Starting phenix.real_space_refine on Fri Nov 15 21:55:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/11_2024/8hgp_34745.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/11_2024/8hgp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/11_2024/8hgp_34745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/11_2024/8hgp_34745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/11_2024/8hgp_34745.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/11_2024/8hgp_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.86, 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: 2.64 Conformation dependent library (CDL) restraints added in 1.3 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: 1.28 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: 2.79 Time building geometry restraints manager: 2.96 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: 3.000 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.440 Find NCS groups from input model: 0.150 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.100 ------------------------------------------------------------------------------- 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 : 1.072 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: 0.2610 time to fit residues: 136.2098 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 : 1.041 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 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 : 1.057 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: 0.5722 (pp30) cc_final: 0.4539 (mm-40) REVERT: B 31 MET cc_start: 0.7888 (mtp) cc_final: 0.7299 (ptp) REVERT: B 32 LYS cc_start: 0.7958 (mptt) cc_final: 0.7555 (mmtt) REVERT: B 46 LEU cc_start: 0.8741 (mt) cc_final: 0.8456 (mt) REVERT: B 54 GLN cc_start: 0.6980 (mt0) cc_final: 0.6606 (tp-100) REVERT: B 56 VAL cc_start: 0.8067 (t) cc_final: 0.7637 (t) REVERT: B 59 ASN cc_start: 0.6695 (m-40) cc_final: 0.6189 (m-40) REVERT: B 73 PHE cc_start: 0.8085 (p90) cc_final: 0.7816 (p90) REVERT: B 74 LEU cc_start: 0.8384 (mt) cc_final: 0.8150 (mt) REVERT: B 75 GLN cc_start: 0.7836 (pt0) cc_final: 0.7530 (pt0) REVERT: B 79 GLU cc_start: 0.7102 (tt0) cc_final: 0.6481 (tt0) REVERT: B 81 GLN cc_start: 0.6785 (mt0) cc_final: 0.6280 (mt0) REVERT: B 92 ARG cc_start: 0.7622 (mtt90) cc_final: 0.7179 (mmm-85) REVERT: B 93 GLN cc_start: 0.8497 (pp30) cc_final: 0.7693 (tm-30) REVERT: B 94 VAL cc_start: 0.8927 (t) cc_final: 0.8589 (t) REVERT: B 105 THR cc_start: 0.7710 (p) cc_final: 0.6794 (t) REVERT: B 106 GLN cc_start: 0.7646 (mt0) cc_final: 0.7092 (mp-120) REVERT: B 116 VAL cc_start: 0.6853 (t) cc_final: 0.6475 (p) REVERT: B 160 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7078 (tp40) REVERT: B 171 ASP cc_start: 0.7925 (t70) cc_final: 0.6730 (t70) REVERT: B 173 PHE cc_start: 0.6843 (m-10) cc_final: 0.6433 (m-10) REVERT: B 185 ASP cc_start: 0.7009 (t0) cc_final: 0.6763 (t0) REVERT: B 193 HIS cc_start: 0.7939 (m90) cc_final: 0.7303 (m90) REVERT: B 211 ASP cc_start: 0.8025 (m-30) cc_final: 0.7710 (m-30) REVERT: B 213 GLN cc_start: 0.7536 (tm-30) cc_final: 0.7225 (tm-30) REVERT: B 237 HIS cc_start: 0.7553 (t-90) cc_final: 0.7347 (t-90) REVERT: B 248 LYS cc_start: 0.8585 (mmtt) cc_final: 0.7975 (mmtt) REVERT: B 251 ASP cc_start: 0.7597 (p0) cc_final: 0.7354 (p0) REVERT: B 253 LEU cc_start: 0.7425 (mt) cc_final: 0.6965 (mt) REVERT: B 265 GLU cc_start: 0.6917 (pm20) cc_final: 0.6578 (pm20) REVERT: B 271 LEU cc_start: 0.8519 (mp) cc_final: 0.8246 (mt) REVERT: B 275 ASN cc_start: 0.8180 (t0) cc_final: 0.7368 (t0) REVERT: B 282 MET cc_start: 0.8009 (mtp) cc_final: 0.7706 (mtp) REVERT: B 300 PRO cc_start: 0.7930 (Cg_exo) cc_final: 0.7498 (Cg_endo) REVERT: B 303 TYR cc_start: 0.7873 (m-80) cc_final: 0.7212 (m-80) REVERT: B 332 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6512 (mp0) REVERT: B 376 PHE cc_start: 0.8113 (m-10) cc_final: 0.7563 (m-10) REVERT: B 377 LEU cc_start: 0.8325 (tp) cc_final: 0.8061 (tt) REVERT: B 407 THR cc_start: 0.7637 (p) cc_final: 0.7353 (m) REVERT: B 411 TYR cc_start: 0.7174 (t80) cc_final: 0.6676 (t80) REVERT: B 420 PRO cc_start: 0.8341 (Cg_endo) cc_final: 0.7957 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7703 (p0) cc_final: 0.7437 (p0) REVERT: B 422 LEU cc_start: 0.8634 (tp) cc_final: 0.7734 (pp) REVERT: B 426 GLN cc_start: 0.7642 (pt0) cc_final: 0.6854 (pp30) REVERT: B 430 VAL cc_start: 0.7360 (p) cc_final: 0.7043 (t) REVERT: B 434 ARG cc_start: 0.7439 (mtt90) cc_final: 0.7183 (mpt-90) REVERT: B 436 LEU cc_start: 0.7912 (mt) cc_final: 0.7376 (mt) REVERT: B 443 LEU cc_start: 0.7820 (tp) cc_final: 0.7365 (mm) REVERT: B 444 THR cc_start: 0.7337 (m) cc_final: 0.6684 (m) REVERT: B 452 TRP cc_start: 0.7735 (p90) cc_final: 0.7238 (p90) REVERT: B 463 SER cc_start: 0.7325 (t) cc_final: 0.6868 (m) REVERT: B 481 PRO cc_start: 0.8291 (Cg_endo) cc_final: 0.7698 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8533 (m100) cc_final: 0.8302 (m100) REVERT: B 488 ASN cc_start: 0.7902 (t0) cc_final: 0.7638 (t0) REVERT: B 494 LEU cc_start: 0.8513 (mt) cc_final: 0.8273 (mm) REVERT: B 517 ARG cc_start: 0.8343 (mtt180) cc_final: 0.7942 (mtm110) REVERT: B 556 ASN cc_start: 0.8057 (t0) cc_final: 0.7441 (t0) REVERT: B 566 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6544 (tm-30) REVERT: B 577 PHE cc_start: 0.8151 (m-80) cc_final: 0.7886 (m-80) REVERT: B 580 GLU cc_start: 0.8462 (tp30) cc_final: 0.8067 (tp30) REVERT: B 592 ASP cc_start: 0.7748 (t0) cc_final: 0.7515 (m-30) REVERT: A 29 LYS cc_start: 0.7956 (pttm) cc_final: 0.7579 (pttm) REVERT: A 36 ASN cc_start: 0.8239 (p0) cc_final: 0.7779 (p0) REVERT: A 46 ASP cc_start: 0.7437 (t70) cc_final: 0.6673 (t70) REVERT: A 47 HIS cc_start: 0.7908 (t70) cc_final: 0.6702 (t70) REVERT: A 51 LEU cc_start: 0.8764 (tp) cc_final: 0.8533 (tp) REVERT: A 55 PHE cc_start: 0.7915 (m-10) cc_final: 0.7493 (m-10) REVERT: A 62 LEU cc_start: 0.8473 (mt) cc_final: 0.8241 (mm) REVERT: A 74 TYR cc_start: 0.7816 (m-80) cc_final: 0.6901 (m-80) REVERT: A 80 LYS cc_start: 0.8234 (mttm) cc_final: 0.7828 (mttm) REVERT: A 83 GLN cc_start: 0.7957 (mm110) cc_final: 0.7456 (mm110) REVERT: A 93 LEU cc_start: 0.8241 (mp) cc_final: 0.8018 (mt) REVERT: A 114 GLU cc_start: 