cc_start: 0.7963 (p90) cc_final: 0.7559 (p90) REVERT: B 467 LEU cc_start: 0.7211 (tp) cc_final: 0.6349 (pp) REVERT: B 481 PRO cc_start: 0.8099 (Cg_endo) cc_final: 0.7709 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8454 (m100) cc_final: 0.8109 (m100) REVERT: B 484 GLN cc_start: 0.8719 (mt0) cc_final: 0.8301 (mp10) REVERT: B 488 ASN cc_start: 0.8429 (t0) cc_final: 0.8012 (t0) REVERT: B 493 LEU cc_start: 0.8177 (tp) cc_final: 0.7427 (tp) REVERT: B 513 GLN cc_start: 0.8197 (pm20) cc_final: 0.7987 (mp10) REVERT: B 556 ASN cc_start: 0.8295 (t0) cc_final: 0.7802 (t0) REVERT: B 577 PHE cc_start: 0.8366 (m-80) cc_final: 0.7924 (m-80) REVERT: B 580 GLU cc_start: 0.8406 (tp30) cc_final: 0.7996 (tp30) REVERT: A 28 LYS cc_start: 0.7727 (mtmm) cc_final: 0.7183 (ptpp) REVERT: A 45 GLU cc_start: 0.8419 (mp0) cc_final: 0.8084 (mp0) REVERT: A 46 ASP cc_start: 0.7215 (t70) cc_final: 0.6742 (t70) REVERT: A 47 HIS cc_start: 0.7916 (t70) cc_final: 0.6866 (t70) REVERT: A 51 LEU cc_start: 0.8921 (tp) cc_final: 0.8533 (tp) REVERT: A 55 PHE cc_start: 0.7907 (m-10) cc_final: 0.7669 (m-10) REVERT: A 74 TYR cc_start: 0.8092 (m-80) cc_final: 0.7066 (m-80) REVERT: A 76 LEU cc_start: 0.8391 (mt) cc_final: 0.8151 (mt) REVERT: A 77 SER cc_start: 0.8035 (m) cc_final: 0.6961 (p) REVERT: A 80 LYS cc_start: 0.8393 (mttm) cc_final: 0.8032 (mttm) REVERT: A 85 VAL cc_start: 0.8173 (t) cc_final: 0.7907 (p) REVERT: A 98 ARG cc_start: 0.7495 (tpp80) cc_final: 0.7120 (tpp80) REVERT: A 112 TYR cc_start: 0.7260 (m-10) cc_final: 0.6785 (m-10) REVERT: A 114 GLU cc_start: 0.7374 (tt0) cc_final: 0.6642 (tt0) REVERT: A 119 LEU cc_start: 0.7823 (tp) cc_final: 0.7473 (tp) REVERT: A 143 ILE cc_start: 0.9139 (mt) cc_final: 0.8750 (mm) REVERT: A 163 GLN cc_start: 0.8179 (pt0) cc_final: 0.7819 (pt0) REVERT: A 176 MET cc_start: 0.8547 (ptp) cc_final: 0.7991 (ptp) REVERT: A 196 ASN cc_start: 0.8926 (m-40) cc_final: 0.8572 (m110) REVERT: A 209 LYS cc_start: 0.8279 (mttt) cc_final: 0.7742 (mtmt) REVERT: A 212 LYS cc_start: 0.7299 (ttmm) cc_final: 0.6808 (ttmm) REVERT: A 254 PHE cc_start: 0.7297 (m-10) cc_final: 0.7047 (m-10) REVERT: A 257 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7970 (mm-30) REVERT: A 261 LYS cc_start: 0.7301 (ptmt) cc_final: 0.6810 (ptmt) REVERT: A 268 MET cc_start: 0.6296 (mtm) cc_final: 0.5007 (mtm) REVERT: A 277 MET cc_start: 0.6433 (mtt) cc_final: 0.5264 (mtt) REVERT: A 293 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7151 (mtpp) REVERT: A 298 ASN cc_start: 0.8750 (p0) cc_final: 0.8377 (p0) REVERT: A 338 ASN cc_start: 0.7591 (p0) cc_final: 0.7234 (p0) REVERT: A 340 ILE cc_start: 0.7220 (mp) cc_final: 0.6959 (mp) REVERT: A 360 LYS cc_start: 0.8664 (tttt) cc_final: 0.8398 (tttt) REVERT: A 377 ARG cc_start: 0.7777 (ptm-80) cc_final: 0.7255 (ptm-80) REVERT: A 396 LYS cc_start: 0.8536 (tppp) cc_final: 0.7882 (tppp) REVERT: A 404 PHE cc_start: 0.7550 (p90) cc_final: 0.6785 (p90) REVERT: A 417 LEU cc_start: 0.7656 (mt) cc_final: 0.7412 (mp) REVERT: A 421 GLU