0.7561 (tt0) cc_final: 0.7056 (tt0) REVERT: A 143 ILE cc_start: 0.8935 (mt) cc_final: 0.8641 (mm) REVERT: A 163 GLN cc_start: 0.8624 (pt0) cc_final: 0.7996 (tt0) REVERT: A 172 PHE cc_start: 0.7632 (m-10) cc_final: 0.7431 (m-80) REVERT: A 176 MET cc_start: 0.8040 (ptp) cc_final: 0.7546 (ptt) REVERT: A 209 LYS cc_start: 0.8071 (mttt) cc_final: 0.7456 (mtmm) REVERT: A 226 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7251 (mtpt) REVERT: A 227 SER cc_start: 0.8170 (t) cc_final: 0.7930 (p) REVERT: A 233 HIS cc_start: 0.7525 (t-90) cc_final: 0.6898 (t-90) REVERT: A 253 LYS cc_start: 0.8059 (tptm) cc_final: 0.7330 (tptm) REVERT: A 256 ASP cc_start: 0.7071 (t70) cc_final: 0.6703 (t0) REVERT: A 261 LYS cc_start: 0.7444 (mttm) cc_final: 0.6933 (mttm) REVERT: A 262 ASP cc_start: 0.7655 (t0) cc_final: 0.7290 (t0) REVERT: A 268 MET cc_start: 0.6289 (mtm) cc_final: 0.5134 (mtm) REVERT: A 277 MET cc_start: 0.6388 (mtt) cc_final: 0.5396 (mtt) REVERT: A 285 TYR cc_start: 0.5899 (m-10) cc_final: 0.5671 (m-10) REVERT: A 293 LYS cc_start: 0.7978 (mtpp) cc_final: 0.7032 (mmmt) REVERT: A 316 TYR cc_start: 0.7592 (t80) cc_final: 0.7118 (t80) REVERT: A 318 MET cc_start: 0.7815 (tpp) cc_final: 0.6988 (tpp) REVERT: A 338 ASN cc_start: 0.6939 (p0) cc_final: 0.6168 (p0) REVERT: A 345 PHE cc_start: 0.8248 (m-80) cc_final: 0.7868 (m-80) REVERT: A 358 HIS cc_start: 0.8240 (m90) cc_final: 0.7683 (m90) REVERT: A 360 LYS cc_start: 0.8711 (tttt) cc_final: 0.8339 (tttt) REVERT: A 368 ASP cc_start: 0.5110 (m-30) cc_final: 0.4027 (m-30) REVERT: A 369 LEU cc_start: 0.7153 (mt) cc_final: 0.6918 (mm) REVERT: A 396 LYS cc_start: 0.8217 (tppp) cc_final: 0.7778 (tppp) REVERT: A 404 PHE cc_start: 0.7340 (p90) cc_final: 0.6032 (p90) REVERT: A 421 GLU cc_start: 0.8627 (tt0) cc_final: 0.7952 (tt0) REVERT: A 430 THR cc_start: 0.7584 (m) cc_final: 0.6292 (t) REVERT: A 432 GLN cc_start: 0.8652 (tp40) cc_final: 0.8184 (tp-100) REVERT: A 433 HIS cc_start: 0.8430 (m90) cc_final: 0.8112 (m90) REVERT: A 476 ASN cc_start: 0.7676 (t0) cc_final: 0.7321 (t0) REVERT: A 489 LYS cc_start: 0.7814 (ttmm) cc_final: 0.7581 (mtpp) REVERT: A 496 GLU cc_start: 0.7742 (mp0) cc_final: 0.7427 (mp0) REVERT: A 521 ARG cc_start: 0.7864 (ptt180) cc_final: 0.7544 (tmm-80) REVERT: A 551 GLU cc_start: 0.8605 (pt0) cc_final: 0.8095 (pm20) REVERT: C 5 LYS cc_start: 0.8093 (mttt) cc_final: 0.7837 (tppp) REVERT: C 18 GLN cc_start: 0.7750 (tt0) cc_final: 0.7250 (pm20) REVERT: C 22 LEU cc_start: 0.7634 (mt) cc_final: 0.7303 (mt) REVERT: C 25 MET cc_start: 0.8075 (mmp) cc_final: 0.7386 (mmp) outliers start: 1 outliers final: 1 residues processed: 377 average time/residue: 0.2603 time to fit residues: 129.0121 Evaluate side-chains 345 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 344 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 0.0970 chunk 87 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.0570 chunk 35 optimal weight: 0.0870 chunk 84 optimal weight: 0.0370 overall best weight: 0.0952 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9358 Z= 0.152 Angle : 0.580 9.547 12680 Z= 0.293 Chirality : 0.046 0.255 1417 Planarity : 0.004 0.043 1669 Dihedral : 8.202 84.394 1426 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % 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: -3.13 (0.22), residues: 1164 helix: -2.19 (0.72), residues: 51 sheet: -2.23 (0.62), residues: 61 loop : -2.31 (0.17), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 415 HIS 0.006 0.001 HIS A 145 PHE 0.022 0.001 PHE B 486 TYR 0.012 0.001 TYR B 301 ARG 0.005 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 368 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.049 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: 0.5725 (pp30) cc_final: 0.4588 (mm-40) REVERT: B 31 MET cc_start: 0.7913 (mtp) cc_final: 0.7299 (ptp) REVERT: B 44 ASP cc_start: 0.7298 (t0) cc_final: 0.6733 (t0) REVERT: B 46 LEU cc_start: 0.8737 (mt) cc_final: 0.8490 (mt) REVERT: B 54 GLN cc_start: 0.6902 (mt0) cc_final: 0.6564 (tp-100) REVERT: B 56 VAL cc_start: 0.8107 (t) cc_final: 0.7759 (m) REVERT: B 59 ASN cc_start: 0.6509 (m-40) cc_final: 0.6202 (m-40) REVERT: B 65 LEU cc_start: 0.8321 (mt) cc_final: 0.8111 (mt) REVERT: B 73 PHE cc_start: 0.8056 (p90) cc_final: 0.7707 (p90) REVERT: B 74 LEU cc_start: 0.8390 (mt) cc_final: 0.8180 (mt) REVERT: B 75 GLN cc_start: 0.7808 (pt0) cc_final: 0.7515 (pt0) REVERT: B 79 GLU cc_start: 0.7016 (tt0) cc_final: 0.6296 (tt0) REVERT: B 81 GLN cc_start: 0.6824 (mt0) cc_final: 0.6243 (mt0) REVERT: B 93 GLN cc_start: 0.8513 (pp30) cc_final: 0.8146 (tm-30) REVERT: B 100 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.7340 (mmm-85) REVERT: B 103 ARG cc_start: 0.7319 (ttm110) cc_final: 0.6605 (ttm110) REVERT: B 105 THR cc_start: 0.7820 (p) cc_final: 0.6899 (t) REVERT: B 106 GLN cc_start: 0.7639 (mt0) cc_final: 0.7083 (mp-120) REVERT: B 143 ARG cc_start: 0.7593 (mtt180) cc_final: 0.7236 (mtt180) REVERT: B 155 ILE cc_start: 0.7956 (mt) cc_final: 0.7682 (mm) REVERT: B 158 ASN cc_start: 0.7486 (m-40) cc_final: 0.7252 (m110) REVERT: B 160 GLN cc_start: 0.7467 (mm-40) cc_final: 0.7183 (tp40) REVERT: B 173 PHE cc_start: 0.6929 (m-10) cc_final: 0.6320 (m-10) REVERT: B 185 ASP cc_start: 0.6988 (t0) cc_final: 0.6523 (t0) REVERT: B 193 HIS cc_start: 0.7918 (m90) cc_final: 0.7303 (m90) REVERT: B 211 ASP cc_start: 0.7949 (m-30) cc_final: 0.7363 (m-30) REVERT: B 226 ARG cc_start: 0.7858 (tpp-160) cc_final: 0.7486 (mmm160) REVERT: B 248 LYS cc_start: 0.8545 (mmtt) cc_final: 0.7959 (mmtt) REVERT: B 251 ASP cc_start: 0.7557 (p0) cc_final: 0.7300 (p0) REVERT: B 265 GLU cc_start: 0.6966 (pm20) cc_final: 0.6372 (pm20) REVERT: B 267 HIS cc_start: 0.7582 (m170) cc_final: 0.7248 (m170) REVERT: B 271 LEU cc_start: 0.8597 (mp) cc_final: 0.8317 (mt) REVERT: B 274 TYR cc_start: 0.6758 (t80) cc_final: 0.5895 (t80) REVERT: B 275 ASN cc_start: 0.7805 (t0) cc_final: 0.7497 (t0) REVERT: B 282 MET cc_start: 0.8271 (mtp) cc_final: 0.7793 (mtp) REVERT: B 288 ARG cc_start: 0.7833 (mmt-90) cc_final: 0.7572 (mtt90) REVERT: B 303 TYR cc_start: 0.7870 (m-80) cc_final: 0.7177 (m-80) REVERT: B 313 LEU cc_start: 0.7909 (mt) cc_final: 0.7642 (pt) REVERT: B 332 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6473 (mp0) REVERT: B 377 LEU cc_start: 0.8299 (tp) cc_final: 0.8029 (tt) REVERT: B 407 THR cc_start: 0.7588 (p) cc_final: 0.7127 (m) REVERT: B 411 TYR cc_start: 0.7221 (t80) cc_final: 0.6402 (t80) REVERT: B 420 PRO cc_start: 0.8338 (Cg_endo) cc_final: 0.8091 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7670 (p0) cc_final: 0.7432 (p0) REVERT: B 422 LEU cc_start: 0.8578 (tp) cc_final: 0.8291 (mt) REVERT: B 426 GLN cc_start: 0.7751 (pt0) cc_final: 0.7000 (pp30) REVERT: B 436 LEU cc_start: 0.7975 (mt) cc_final: 0.7467 (mt) REVERT: B 443 LEU cc_start: 0.7791 (tp) cc_final: 0.7292 (mm) REVERT: B 444 THR cc_start: 0.7133 (m) cc_final: 0.6483 (m) REVERT: B 451 SER cc_start: 0.8037 (p) cc_final: 0.7692 (m) REVERT: B 481 PRO cc_start: 0.8226 (Cg_endo) cc_final: 0.7663 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8621 (m100) cc_final: 0.8351 (m100) REVERT: B 487 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7338 (tpp80) REVERT: B 494 LEU cc_start: 0.8515 (mt) cc_final: 0.8199 (mt) REVERT: B 517 ARG cc_start: 0.8354 (mtt180) cc_final: 0.8131 (mtt180) REVERT: B 556 ASN cc_start: 0.7991 (t0) cc_final: 0.7366 (t0) REVERT: B 566 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6505 (tm-30) REVERT: B 577 PHE cc_start: 0.8153 (m-80) cc_final: 0.7888 (m-80) REVERT: B 580 GLU cc_start: 0.8433 (tp30) cc_final: 0.8100 (tp30) REVERT: B 592 ASP cc_start: 0.7769 (t0) cc_final: 0.7491 (m-30) REVERT: A 28 LYS cc_start: 0.7758 (mtmm) cc_final: 0.7547 (ptpp) REVERT: A 29 LYS cc_start: 0.7800 (pttm) cc_final: 0.7399 (pttt) REVERT: A 36 ASN cc_start: 0.8203 (p0) cc_final: 0.7831 (p0) REVERT: A 46 ASP cc_start: 0.7245 (t70) cc_final: 0.6600 (t70) REVERT: A 47 HIS cc_start: 0.7832 (t70) cc_final: 0.6686 (t70) REVERT: A 51 LEU cc_start: 0.8766 (tp) cc_final: 0.8516 (tp) REVERT: A 55 PHE cc_start: 0.7862 (m-10) cc_final: 0.7508 (m-10) REVERT: A 61 VAL cc_start: 0.8218 (m) cc_final: 0.7968 (p) REVERT: A 65 LEU cc_start: 0.7814 (tp) cc_final: 0.7438 (tt) REVERT: A 74 TYR cc_start: 0.7846 (m-80) cc_final: 0.6892 (m-80) REVERT: A 80 LYS cc_start: 0.8187 (mttm) cc_final: 0.7973 (mttm) REVERT: A 83 GLN cc_start: 0.7896 (mm110) cc_final: 0.7108 (mm110) REVERT: A 85 VAL cc_start: 0.8125 (t) cc_final: 0.7882 (p) REVERT: A 103 ASN cc_start: 0.7268 (m-40) cc_final: 0.6356 (m-40) REVERT: A 110 ASN cc_start: 0.7947 (m-40) cc_final: 0.7474 (p0) REVERT: A 132 LEU cc_start: 0.7624 (mm) cc_final: 0.7101 (mm) REVERT: A 143 ILE cc_start: 0.8907 (mt) cc_final: 0.8591 (mm) REVERT: A 163 GLN cc_start: 0.8567 (pt0) cc_final: 0.8004 (tt0) REVERT: A 172 PHE cc_start: 0.7614 (m-10) cc_final: 0.7379 (m-80) REVERT: A 176 MET cc_start: 0.8047 (ptp) cc_final: 0.7668 (ptt) REVERT: A 209 LYS cc_start: 0.8065 (mttt) cc_final: 0.7477 (mtmm) REVERT: A 226 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7227 (mtpt) REVERT: A 227 SER cc_start: 0.8149 (t) cc_final: 0.7934 (p) REVERT: A 229 SER cc_start: 0.8292 (p) cc_final: 0.7951 (t) REVERT: A 230 ASP cc_start: 0.8435 (m-30) cc_final: 0.8206 (m-30) REVERT: A 233 HIS cc_start: 0.7307 (t-90) cc_final: 0.6909 (t-90) REVERT: A 253 LYS cc_start: 0.8064 (tptm) cc_final: 0.7424 (tptm) REVERT: A 254 PHE cc_start: 0.7284 (m-10) cc_final: 0.5938 (m-80) REVERT: A 255 ARG cc_start: 0.6789 (ttt-90) cc_final: 0.6471 (ttp80) REVERT: A 261 LYS cc_start: 0.7440 (mttm) cc_final: 0.7238 (ptmt) REVERT: A 262 ASP cc_start: 0.7561 (t0) cc_final: 0.7120 (t0) REVERT: A 268 MET cc_start: 0.6244 (mtm) cc_final: 0.5098 (mtm) REVERT: A 277 MET cc_start: 0.6353 (mtt) cc_final: 0.5358 (mtt) REVERT: A 290 THR cc_start: 0.6846 (t) cc_final: 0.6621 (t) REVERT: A 293 LYS cc_start: 0.7710 (mtpp) cc_final: 0.7249 (tppt) REVERT: A 316 TYR cc_start: 0.7522 (t80) cc_final: 0.7057 (t80) REVERT: A 318 MET cc_start: 0.7714 (tpp) cc_final: 0.6886 (tpp) REVERT: A 338 ASN cc_start: 0.7139 (p0) cc_final: 0.6920 (p0) REVERT: A 358 HIS cc_start: 0.8282 (m90) cc_final: 0.7744 (m90) REVERT: A 360 LYS cc_start: 0.8698 (tttt) cc_final: 0.8341 (tttt) REVERT: A 368 ASP cc_start: 0.4905 (m-30) cc_final: 0.4390 (m-30) REVERT: A 396 LYS cc_start: 0.8193 (tppp) cc_final: 0.7734 (tppp) REVERT: A 406 LEU cc_start: 0.7550 (tp) cc_final: 0.6912 (mt) REVERT: A 421 GLU cc_start: 0.8608 (tt0) cc_final: 0.7973 (tt0) REVERT: A 430 THR cc_start: 0.7571 (m) cc_final: 0.7007 (t) REVERT: A 431 LYS cc_start: 0.8150 (mtmm) cc_final: 0.7687 (mtmt) REVERT: A 432 GLN cc_start: 0.8640 (tp40) cc_final: 0.8308 (tp-100) REVERT: A 433 HIS cc_start: 0.8388 (m90) cc_final: 0.8147 (m90) REVERT: A 476 ASN cc_start: 0.7628 (t0) cc_final: 0.7266 (t0) REVERT: A 489 LYS cc_start: 0.7693 (ttmm) cc_final: 0.7472 (mmmm) REVERT: A 496 GLU cc_start: 0.7762 (mp0) cc_final: 0.7496 (mp0) REVERT: A 551 GLU cc_start: 0.8641 (pt0) cc_final: 0.8175 (pm20) REVERT: C 5 LYS cc_start: 0.8123 (mttt) cc_final: 0.7867 (tppp) REVERT: C 18 GLN cc_start: 0.7764 (tt0) cc_final: 0.7248 (pm20) REVERT: C 22 LEU cc_start: 0.7537 (mt) cc_final: 0.7285 (mt) REVERT: C 25 MET cc_start: 0.8060 (mmp) cc_final: 0.7476 (mmp) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.2594 time to fit residues: 126.0673 Evaluate side-chains 348 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.0010 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 0.0980 chunk 112 optimal weight: 0.0000 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 30 optimal weight: 0.0980 overall best weight: 0.1590 ------------------------------------------------------------------------------- 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** A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9358 Z= 0.147 Angle : 0.557 9.770 12680 Z= 0.279 Chirality : 0.045 0.255 1417 Planarity : 0.004 0.043 1669 Dihedral : 7.236 74.146 1426 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -2.81 (0.22), residues: 1164 helix: -1.34 (0.86), residues: 42 sheet: -1.38 (0.64), residues: 69 loop : -2.16 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 452 HIS 0.003 0.000 HIS A 507 PHE 0.017 0.001 PHE A 180 TYR 0.016 0.001 TYR A 113 ARG 0.006 0.000 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 361 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.093 