cc_start: 0.8602 (tt0) cc_final: 0.7718 (tt0) REVERT: A 429 ARG cc_start: 0.8216 (mtt180) cc_final: 0.7471 (mtt-85) REVERT: A 431 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7825 (mtpt) REVERT: A 432 GLN cc_start: 0.8601 (tp40) cc_final: 0.7924 (tm-30) REVERT: A 433 HIS cc_start: 0.8181 (m90) cc_final: 0.7845 (m90) REVERT: A 445 ILE cc_start: 0.8003 (pt) cc_final: 0.7716 (pt) REVERT: A 454 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8179 (mmtt) REVERT: A 456 ILE cc_start: 0.8614 (mm) cc_final: 0.8189 (pt) REVERT: A 457 SER cc_start: 0.8041 (m) cc_final: 0.7295 (t) REVERT: A 476 ASN cc_start: 0.7808 (t0) cc_final: 0.7357 (t0) REVERT: A 487 LYS cc_start: 0.7872 (ptpp) cc_final: 0.7643 (ptpp) REVERT: A 489 LYS cc_start: 0.7506 (tptm) cc_final: 0.7053 (mtpp) REVERT: A 496 GLU cc_start: 0.7581 (mp0) cc_final: 0.7232 (mp0) REVERT: A 551 GLU cc_start: 0.8624 (pt0) cc_final: 0.8200 (pm20) REVERT: A 559 HIS cc_start: 0.7684 (t70) cc_final: 0.7275 (t-170) REVERT: C 18 GLN cc_start: 0.8050 (tt0) cc_final: 0.7562 (tt0) REVERT: C 25 MET cc_start: 0.7875 (mmp) cc_final: 0.7421 (mmp) REVERT: C 31 ARG cc_start: 0.7000 (ttp-170) cc_final: 0.6441 (ttm170) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.2719 time to fit residues: 130.7647 Evaluate side-chains 343 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 83 GLN A 280 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.122123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.096954 restraints weight = 16367.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102269 restraints weight = 9220.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.106022 restraints weight = 5836.007| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9358 Z= 0.258 Angle : 0.707 10.991 12680 Z= 0.360 Chirality : 0.049 0.267 1417 Planarity : 0.005 0.068 1669 Dihedral : 7.348 75.540 1426 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.10 % Allowed : 0.69 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.24), residues: 1164 helix: -2.47 (0.59), residues: 60 sheet: -1.42 (0.68), residues: 64 loop : -1.79 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 410 HIS 0.008 0.002 HIS A 183 PHE 0.018 0.002 PHE B 486 TYR 0.021 0.002 TYR A 117 ARG 0.009 0.001 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 1.002 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.7582 (mtp) cc_final: 0.6728 (ptp) REVERT: B 44 ASP cc_start: 0.7693 (t0) cc_final: 0.6866 (t0) REVERT: B 47 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7421 (ttp80) REVERT: B 55 VAL cc_start: 0.7818 (t) cc_final: 0.7263 (p) REVERT: B 59 ASN cc_start: 0.7481 (m-40) cc_final: 0.7009 (m-40) REVERT: B 61 GLU cc_start: 0.6981 (tm-30) cc_final: 0.4092 (tm-30) REVERT: B 65 LEU cc_start: 0.8253 (mt) cc_final: 0.7787 (mt) REVERT: B 75 GLN cc_start: 0.8045 (pt0) cc_final: 0.7302 (pp30) REVERT: B 78 GLN cc_start: 0.7741 (pm20) cc_final: 0.7363 (pm20) REVERT: B 100 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7736 (mmm-85) REVERT: B 103 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7035 (ttm110) REVERT: B 106 GLN cc_start: 0.7876 (mt0) cc_final: 0.7513 (mp-120) REVERT: B 185 ASP cc_start: 0.7239 (t0) cc_final: 0.6955 (t0) REVERT: B 193 HIS cc_start: 0.7752 (m90) cc_final: 0.7315 (m90) REVERT: B 208 SER cc_start: 0.7929 (m) cc_final: 0.7663 (t) REVERT: B 237 HIS cc_start: 0.7510 (t-90) cc_final: 0.7302 (t-90) REVERT: B 248 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8017 (mmtt) REVERT: B 258 PHE cc_start: 0.7488 (m-80) cc_final: 0.6996 (m-80) REVERT: B 265 GLU cc_start: 0.7241 (pm20) cc_final: 0.6546 (pm20) REVERT: B 266 LEU cc_start: 0.8269 (tp) cc_final: 0.7530 (tp) REVERT: B 267 HIS cc_start: 0.7635 (m170) cc_final: 0.6756 (m170) REVERT: B 271 LEU cc_start: 0.8575 (pt) cc_final: 0.8303 (pp) REVERT: B 274 TYR cc_start: 0.6796 (t80) cc_final: 0.6200 (t80) REVERT: B 282 MET cc_start: 0.8390 (mtp) cc_final: 0.7944 (mtp) REVERT: B 303 TYR cc_start: 0.8120 (m-80) cc_final: 0.7573 (m-80) REVERT: B 313 LEU cc_start: 0.8306 (mt) cc_final: 0.7982 (pt) REVERT: B 319 ASN cc_start: 0.7645 (m-40) cc_final: 0.7387 (m-40) REVERT: B 323 THR cc_start: 0.7491 (t) cc_final: 0.7108 (p) REVERT: B 332 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7134 (mt-10) REVERT: B 364 PHE cc_start: 0.8748 (m-80) cc_final: 0.8269 (m-80) REVERT: B 398 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7714 (mp10) REVERT: B 407 THR cc_start: 0.7941 (p) cc_final: 0.7489 (m) REVERT: B 411 TYR cc_start: 0.7269 (t80) cc_final: 0.6541 (t80) REVERT: B 426 GLN cc_start: 0.8021 (pt0) cc_final: 0.7419 (pp30) REVERT: B 429 GLN cc_start: 0.6601 (mt0) cc_final: 0.6111 (mm-40) REVERT: B 430 VAL cc_start: 0.7779 (p) cc_final: 0.7456 (t) REVERT: B 436 LEU cc_start: 0.7925 (mt) cc_final: 0.7720 (mt) REVERT: B 444 THR cc_start: 0.7530 (m) cc_final: 0.6391 (m) REVERT: B 452 TRP cc_start: 0.7997 (p90) cc_final: 0.7321 (p90) REVERT: B 467 LEU cc_start: 0.7303 (tp) cc_final: 0.6477 (pp) REVERT: B 481 PRO cc_start: 0.8034 (Cg_endo) cc_final: 0.7433 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8488 (m100) cc_final: 0.7998 (m100) REVERT: B 484 GLN cc_start: 0.8803 (mt0) cc_final: 0.8330 (mp10) REVERT: B 486 PHE cc_start: 0.8375 (m-80) cc_final: 0.7197 (m-80) REVERT: B 493 LEU cc_start: 0.8393 (tp) cc_final: 0.7623 (tp) REVERT: B 538 GLN cc_start: 0.8267 (mt0) cc_final: 0.7158 (pp30) REVERT: B 577 PHE cc_start: 0.8420 (m-80) cc_final: 0.8046 (m-80) REVERT: B 580 GLU cc_start: 0.8365 (tp30) cc_final: 0.7962 (tp30) REVERT: A 28 LYS cc_start: 0.7750 (mtmm) cc_final: 0.7194 (ptpp) REVERT: A 45 GLU cc_start: 0.8455 (mp0) cc_final: 0.8080 (mp0) REVERT: A 46 ASP cc_start: 0.7228 (t70) cc_final: 0.6783 (t70) REVERT: A 47 HIS cc_start: 0.7957 (t70) cc_final: 0.6869 (t70) REVERT: A 51 LEU cc_start: 0.9007 (tp) cc_final: 0.8568 (tp) REVERT: A 54 MET cc_start: 0.8161 (tpt) cc_final: 0.7944 (tpt) REVERT: A 74 TYR cc_start: 0.8143 (m-80) cc_final: 0.7076 (m-80) REVERT: A 76 LEU cc_start: 0.8229 (mt) cc_final: 