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: B 24 GLN cc_start: 0.5903 (pp30) cc_final: 0.4683 (mm-40) REVERT: B 31 MET cc_start: 0.7870 (mtp) cc_final: 0.7159 (ptp) REVERT: B 44 ASP cc_start: 0.7342 (t0) cc_final: 0.6540 (t0) REVERT: B 46 LEU cc_start: 0.8759 (mt) cc_final: 0.8449 (mt) REVERT: B 47 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7391 (ttp80) REVERT: B 54 GLN cc_start: 0.6957 (mt0) cc_final: 0.6620 (tp-100) REVERT: B 56 VAL cc_start: 0.8061 (t) cc_final: 0.7777 (m) REVERT: B 65 LEU cc_start: 0.8330 (mt) cc_final: 0.8096 (mt) REVERT: B 73 PHE cc_start: 0.8073 (p90) cc_final: 0.7652 (p90) REVERT: B 75 GLN cc_start: 0.7827 (pt0) cc_final: 0.7512 (pt0) REVERT: B 79 GLU cc_start: 0.7160 (tt0) cc_final: 0.6462 (tt0) REVERT: B 81 GLN cc_start: 0.6827 (mt0) cc_final: 0.6285 (mt0) REVERT: B 93 GLN cc_start: 0.8518 (pp30) cc_final: 0.8165 (tm-30) REVERT: B 100 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7399 (mmm-85) REVERT: B 103 ARG cc_start: 0.7330 (mmt90) cc_final: 0.6784 (tpp80) REVERT: B 105 THR cc_start: 0.7856 (p) cc_final: 0.6951 (t) REVERT: B 106 GLN cc_start: 0.7711 (mt0) cc_final: 0.7112 (mp-120) REVERT: B 112 TYR cc_start: 0.7163 (m-80) cc_final: 0.6756 (m-80) REVERT: B 143 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7252 (mtt180) REVERT: B 155 ILE cc_start: 0.7943 (mt) cc_final: 0.7570 (mt) REVERT: B 160 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7211 (tp40) REVERT: B 173 PHE cc_start: 0.6903 (m-10) cc_final: 0.6052 (m-10) REVERT: B 185 ASP cc_start: 0.6984 (t0) cc_final: 0.6518 (t0) REVERT: B 193 HIS cc_start: 0.7917 (m90) cc_final: 0.7297 (m90) REVERT: B 211 ASP cc_start: 0.7920 (m-30) cc_final: 0.7324 (m-30) REVERT: B 226 ARG cc_start: 0.8060 (tpp-160) cc_final: 0.7456 (mmm160) REVERT: B 248 LYS cc_start: 0.8530 (mmtt) cc_final: 0.7923 (mmtt) REVERT: B 251 ASP cc_start: 0.7551 (p0) cc_final: 0.7350 (p0) REVERT: B 265 GLU cc_start: 0.6863 (pm20) cc_final: 0.6373 (pm20) REVERT: B 266 LEU cc_start: 0.8301 (tp) cc_final: 0.8091 (tp) REVERT: B 267 HIS cc_start: 0.7611 (m170) cc_final: 0.7101 (m170) REVERT: B 271 LEU cc_start: 0.8588 (mp) cc_final: 0.8280 (mt) REVERT: B 274 TYR cc_start: 0.6727 (t80) cc_final: 0.6169 (t80) REVERT: B 275 ASN cc_start: 0.8087 (t0) cc_final: 0.7593 (t0) REVERT: B 282 MET cc_start: 0.8363 (mtp) cc_final: 0.7814 (mtp) REVERT: B 286 GLU cc_start: 0.7648 (mp0) cc_final: 0.7437 (mp0) REVERT: B 288 ARG cc_start: 0.7854 (mmt-90) cc_final: 0.7328 (mmp80) REVERT: B 303 TYR cc_start: 0.7909 (m-80) cc_final: 0.7263 (m-80) REVERT: B 323 THR cc_start: 0.7305 (t) cc_final: 0.6882 (p) REVERT: B 332 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7070 (mt-10) REVERT: B 377 LEU cc_start: 0.8296 (tp) cc_final: 0.8025 (tt) REVERT: B 398 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7852 (mm-40) REVERT: B 407 THR cc_start: 0.7614 (p) cc_final: 0.5591 (m) REVERT: B 411 TYR cc_start: 0.7277 (t80) cc_final: 0.6420 (t80) REVERT: B 420 PRO cc_start: 0.8299 (Cg_endo) cc_final: 0.7838 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7636 (p0) cc_final: 0.7336 (p0) REVERT: B 426 GLN cc_start: 0.7740 (pt0) cc_final: 0.7014 (pp30) REVERT: B 430 VAL cc_start: 0.7757 (p) cc_final: 0.7508 (t) REVERT: B 432 ARG cc_start: 0.6981 (mmt-90) cc_final: 0.6197 (mmt-90) REVERT: B 436 LEU cc_start: 0.8021 (mt) cc_final: 0.7423 (mt) REVERT: B 443 LEU cc_start: 0.7775 (tp) cc_final: 0.7257 (mm) REVERT: B 444 THR cc_start: 0.7138 (m) cc_final: 0.6443 (m) REVERT: B 452 TRP cc_start: 0.7751 (p90) cc_final: 0.7201 (p90) REVERT: B 467 LEU cc_start: 0.7029 (tp) cc_final: 0.6807 (tp) REVERT: B 481 PRO cc_start: 0.8281 (Cg_endo) cc_final: 0.7653 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8600 (m100) cc_final: 0.8273 (m100) REVERT: B 485 LEU cc_start: 0.8555 (mt) cc_final: 0.8327 (mt) REVERT: B 486 PHE cc_start: 0.7946 (m-10) cc_final: 0.7537 (m-10) REVERT: B 487 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.6755 (ttm110) REVERT: B 488 ASN cc_start: 0.7884 (t0) cc_final: 0.7429 (t0) REVERT: B 494 LEU cc_start: 0.8544 (mt) cc_final: 0.7996 (mm) REVERT: B 517 ARG cc_start: 0.8317 (mtt180) cc_final: 0.8088 (mtt180) REVERT: B 556 ASN cc_start: 0.8031 (t0) cc_final: 0.7403 (t0) REVERT: B 566 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6496 (tm-30) REVERT: B 577 PHE cc_start: 0.8177 (m-80) cc_final: 0.7899 (m-80) REVERT: B 580 GLU cc_start: 0.8444 (tp30) cc_final: 0.8110 (tp30) REVERT: B 592 ASP cc_start: 0.7908 (t0) cc_final: 0.7645 (m-30) REVERT: A 28 LYS cc_start: 0.7726 (mtmm) cc_final: 0.7518 (ptpp) REVERT: A 29 LYS cc_start: 0.7798 (pttm) cc_final: 0.7301 (pttt) REVERT: A 36 ASN cc_start: 0.8241 (p0) cc_final: 0.7844 (p0) REVERT: A 46 ASP cc_start: 0.7268 (t70) cc_final: 0.6645 (t70) REVERT: A 47 HIS cc_start: 0.7840 (t70) cc_final: 0.6713 (t70) REVERT: A 51 LEU cc_start: 0.8855 (tp) cc_final: 0.8590 (tp) REVERT: A 55 PHE cc_start: 0.7828 (m-10) cc_final: 0.7531 (m-10) REVERT: A 61 VAL cc_start: 0.8268 (m) cc_final: 0.8018 (p) REVERT: A 74 TYR cc_start: 0.7872 (m-80) cc_final: 0.6873 (m-80) REVERT: A 80 LYS cc_start: 0.8233 (mttm) cc_final: 0.8006 (mttm) REVERT: A 85 VAL cc_start: 0.8107 (t) cc_final: 0.7878 (p) REVERT: A 103 ASN cc_start: 0.7250 (m-40) cc_final: 0.6740 (m-40) REVERT: A 110 ASN cc_start: 0.7927 (m-40) cc_final: 0.7602 (p0) REVERT: A 114 GLU cc_start: 0.7461 (tt0) cc_final: 0.6909 (tt0) REVERT: A 132 LEU cc_start: 0.7769 (mm) cc_final: 0.7289 (mm) REVERT: A 143 ILE cc_start: 0.8914 (mt) cc_final: 0.8605 (mm) REVERT: A 163 GLN cc_start: 0.8704 (pt0) cc_final: 0.8249 (tt0) REVERT: A 172 PHE cc_start: 0.7722 (m-10) cc_final: 0.7456 (m-80) REVERT: A 176 MET cc_start: 0.8130 (ptp) cc_final: 0.7727 (ptt) REVERT: A 178 MET cc_start: 0.7993 (pmm) cc_final: 0.7790 (pmm) REVERT: A 209 LYS cc_start: 0.8101 (mttt) cc_final: 0.7531 (mtmt) REVERT: A 226 LYS cc_start: 0.7788 (mtpt) cc_final: 0.7171 (mtpt) REVERT: A 227 SER cc_start: 0.8084 (t) cc_final: 0.7872 (p) REVERT: A 230 ASP cc_start: 0.8393 (m-30) cc_final: 0.8104 (m-30) REVERT: A 233 HIS cc_start: 0.7538 (t-90) cc_final: 0.7270 (t-90) REVERT: A 254 PHE cc_start: 0.7313 (m-10) cc_final: 0.7039 (m-80) REVERT: A 255 ARG cc_start: 0.6719 (ttt-90) cc_final: 0.6311 (ttp80) REVERT: A 257 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7692 (mm-30) REVERT: A 261 LYS cc_start: 0.7508 (mttm) cc_final: 0.7247 (ptmt) REVERT: A 268 MET cc_start: 0.6275 (mtm) cc_final: 0.5139 (mtm) REVERT: A 277 MET cc_start: 0.6361 (mtt) cc_final: 0.5346 (mtt) REVERT: A 290 THR cc_start: 0.6891 (t) cc_final: 0.6483 (t) REVERT: A 293 LYS cc_start: 0.7744 (mtpp) cc_final: 0.7263 (tppt) REVERT: A 338 ASN cc_start: 0.7378 (p0) cc_final: 0.6649 (p0) REVERT: A 345 PHE cc_start: 0.8232 (m-80) cc_final: 0.7828 (m-80) REVERT: A 358 HIS cc_start: 0.8381 (m90) cc_final: 0.7822 (m90) REVERT: A 360 LYS cc_start: 0.8719 (tttt) cc_final: 0.8355 (tttt) REVERT: A 368 ASP cc_start: 0.4915 (m-30) cc_final: 0.4350 (m-30) REVERT: A 396 LYS cc_start: 0.8208 (tppp) cc_final: 0.7750 (tppp) REVERT: A 404 PHE cc_start: 0.7203 (p90) cc_final: 0.6302 (p90) REVERT: A 421 GLU cc_start: 0.8582 (tt0) cc_final: 0.7935 (tt0) REVERT: A 431 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7853 (mtmt) REVERT: A 432 GLN cc_start: 0.8628 (tp40) cc_final: 0.8369 (tp-100) REVERT: A 433 HIS cc_start: 0.8410 (m90) cc_final: 0.8124 (m90) REVERT: A 457 SER cc_start: 0.7533 (m) cc_final: 0.7267 (m) REVERT: A 460 ASP cc_start: 0.6910 (t70) cc_final: 0.6608 (t70) REVERT: A 476 ASN cc_start: 0.7624 (t0) cc_final: 0.7212 (t0) REVERT: A 496 GLU cc_start: 0.7728 (mp0) cc_final: 0.7456 (mp0) REVERT: A 521 ARG cc_start: 0.7729 (ptt180) cc_final: 0.7241 (tmm-80) REVERT: A 551 GLU cc_start: 0.8618 (pt0) cc_final: 0.8161 (pm20) REVERT: C 5 LYS cc_start: 0.8027 (mttt) cc_final: 0.7772 (tppp) REVERT: C 22 LEU cc_start: 0.7643 (mt) cc_final: 0.7375 (mt) REVERT: C 25 MET cc_start: 0.8070 (mmp) cc_final: 0.7431 (mmp) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.2649 time to fit residues: 124.8788 Evaluate side-chains 340 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 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 158 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 435 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.3679 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= 0.221 Angle : 0.640 10.274 12680 Z= 0.324 Chirality : 0.047 0.280 1417 Planarity : 0.005 0.061 1669 Dihedral : 6.900 72.030 1426 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % 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: -2.60 (0.23), residues: 1164 helix: -1.40 (0.76), residues: 48 sheet: -0.95 (0.70), residues: 64 loop : -2.01 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 477 HIS 0.007 0.001 HIS A 507 PHE 0.009 0.001 PHE A 180 TYR 0.018 0.002 TYR A 316 ARG 0.012 0.001 ARG B 434 *********************** 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 376 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 1.072 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: 0.6592 (pp30) cc_final: 0.4965 (mm-40) REVERT: B 31 MET cc_start: 0.7460 (mtp) cc_final: 0.7023 (ptp) REVERT: B 44 ASP cc_start: 0.7525 (t0) cc_final: 0.6605 (t0) REVERT: B 46 LEU cc_start: 0.8844 (mt) cc_final: 0.8383 (mt) REVERT: B 47 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7545 (ttp80) REVERT: B 54 GLN cc_start: 0.7190 (mt0) cc_final: 0.6895 (mp10) REVERT: B 55 VAL cc_start: 0.7483 (t) cc_final: 0.6743 (t) REVERT: B 59 ASN cc_start: 0.7251 (m-40) cc_final: 0.6760 (m-40) REVERT: B 61 GLU cc_start: 0.6908 (tm-30) cc_final: 0.5702 (tm-30) REVERT: B 64 TYR cc_start: 0.7765 (m-80) cc_final: 0.7302 (m-80) REVERT: B 65 LEU cc_start: 0.8302 (mt) cc_final: 0.8046 (mt) REVERT: B 70 SER cc_start: 0.8516 (p) cc_final: 0.8309 (p) REVERT: B 73 PHE cc_start: 0.8219 (p90) cc_final: 0.7920 (p90) REVERT: B 75 GLN cc_start: 0.7866 (pt0) cc_final: 0.7534 (pt0) REVERT: B 79 GLU cc_start: 0.6995 (tt0) cc_final: 0.6290 (tt0) REVERT: B 81 GLN cc_start: 0.6866 (mt0) cc_final: 0.6424 (mt0) REVERT: B 93 GLN cc_start: 0.8550 (pp30) cc_final: 0.8306 (tm-30) REVERT: B 100 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7663 (mmm-85) REVERT: B 103 ARG cc_start: 0.7442 (mmt90) cc_final: 0.7016 (ttm110) REVERT: B 105 THR cc_start: 0.7988 (p) cc_final: 0.7547 (t) REVERT: B 106 GLN cc_start: 0.7736 (mt0) cc_final: 0.7331 (mp10) REVERT: B 112 TYR cc_start: 0.7565 (m-80) cc_final: 0.6855 (m-80) REVERT: B 143 ARG cc_start: 0.7645 (mtt180) cc_final: 0.7023 (mtt180) REVERT: B 173 PHE cc_start: 0.7252 (m-10) cc_final: 0.7001 (m-10) REVERT: B 184 ILE cc_start: 0.8584 (mm) cc_final: 0.8345 (mm) REVERT: B 193 HIS cc_start: 0.7938 (m90) cc_final: 0.7331 (m90) REVERT: B 208 SER cc_start: 0.7792 (m) cc_final: 0.7534 (t) REVERT: B 248 LYS cc_start: 0.8593 (mmtt) cc_final: 0.7955 (mmtt) REVERT: B 251 ASP cc_start: 0.7517 (p0) cc_final: 0.7281 (p0) REVERT: B 267 HIS cc_start: 0.7624 (m170) cc_final: 0.7276 (m170) REVERT: B 271 LEU cc_start: 0.8619 (mp) cc_final: 0.8417 (mt) REVERT: B 274 TYR cc_start: 0.6779 (t80) cc_final: 0.6393 (t80) REVERT: B 275 ASN cc_start: 0.8016 (t0) cc_final: 0.7511 (t0) REVERT: B 282 MET cc_start: 0.8326 (mtp) cc_final: 0.7833 (mtp) REVERT: B 303 TYR cc_start: 0.8184 (m-80) cc_final: 0.7585 (m-80) REVERT: B 311 CYS cc_start: 0.4309 (p) cc_final: 0.3407 (m) REVERT: B 332 GLU cc_start: 0.7299 (mt-10) cc_final: 0.7079 (mt-10) REVERT: B 364 PHE cc_start: 0.8603 (m-80) cc_final: 0.7800 (m-80) REVERT: B 398 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7965 (mm-40) REVERT: B 411 TYR cc_start: 0.7370 (t80) cc_final: 0.6619 (t80) REVERT: B 420 PRO cc_start: 0.8346 (Cg_endo) cc_final: 0.8133 (Cg_exo) REVERT: B 422 LEU cc_start: 0.8552 (tp) cc_final: 0.7932 (mt) REVERT: B 425 PHE cc_start: 0.7975 (m-80) cc_final: 0.7590 (m-80) REVERT: B 426 GLN cc_start: 0.7794 (pt0) cc_final: 0.7151 (pp30) REVERT: B 432 ARG cc_start: 0.7136 (mmt-90) cc_final: 0.6756 (ttm-80) REVERT: B 444 THR cc_start: 0.7330 (m) cc_final: 0.6940 (m) REVERT: B 452 TRP cc_start: 0.7864 (p90) cc_final: 0.7247 (p90) REVERT: B 467 LEU cc_start: 0.7176 (tp) cc_final: 0.6956 (tp) REVERT: B 481 PRO cc_start: 0.8241 (Cg_endo) cc_final: 0.7694 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8653 (m100) cc_final: 0.8446 (m100) REVERT: B 487 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7530 (mmt90) REVERT: B 488 ASN cc_start: 0.7794 (t0) cc_final: 0.7344 (t0) REVERT: B 494 LEU cc_start: 0.8695 (mt) cc_final: 0.8369 (mt) REVERT: B 517 ARG cc_start: 0.8390 (mtt180) cc_final: 0.8148 (mtt180) REVERT: B 527 GLN cc_start: 0.7199 (pm20) cc_final: 0.5590 (pm20) REVERT: B 556 ASN cc_start: 0.8148 (t0) cc_final: 0.7493 (t0) REVERT: B 566 GLU cc_start: 0.7632 (mm-30) cc_final: 0.6460 (tm-30) REVERT: B 577 PHE cc_start: 0.8261 (m-80) cc_final: 0.7953 (m-80) REVERT: B 580 GLU cc_start: 0.8433 (tp30) cc_final: 0.8093 (tp30) REVERT: A 28 LYS cc_start: 0.7831 (mtmm) cc_final: 0.7537 (ptpp) REVERT: A 29 LYS cc_start: 0.8031 (pttm) cc_final: 0.7498 (pttt) REVERT: A 36 ASN cc_start: 0.8338 (p0) cc_final: 0.7885 (p0) REVERT: A 46 ASP cc_start: 0.7403 (t70) cc_final: 0.6811 (t70) REVERT: A 47 HIS cc_start: 0.7980 (t70) cc_final: 0.6899 (t70) REVERT: A 51 LEU cc_start: 0.8979 (tp) cc_final: 0.8683 (tp) REVERT: A 55 PHE cc_start: 0.8016 (m-10) cc_final: 0.7654 (m-10) REVERT: A 61 VAL cc_start: 0.8187 (m) cc_final: 0.7933 (p) REVERT: A 65 LEU cc_start: 0.7714 (tp) cc_final: 0.7432 (tt) REVERT: A 74 TYR cc_start: 0.8073 (m-80) cc_final: 0.7006 (m-80) REVERT: A 80 LYS cc_start: 0.8324 (mttm) cc_final: 0.8058 (mttm) REVERT: A 83 GLN cc_start: 0.7901 (mm110) cc_final: 0.7111 (mm110) REVERT: A 85 VAL cc_start: 0.8061 (t) cc_final: 0.7747 (p) REVERT: A 98 ARG cc_start: 0.7609 (ttt90) cc_final: 0.7127 (tpp80) REVERT: A 102 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6875 (mt-10) REVERT: A 103 ASN cc_start: 0.7333 (m-40) cc_final: 0.6423 (m-40) REVERT: A 114 GLU cc_start: 0.7821 (tt0) cc_final: 0.7139 (tt0) REVERT: A 132 LEU cc_start: 0.7560 (mm) cc_final: 0.7072 (mm) REVERT: A 143 ILE cc_start: 0.9000 (mt) cc_final: 0.8559 (mm) REVERT: A 162 ILE cc_start: 0.8576 (mm) cc_final: 0.8261 (mm) REVERT: A 163 GLN cc_start: 0.8494 (pt0) cc_final: 0.8173 (tt0) REVERT: A 172 PHE cc_start: 0.7884 (m-10) cc_final: 0.7644 (m-10) REVERT: A 176 MET cc_start: 0.8399 (ptp) cc_final: 0.7978 (ptt) REVERT: A 209 LYS cc_start: 0.8253 (mttt) cc_final: 0.7656 (mtmt) REVERT: A 230 ASP cc_start: 0.8442 (m-30) cc_final: 0.6769 (t70) REVERT: A 252 ARG cc_start: 0.7377 (mtp85) cc_final: 0.6903 (mtp85) REVERT: A 257 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8028 (mm-30) REVERT: A 261 LYS cc_start: 0.7569 (mttm) cc_final: 0.7270 (ptmt) REVERT: A 268 MET cc_start: 0.6289 (mtm) cc_final: 0.5230 (mtm) REVERT: A 277 MET cc_start: 0.6466 (mtt) cc_final: 0.5458 (mtt) REVERT: A 293 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7302 (tppt) REVERT: A 338 ASN cc_start: 0.7413 (p0) cc_final: 0.6373 (p0) REVERT: A 340 ILE cc_start: 0.7413 (mp) cc_final: 0.7147 (mp) REVERT: A 344 GLU cc_start: 0.7317 (tt0) cc_final: 0.7078 (tt0) REVERT: A 345 PHE cc_start: 0.8423 (m-80) cc_final: 0.7690 (m-80) REVERT: A 360 LYS cc_start: 0.8671 (tttt) cc_final: 0.8353 (tttt) REVERT: A 368 ASP cc_start: 0.4978 (m-30) cc_final: 0.4512 (m-30) REVERT: A 396 LYS cc_start: 0.8337 (tppp) cc_final: 0.7849 (tppp) REVERT: A 404 PHE cc_start: 0.7506 (p90) cc_final: 0.6405 (p90) REVERT: A 421 GLU cc_start: 0.8603 (tt0) cc_final: 0.7596 (tt0) REVERT: A 429 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7417 (mtt-85) REVERT: A 430 THR cc_start: 0.7530 (m) cc_final: 0.6459 (m) REVERT: A 431 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7982 (mtpt) REVERT: A 432 GLN cc_start: 0.8589 (tp40) cc_final: 0.8172 (tp-100) REVERT: A 433 HIS cc_start: 0.8404 (m90) cc_final: 0.8105 (m90) REVERT: A 451 ARG cc_start: 0.7124 (mtt90) cc_final: 0.6884 (ptp-170) REVERT: A 456 ILE cc_start: 0.8429 (mm) cc_final: 0.7582 (pt) REVERT: A 457 SER cc_start: 0.7928 (m) cc_final: 0.7506 (m) REVERT: A 476 ASN cc_start: 0.7735 (t0) cc_final: 0.7340 (t0) REVERT: A 496 GLU cc_start: 0.7770 (mp0) cc_final: 0.7476 (mp0) REVERT: A 551 GLU cc_start: 0.8634 (pt0) cc_final: 0.8222 (pm20) REVERT: C 22 LEU cc_start: 0.7829 (mt) cc_final: 0.7539 (mt) REVERT: C 25 MET cc_start: 0.8093 (mmp) cc_final: 0.7474 (mmp) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.2698 time to fit residues: 132.7262 Evaluate side-chains 350 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 chunk 112 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN 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 468 ASN A 565 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9358 Z= 0.264 Angle : 0.672 9.278 12680 Z= 0.343 Chirality : 0.048 0.277 1417 Planarity : 0.005 0.047 1669 Dihedral : 7.129 75.603 1426 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 0.10 % Allowed : 1.76 % Favored : 98.14 % 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: -2.52 (0.23), residues: 1164 helix: -1.83 (0.71), residues: 48 sheet: -0.84 (0.66), residues: 69 loop : -1.93 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 200 HIS 0.008 0.001 HIS A 507 PHE 0.016 0.002 PHE B 486 TYR 0.043 0.002 TYR A 117 ARG 0.010 0.001 ARG A 531 *********************** 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 384 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 383 time to evaluate : 0.979 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: 0.6656 (pp30) cc_final: 0.5638 (tm-30) REVERT: B 31 MET cc_start: 0.7477 (mtp) cc_final: 0.6360 (ptp) REVERT: B 44 ASP cc_start: 0.7450 (t0) cc_final: 0.6678 (t0) REVERT: B 45 MET cc_start: 0.8412 (tmm) cc_final: 0.8205 (tmm) REVERT: B 46 LEU cc_start: 0.8829 (mt) cc_final: 0.8286 (mt) REVERT: B 47 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7561 (ttp80) REVERT: B 55 VAL cc_start: 0.7739 (t) cc_final: 0.7217 (p) REVERT: B 59 ASN cc_start: 0.7304 (m-40) cc_final: 0.6794 (m-40) REVERT: B 60 LEU cc_start: 0.7797 (tp) cc_final: 0.7572 (tt) REVERT: B 61 GLU cc_start: 0.6908 (tm-30) cc_final: 0.4950 (tm-30) REVERT: B 64 TYR cc_start: 0.7862 (m-80) cc_final: 0.7411 (m-80) REVERT: B 65 LEU cc_start: 0.8210 (mt) cc_final: 0.7969 (mt) REVERT: B 70 SER cc_start: 0.8586 (p) cc_final: 0.8340 (p) REVERT: B 75 GLN cc_start: 0.7940 (pt0) cc_final: 0.7633 (pt0) REVERT: B 78 GLN cc_start: 0.7552 (pm20) cc_final: 0.7191 (pm20) REVERT: B 81 GLN cc_start: 0.6734 (mt0) cc_final: 0.6256 (mt0) REVERT: B 93 GLN cc_start: 0.8560 (pp30) cc_final: 0.7749 (tm-30) REVERT: B 100 