0.7963 (mt) REVERT: A 77 SER cc_start: 0.8083 (m) cc_final: 0.6944 (p) REVERT: A 80 LYS cc_start: 0.8408 (mttm) cc_final: 0.8135 (mttm) REVERT: A 85 VAL cc_start: 0.8191 (t) cc_final: 0.7950 (p) REVERT: A 112 TYR cc_start: 0.7279 (m-10) cc_final: 0.6695 (m-10) REVERT: A 119 LEU cc_start: 0.7713 (tp) cc_final: 0.7394 (tp) REVERT: A 135 LEU cc_start: 0.8401 (tp) cc_final: 0.8149 (tp) REVERT: A 137 MET cc_start: 0.8415 (mtm) cc_final: 0.8127 (mtm) REVERT: A 143 ILE cc_start: 0.9133 (mt) cc_final: 0.8743 (mm) REVERT: A 176 MET cc_start: 0.8562 (ptp) cc_final: 0.8079 (ptp) REVERT: A 196 ASN cc_start: 0.8922 (m-40) cc_final: 0.8584 (m110) REVERT: A 209 LYS cc_start: 0.8270 (mttt) cc_final: 0.7673 (mtmm) REVERT: A 212 LYS cc_start: 0.7207 (ttmm) cc_final: 0.6750 (ttmm) REVERT: A 257 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7959 (mm-30) REVERT: A 268 MET cc_start: 0.6375 (mtm) cc_final: 0.5066 (mtm) REVERT: A 277 MET cc_start: 0.6497 (mtt) cc_final: 0.5256 (mtt) REVERT: A 298 ASN cc_start: 0.8852 (p0) cc_final: 0.8518 (p0) REVERT: A 316 TYR cc_start: 0.7470 (t80) cc_final: 0.7138 (t80) REVERT: A 338 ASN cc_start: 0.7578 (p0) cc_final: 0.6363 (p0) REVERT: A 340 ILE cc_start: 0.7139 (mp) cc_final: 0.6880 (mp) REVERT: A 345 PHE cc_start: 0.8361 (m-80) cc_final: 0.7755 (m-80) REVERT: A 360 LYS cc_start: 0.8562 (tttt) cc_final: 0.8320 (tttt) REVERT: A 396 LYS cc_start: 0.8584 (tppp) cc_final: 0.7915 (tppp) REVERT: A 404 PHE cc_start: 0.7575 (p90) cc_final: 0.6741 (p90) REVERT: A 420 PHE cc_start: 0.8484 (m-80) cc_final: 0.8270 (m-80) REVERT: A 421 GLU cc_start: 0.8646 (tt0) cc_final: 0.7869 (tt0) REVERT: A 429 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7525 (mtt-85) REVERT: A 431 LYS cc_start: 0.8190 (mtmm) cc_final: 0.7598 (mtmm) REVERT: A 432 GLN cc_start: 0.8600 (tp40) cc_final: 0.8339 (tm-30) REVERT: A 454 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8207 (mmtt) REVERT: A 457 SER cc_start: 0.8083 (m) cc_final: 0.7362 (t) REVERT: A 476 ASN cc_start: 0.7860 (t0) cc_final: 0.7422 (t0) REVERT: A 487 LYS cc_start: 0.7867 (ptpp) cc_final: 0.7653 (ptpp) REVERT: A 489 LYS cc_start: 0.7490 (tptm) cc_final: 0.7146 (mtpp) REVERT: A 496 GLU cc_start: 0.7554 (mp0) cc_final: 0.7237 (mp0) REVERT: A 551 GLU cc_start: 0.8580 (pt0) cc_final: 0.8139 (pm20) REVERT: A 554 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8285 (mt-10) REVERT: A 559 HIS cc_start: 0.7671 (t70) cc_final: 0.7260 (t-170) REVERT: C 18 GLN cc_start: 0.8003 (tt0) cc_final: 0.7334 (tt0) REVERT: C 25 MET cc_start: 0.7825 (mmp) cc_final: 0.7330 (mmp) REVERT: C 31 ARG cc_start: 0.7091 (ttp-170) cc_final: 0.6658 (ttp-110) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.2450 time to fit residues: 114.7926 Evaluate side-chains 344 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.0470 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 63 optimal weight: 0.1980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 257 HIS ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 280 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.124915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099520 restraints weight = 16418.