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7694 (mmm-85) REVERT: B 103 ARG cc_start: 0.7315 (mmt90) cc_final: 0.6939 (ttm110) REVERT: B 105 THR cc_start: 0.8020 (p) cc_final: 0.7667 (t) REVERT: B 106 GLN cc_start: 0.7784 (mt0) cc_final: 0.7397 (mp10) REVERT: B 109 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7650 (mm-30) REVERT: B 112 TYR cc_start: 0.7635 (m-80) cc_final: 0.6913 (m-80) REVERT: B 139 GLU cc_start: 0.7322 (mp0) cc_final: 0.7110 (mp0) REVERT: B 143 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7335 (mtt180) REVERT: B 153 VAL cc_start: 0.7643 (t) cc_final: 0.7348 (t) REVERT: B 160 GLN cc_start: 0.6925 (tp40) cc_final: 0.6646 (tp40) REVERT: B 167 ILE cc_start: 0.8562 (mm) cc_final: 0.8047 (mm) REVERT: B 169 TRP cc_start: 0.8326 (m100) cc_final: 0.6848 (m100) REVERT: B 171 ASP cc_start: 0.8314 (t0) cc_final: 0.7677 (t0) REVERT: B 182 THR cc_start: 0.7675 (p) cc_final: 0.7377 (p) REVERT: B 185 ASP cc_start: 0.7065 (t0) cc_final: 0.6588 (t0) REVERT: B 193 HIS cc_start: 0.7954 (m90) cc_final: 0.7386 (m90) REVERT: B 208 SER cc_start: 0.7791 (m) cc_final: 0.7511 (t) REVERT: B 211 ASP cc_start: 0.7899 (m-30) cc_final: 0.7430 (m-30) REVERT: B 248 LYS cc_start: 0.8595 (mmtt) cc_final: 0.7908 (mmtt) REVERT: B 251 ASP cc_start: 0.7482 (p0) cc_final: 0.7220 (p0) REVERT: B 267 HIS cc_start: 0.7611 (m170) cc_final: 0.7180 (m170) REVERT: B 274 TYR cc_start: 0.6779 (t80) cc_final: 0.6335 (t80) REVERT: B 282 MET cc_start: 0.8353 (mtp) cc_final: 0.7883 (mtp) REVERT: B 288 ARG cc_start: 0.7909 (mmt90) cc_final: 0.7517 (mtt90) REVERT: B 303 TYR cc_start: 0.8257 (m-80) cc_final: 0.7610 (m-80) REVERT: B 311 CYS cc_start: 0.4252 (p) cc_final: 0.3470 (m) REVERT: B 319 ASN cc_start: 0.7670 (m-40) cc_final: 0.7452 (m-40) REVERT: B 332 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7087 (mt-10) REVERT: B 364 PHE cc_start: 0.8744 (m-80) cc_final: 0.7997 (m-80) REVERT: B 398 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7995 (mm-40) REVERT: B 405 GLU cc_start: 0.6605 (tp30) cc_final: 0.6157 (tp30) REVERT: B 407 THR cc_start: 0.7832 (p) cc_final: 0.7070 (m) REVERT: B 411 TYR cc_start: 0.7231 (t80) cc_final: 0.6519 (t80) REVERT: B 420 PRO cc_start: 0.8331 (Cg_endo) cc_final: 0.8105 (Cg_exo) REVERT: B 426 GLN cc_start: 0.7856 (pt0) cc_final: 0.7201 (pp30) REVERT: B 430 VAL cc_start: 0.7942 (t) cc_final: 0.7371 (p) REVERT: B 444 THR cc_start: 0.7393 (m) cc_final: 0.6966 (m) REVERT: B 452 TRP cc_start: 0.7944 (p90) cc_final: 0.7307 (p90) REVERT: B 481 PRO cc_start: 0.8242 (Cg_endo) cc_final: 0.7732 (Cg_exo) REVERT: B 483 ASP cc_start: 0.8556 (m-30) cc_final: 0.7829 (t0) REVERT: B 487 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.6794 (ttm-80) REVERT: B 488 ASN cc_start: 0.7796 (t0) cc_final: 0.7310 (t0) REVERT: B 493 LEU cc_start: 0.8173 (tp) cc_final: 0.7873 (tp) REVERT: B 517 ARG cc_start: 0.8379 (mtt180) cc_final: 0.8097 (mtt180) REVERT: B 527 GLN cc_start: 0.7119 (pm20) cc_final: 0.6009 (pm20) REVERT: B 556 ASN cc_start: 0.8204 (t0) cc_final: 0.7553 (t0) REVERT: B 566 GLU cc_start: 0.7701 (mm-30) cc_final: 0.6407 (tm-30) REVERT: B 577 PHE cc_start: 0.8393 (m-80) cc_final: 0.8019 (m-80) REVERT: B 580 GLU cc_start: 0.8404 (tp30) cc_final: 0.7966 (tp30) REVERT: A 28 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7582 (ptpp) REVERT: A 36 ASN cc_start: 0.8395 (p0) cc_final: 0.7891 (p0) REVERT: A 46 ASP cc_start: 0.7364 (t70) cc_final: 0.6704 (t70) REVERT: A 47 HIS cc_start: 0.8073 (t70) cc_final: 0.7065 (t70) REVERT: A 51 LEU cc_start: 0.9017 (tp) cc_final: 0.8670 (tp) REVERT: A 55 PHE cc_start: 0.8012 (m-10) cc_final: 0.7770 (m-10) REVERT: A 74 TYR cc_start: 0.8152 (m-80) cc_final: 0.7078 (m-80) REVERT: A 77 SER cc_start: 0.8161 (m) cc_final: 0.7184 (p) REVERT: A 80 LYS cc_start: 0.8332 (mttm) cc_final: 0.7986 (mttm) REVERT: A 85 VAL cc_start: 0.8053 (t) cc_final: 0.7700 (p) REVERT: A 98 ARG cc_start: 0.7510 (ttt90) cc_final: 0.7278 (tpp80) REVERT: A 132 LEU cc_start: 0.7583 (mm) cc_final: 0.7068 (mm) REVERT: A 137 MET cc_start: 0.8243 (mtm) cc_final: 0.7763 (mtm) REVERT: A 143 ILE cc_start: 0.9067 (mt) cc_final: 0.8634 (mm) REVERT: A 176 MET cc_start: 0.8630 (ptp) cc_final: 0.8047 (ptt) REVERT: A 209 LYS cc_start: 0.8270 (mttt) cc_final: 0.7698 (mtmm) REVERT: A 230 ASP cc_start: 0.8304 (m-30) cc_final: 0.6819 (p0) REVERT: A 257 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8013 (mm-30) REVERT: A 261 LYS cc_start: 0.7556 (mttm) cc_final: 0.7232 (ptmt) REVERT: A 268 MET cc_start: 0.6346 (mtm) cc_final: 0.5167 (mtm) REVERT: A 277 MET cc_start: 0.6616 (mtt) cc_final: 0.5508 (mtt) REVERT: A 293 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7001 (mtpp) REVERT: A 338 ASN cc_start: 0.7407 (p0) cc_final: 0.7109 (p0) REVERT: A 340 ILE cc_start: 0.7314 (mp) cc_final: 0.7095 (mp) REVERT: A 360 LYS cc_start: 0.8701 (tttt) cc_final: 0.8372 (tttt) REVERT: A 368 ASP cc_start: 0.5109 (m-30) cc_final: 0.4605 (m-30) REVERT: A 396 LYS cc_start: 0.8467 (tppp) cc_final: 0.7894 (tppp) REVERT: A 404 PHE cc_start: 0.7442 (p90) cc_final: 0.6407 (p90) REVERT: A 408 GLN cc_start: 0.6745 (mp10) cc_final: 0.6519 (mp10) REVERT: A 417 LEU cc_start: 0.7436 (mt) cc_final: 0.7119 (mp) REVERT: A 421 GLU cc_start: 0.8634 (tt0) cc_final: 0.7546 (tt0) REVERT: A 429 ARG cc_start: 0.8075 (mtt180) cc_final: 0.7536 (mtt-85) REVERT: A 432 GLN cc_start: 0.8588 (tp40) cc_final: 0.8214 (tp-100) REVERT: A 433 HIS cc_start: 0.8477 (m90) cc_final: 0.8093 (m90) REVERT: A 445 ILE cc_start: 0.7859 (pt) cc_final: 0.7634 (pt) REVERT: A 454 LYS cc_start: 0.8664 (mmtt) cc_final: 0.8107 (mmtt) REVERT: A 456 ILE cc_start: 0.8544 (mm) cc_final: 0.7863 (pt) REVERT: A 457 SER cc_start: 0.8103 (m) cc_final: 0.7743 (m) REVERT: A 460 ASP cc_start: 0.7408 (t70) cc_final: 0.6908 (t70) REVERT: A 463 ILE cc_start: 0.7096 (mt) cc_final: 0.6891 (mp) REVERT: A 475 ILE cc_start: 0.8354 (mm) cc_final: 0.8101 (mt) REVERT: A 476 ASN cc_start: 0.7746 (t0) cc_final: 0.7323 (t0) REVERT: A 496 GLU cc_start: 0.7793 (mp0) cc_final: 0.7505 (mp0) REVERT: A 551 GLU cc_start: 0.8651 (pt0) cc_final: 0.8223 (pm20) REVERT: A 559 HIS cc_start: 0.7783 (t70) cc_final: 0.7287 (t-170) REVERT: C 18 GLN cc_start: 0.7960 (tt0) cc_final: 