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.104845 restraints weight = 9283.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.108616 restraints weight = 5867.580| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9358 Z= 0.226 Angle : 0.696 9.782 12680 Z= 0.351 Chirality : 0.049 0.261 1417 Planarity : 0.005 0.063 1669 Dihedral : 7.257 74.316 1426 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 0.10 % Allowed : 0.00 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.24), residues: 1164 helix: -2.70 (0.56), residues: 66 sheet: -1.46 (0.63), residues: 74 loop : -1.74 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 164 HIS 0.007 0.001 HIS A 183 PHE 0.030 0.002 PHE A 150 TYR 0.027 0.002 TYR B 64 ARG 0.010 0.001 ARG B 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 0.940 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.7533 (mtp) cc_final: 0.6766 (ptp) REVERT: B 44 ASP cc_start: 0.7611 (t0) cc_final: 0.6851 (t0) REVERT: B 47 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7393 (ttp80) REVERT: B 59 ASN cc_start: 0.7506 (m-40) cc_final: 0.7003 (m-40) REVERT: B 61 GLU cc_start: 0.6920 (tm-30) cc_final: 0.4058 (tm-30) REVERT: B 75 GLN cc_start: 0.8052 (pt0) cc_final: 0.7285 (pp30) REVERT: B 100 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7596 (mmm-85) REVERT: B 103 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.7056 (ttm110) REVERT: B 106 GLN cc_start: 0.7806 (mt0) cc_final: 0.7415 (mp-120) REVERT: B 173 PHE cc_start: 0.7124 (m-10) cc_final: 0.6904 (m-10) REVERT: B 185 ASP cc_start: 0.7205 (t0) cc_final: 0.6937 (t0) REVERT: B 193 HIS cc_start: 0.7787 (m90) cc_final: 0.7371 (m90) REVERT: B 217 ARG cc_start: 0.7225 (mtp-110) cc_final: 0.6768 (mtt90) REVERT: B 248 LYS cc_start: 0.8656 (mmtt) cc_final: 0.7953 (mmtt) REVERT: B 258 PHE cc_start: 0.7475 (m-80) cc_final: 0.7008 (m-80) REVERT: B 265 GLU cc_start: 0.7258 (pm20) cc_final: 0.6560 (pm20) REVERT: B 266 LEU cc_start: 0.8180 (tp) cc_final: 0.7445 (tp) REVERT: B 267 HIS cc_start: 0.7614 (m170) cc_final: 0.6764 (m170) REVERT: B 274 TYR cc_start: 0.6815 (t80) cc_final: 0.6217 (t80) REVERT: B 282 MET cc_start: 0.8381 (mtp) cc_final: 0.7855 (mtp) REVERT: B 303 TYR cc_start: 0.8096 (m-80) cc_final: 0.7555 (m-80) REVERT: B 313 LEU cc_start: 0.8279 (mt) cc_final: 0.7996 (pt) REVERT: B 319 ASN cc_start: 0.7598 (m-40) cc_final: 0.7344 (m-40) REVERT: B 323 THR cc_start: 0.7495 (t) cc_final: 0.7102 (p) REVERT: B 332 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7132 (mt-10) REVERT: B 350 LEU cc_start: 0.7767 (mt) cc_final: 0.7541 (mt) REVERT: B 364 PHE cc_start: 0.8751 (m-80) cc_final: 0.8197 (m-80) REVERT: B 398 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7737 (mp10) REVERT: B 405 GLU cc_start: 0.6584 (tp30) cc_final: 0.6295 (tp30) REVERT: B 407 THR cc_start: 0.7910 (p) cc_final: 0.7472 (m) REVERT: B 409 TYR cc_start: 0.7040 (p90) cc_final: 0.6811 (p90) REVERT: B 411 TYR cc_start: 0.7217 (t80) cc_final: 0.6512 (t80) REVERT: B 426 GLN cc_start: 0.8003 (pt0) cc_final: 0.7427 (pp30) REVERT: B 436 LEU cc_start: 0.7931 (mt) cc_final: 0.7638 (mt) REVERT: B 452 TRP cc_start: 0.7993 (p90) cc_final: 0.7305 (p90) REVERT: B 463 SER cc_start: 0.7857 (t) cc_final: 0.7549 (p) REVERT: B 467 LEU cc_start: 0.7316 (tp) cc_final: 0.6551 (pp) REVERT: B 481 PRO cc_start: 0.8063 (Cg_endo) cc_final: 0.7488 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8472 (m100) cc_final: 0.8054 (m100) REVERT: B 484 GLN cc_start: 0.8815 (mt0) cc_final: 0.8339 (mp10) REVERT: B 486 PHE cc_start: 0.8201 (m-80) cc_final: 0.7303 (m-80) REVERT: B 493 LEU cc_start: 0.8436 (tp) cc_final: 0.7460 (tp) REVERT: B 494 LEU cc_start: 0.8650 (mt) cc_final: 0.8326 (tt) REVERT: B 538 GLN cc_start: 0.8220 (mt0) cc_final: 0.7018 (tm-30) REVERT: B 577 PHE cc_start: 0.8449 (m-80) cc_final: 0.7972 (m-80) REVERT: B 580 GLU cc_start: 0.8334 (tp30) cc_final: 0.7939 (tp30) REVERT: A 45 GLU cc_start: 0.8458 (mp0) cc_final: 0.8061 (mp0) REVERT: A 46 ASP cc_start: 0.7233 (t70) cc_final: 0.6842 (t70) REVERT: A 47 HIS cc_start: 0.7915 (t70) cc_final: 0.6933 (t70) REVERT: A 51 LEU cc_start: 0.8980 (tp) cc_final: 0.8576 (tp) REVERT: A 54 MET cc_start: 0.8200 (tpt) cc_final: 0.7909 (tpt) REVERT: A 55 PHE cc_start: 0.7951 (m-10) cc_final: 0.7690 (m-10) REVERT: A 74 TYR cc_start: 0.8102 (m-80) cc_final: 0.7069 (m-80) REVERT: A 76 LEU cc_start: 0.8213 (mt) cc_final: 0.7953 (mt) REVERT: A 77 SER cc_start: 0.8045 (m) cc_final: 0.6889 (p) REVERT: A 80 LYS cc_start: 0.8401 (mttm) cc_final: 0.8065 (mttm) REVERT: A 83 GLN cc_start: 0.7640 (mm110) cc_final: 0.7381 (mm110) REVERT: A 85 VAL cc_start: 0.8165 (t) cc_final: 0.7952 (p) REVERT: A 112 TYR cc_start: 0.7265 (m-10) cc_final: 0.6711 (m-10) REVERT: A 114 GLU cc_start: 0.7445 (tt0) cc_final: 0.6617 (tt0) REVERT: A 119 LEU cc_start: 0.7857 (tp) cc_final: 0.7528 (tp) REVERT: A 125 TYR cc_start: 0.6812 (p90) cc_final: 0.6584 (p90) REVERT: A 143 ILE cc_start: 0.9133 (mt) cc_final: 0.8737 (mm) REVERT: A 176 MET cc_start: 0.8508 (ptp) cc_final: 0.8055 (ptp) REVERT: A 196 ASN cc_start: 0.8915 (m-40) cc_final: 0.8581 (m110) REVERT: A 209 LYS cc_start: 0.8230 (mttt) cc_final: 0.7658 (mtmm) REVERT: A 212 LYS cc_start: 0.7208 (ttmm) cc_final: 0.6753 (ttmm) REVERT: A 257 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8099 (mm-30) REVERT: A 261 LYS cc_start: 0.7340 (ptmt) cc_final: 0.6928 (ptmt) REVERT: A 268 MET cc_start: 0.6300 (mtm) cc_final: 0.4987 (mtm) REVERT: A 277 MET cc_start: 0.6440 (mtt) cc_final: 0.5241 (mtt) REVERT: A 298 ASN cc_start: 0.8818 (p0) cc_final: 0.8435 (p0) REVERT: A 316 TYR cc_start: 0.7435 (t80) cc_final: 0.7062 (t80) REVERT: A 338 ASN cc_start: 0.7646 (p0) cc_final: 0.7152 (p0) REVERT: A 340 ILE cc_start: 0.7156 (mp) cc_final: 0.6893 (mp) REVERT: A 344 GLU cc_start: 0.7201 (tt0) cc_final: 0.6985 (tt0) REVERT: A 358 HIS cc_start: 0.8564 (m170) cc_final: 0.8314 (m-70) REVERT: A 360 LYS cc_start: 0.8567 (tttt) cc_final: 0.8337 (tttt) REVERT: A 377 ARG cc_start: 0.7757 (ptm-80) cc_final: 0.7265 (ptp-110) REVERT: A 396 LYS cc_start: 0.8547 (tppp) cc_final: 0.7850 (tppp) REVERT: A 404 PHE cc_start: 0.7547 (p90) cc_final: 0.6694 (p90) REVERT: A 417 LEU cc_start: 0.7801 (mt) cc_final: 0.7482 (mt) REVERT: A 420 PHE cc_start: 0.8469 (m-80) cc_final: 0.8204 (m-80) REVERT: A 421 GLU cc_start: 0.8670 (tt0) cc_final: 0.8088 (tt0) REVERT: A 429 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7482 (mtt-85) REVERT: A 432 GLN cc_start: 0.8634 (tp40) cc_final: 0.8351 (tm-30) REVERT: A 451 ARG cc_start: 0.7790 (ptp90) cc_final: 0.7533 (ptp-170) REVERT: A 456 ILE cc_start: 0.8821 (mm) cc_final: 0.8311 (pt) REVERT: A 457 SER cc_start: 0.8116 (m) cc_final: 0.7454 (t) REVERT: A 476 ASN cc_start: 0.7893 (t0) cc_final: 0.7512 (t0) REVERT: A 487 LYS cc_start: 0.7878 (ptpp) cc_final: 0.7666 (ptpp) REVERT: A 489 LYS cc_start: 0.7444 (tptm) cc_final: 0.7167 (mtpp) REVERT: A 496 GLU cc_start: 0.7556 (mp0) cc_final: 0.7204 (mp0) REVERT: A 551 GLU cc_start: 0.8575 (pt0) cc_final: 0.8136 (pm20) REVERT: A 554 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8270 (mt-10) REVERT: A 559 HIS cc_start: 0.7662 (t70) cc_final: 0.7254 (t-170) REVERT: C 18 GLN cc_start: 0.8006 (tt0) cc_final: 0.7435 (tt0) REVERT: C 25 MET cc_start: 0.7807 (mmp) cc_final: 0.7223 (mmp) REVERT: C 31 ARG cc_start: 0.7066 (ttp-170) cc_final: 0.6402 (ttm170) outliers start: 1 outliers final: 0 residues processed: 353 average time/residue: 0.2459 time to fit residues: 113.1680 Evaluate side-chains 338 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 77 optimal weight: 0.0040 chunk 61 optimal weight: 0.8980 chunk 107 optimal weight: 0.0050 chunk 0 optimal weight: 1.9990 chunk 69 optimal weight: 0.0970 chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 overall best weight: 0.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 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 = 0.3793 r_free = 0.3793 target = 0.128586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102798 restraints weight = 16354.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.108027 restraints weight = 9390.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.111780 restraints weight = 6040.977| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9358 Z= 0.196 Angle : 0.693 9.614 12680 Z= 0.348 Chirality : 0.049 0.454 1417 Planarity : 0.005 0.062 1669 Dihedral : 6.992 69.251 1426 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.24), residues: 1164 helix: -2.26 (0.69), residues: 54 sheet: -1.29 (0.69), residues: 64 loop : -1.69 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 410 HIS 0.007 0.001 HIS A 183 PHE 0.026 0.001 PHE B 108 TYR 0.016 0.001 TYR A 125 ARG 0.011 0.001 ARG B 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3748.91 seconds wall clock time: 65 minutes 39.98 seconds (3939.98 seconds total)