0.7006 (tt0) REVERT: C 25 MET cc_start: 0.8071 (mmp) cc_final: 0.7543 (mmp) outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.2622 time to fit residues: 131.6554 Evaluate side-chains 351 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 0.0870 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 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 584 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9358 Z= 0.257 Angle : 0.686 11.072 12680 Z= 0.348 Chirality : 0.048 0.268 1417 Planarity : 0.005 0.048 1669 Dihedral : 7.326 77.228 1426 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 0.10 % Allowed : 0.78 % Favored : 99.12 % 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: -1.81 (0.74), residues: 48 sheet: -1.19 (0.67), residues: 64 loop : -1.86 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.004 TRP A 200 HIS 0.007 0.001 HIS A 507 PHE 0.012 0.002 PHE B 486 TYR 0.038 0.002 TYR A 117 ARG 0.010 0.001 ARG A 451 *********************** 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 386 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 1.112 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 24 GLN cc_start: 0.6872 (pp30) cc_final: 0.5488 (tm-30) REVERT: B 31 MET cc_start: 0.7454 (mtp) cc_final: 0.6425 (ptp) REVERT: B 44 ASP cc_start: 0.7610 (t0) cc_final: 0.6745 (t0) REVERT: B 45 MET cc_start: 0.8474 (tmm) cc_final: 0.8200 (tmm) REVERT: B 46 LEU cc_start: 0.8803 (mt) cc_final: 0.8219 (mt) REVERT: B 47 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7512 (ttp80) REVERT: B 55 VAL cc_start: 0.7791 (t) cc_final: 0.7318 (p) REVERT: B 61 GLU cc_start: 0.6928 (tm-30) cc_final: 0.4912 (tm-30) REVERT: B 81 GLN cc_start: 0.6744 (mt0) cc_final: 0.6300 (mt0) REVERT: B 93 GLN cc_start: 0.8561 (pp30) cc_final: 0.7246 (tt0) REVERT: B 100 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7852 (mmm-85) REVERT: B 105 THR cc_start: 0.8010 (p) cc_final: 0.7645 (t) REVERT: B 106 GLN cc_start: 0.7780 (mt0) cc_final: 0.7385 (mp10) REVERT: B 139 GLU cc_start: 0.7481 (mp0) cc_final: 0.7259 (mp0) REVERT: B 182 THR cc_start: 0.7783 (p) cc_final: 0.7422 (p) REVERT: B 185 ASP cc_start: 0.7092 (t0) cc_final: 0.6572 (t0) REVERT: B 208 SER cc_start: 0.7880 (m) cc_final: 0.7426 (t) REVERT: B 211 ASP cc_start: 0.7887 (m-30) cc_final: 0.6346 (p0) REVERT: B 237 HIS cc_start: 0.7474 (t-90) cc_final: 0.7241 (t-90) REVERT: B 239 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7590 (mp10) REVERT: B 248 LYS cc_start: 0.8547 (mmtt) cc_final: 0.7930 (mmtt) REVERT: B 267 HIS cc_start: 0.7650 (m170) cc_final: 0.7294 (m170) REVERT: B 274 TYR cc_start: 0.6687 (t80) cc_final: 0.6258 (t80) REVERT: B 282 MET cc_start: 0.8360 (mtp) cc_final: 0.7898 (mtp) REVERT: B 288 ARG cc_start: 0.7946 (mmt90) cc_final: 0.7692 (mtt90) REVERT: B 303 TYR cc_start: 0.8253 (m-80) cc_final: 0.7636 (m-80) REVERT: B 311 CYS cc_start: 0.4179 (p) cc_final: 0.3329 (m) REVERT: B 323 THR cc_start: 0.7598 (t) cc_final: 0.7221 (p) REVERT: B 332 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7057 (mt-10) REVERT: B 351 ARG cc_start: 0.7996 (mmp80) cc_final: 0.7787 (tpp-160) REVERT: B 364 PHE cc_start: 0.8790 (m-80) cc_final: 0.8112 (m-80) REVERT: B 377 LEU cc_start: 0.8224 (tt) cc_final: 0.8023 (tt) REVERT: B 398 GLN cc_start: 0.8265 (mm-40) cc_final: 0.8027 (mm-40) REVERT: B 405 GLU cc_start: 0.6625 (tp30) cc_final: 0.6076 (tp30) REVERT: B 407 THR cc_start: 0.7883 (p) cc_final: 0.7167 (m) REVERT: B 411 TYR cc_start: 0.7285 (t80) cc_final: 0.6475 (t80) REVERT: B 426 GLN cc_start: 0.7836 (pt0) cc_final: 0.7130 (pp30) REVERT: B 430 VAL cc_start: 0.7801 (t) cc_final: 0.7213 (p) REVERT: B 438 ASN cc_start: 0.8828 (m-40) cc_final: 0.8622 (m-40) REVERT: B 444 THR cc_start: 0.7542 (m) cc_final: 0.7202 (m) REVERT: B 451 SER cc_start: 0.8059 (p) cc_final: 0.7776 (m) REVERT: B 452 TRP cc_start: 0.7938 (p90) cc_final: 0.7561 (p90) REVERT: B 481 PRO cc_start: 0.8185 (Cg_endo) cc_final: 0.7682 (Cg_exo) REVERT: B 483 ASP cc_start: 0.8552 (m-30) cc_final: 0.7872 (t0) REVERT: B 487 ARG cc_start: 0.7736 (mmm-85) cc_final: 0.6834 (ttm-80) REVERT: B 488 ASN cc_start: 0.7851 (t0) cc_final: 0.7077 (t0) REVERT: B 491 GLN cc_start: 0.5951 (mt0) cc_final: 0.5428 (mt0) REVERT: B 493 LEU cc_start: 0.8260 (tp) cc_final: 0.7928 (tp) REVERT: B 517 ARG cc_start: 0.8463 (mtt180) cc_final: 0.8162 (mtt180) REVERT: B 527 GLN cc_start: 0.7051 (pm20) cc_final: 0.6489 (pm20) REVERT: B 556 ASN cc_start: 0.8267 (t0) cc_final: 0.7791 (t0) REVERT: B 577 PHE cc_start: 0.8419 (m-80) cc_final: 0.8024 (m-80) REVERT: B 580 GLU cc_start: 0.8382 (tp30) cc_final: 0.7939 (tp30) REVERT: A 28 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7452 (ptpp) REVERT: A 46 ASP cc_start: 0.7334 (t70) cc_final: 0.6752 (t70) REVERT: A 47 HIS cc_start: 0.8109 (t70) cc_final: 0.7093 (t70) REVERT: A 51 LEU cc_start: 0.9053 (tp) cc_final: 0.8670 (tp) REVERT: A 54 MET cc_start: 0.8293 (tpt) cc_final: 0.8065 (tpt) REVERT: A 74 TYR cc_start: 0.8188 (m-80) cc_final: 0.7111 (m-80) REVERT: A 76 LEU cc_start: 0.8341 (mt) cc_final: 0.8071 (mt) REVERT: A 77 SER cc_start: 0.8149 (m) cc_final: 0.7189 (p) REVERT: A 80 LYS cc_start: 0.8309 (mttm) cc_final: 0.8002 (mttm) REVERT: A 83 GLN cc_start: 0.7859 (mm110) cc_final: 0.7335 (mm110) REVERT: A 98 ARG cc_start: 0.7497 (ttt90) cc_final: 0.7202 (tpp80) REVERT: A 107 ILE cc_start: 0.8506 (mm) cc_final: 0.8224 (mm) REVERT: A 119 LEU cc_start: 0.7196 (tp) cc_final: 0.6549 (tp) REVERT: A 132 LEU cc_start: 0.7561 (mm) cc_final: 0.6992 (mm) REVERT: A 143 ILE cc_start: 0.9061 (mt) cc_final: 0.8587 (mm) REVERT: A 163 GLN cc_start: 0.8269 (pt0) cc_final: 0.8052 (tt0) REVERT: A 176 MET cc_start: 0.8653 (ptp) cc_final: 0.7953 (ptp) REVERT: A 196 ASN cc_start: 0.8940 (m-40) cc_final: 0.8623 (m110) REVERT: A 209 LYS cc_start: 0.8220 (mttt) cc_final: 0.7641 (mtmm) REVERT: A 217 GLN cc_start: 0.8383 (pt0) cc_final: 0.7884 (pt0) REVERT: A 252 ARG cc_start: 0.7490 (mtp85) cc_final: 0.7108 (mtp85) REVERT: A 254 PHE cc_start: 0.7353 (m-10) cc_final: 0.7110 (m-10) REVERT: A 256 ASP cc_start: 0.7478 (t70) cc_final: 0.7113 (t0) REVERT: A 257 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8035 (mm-30) REVERT: A 261 LYS cc_start: 0.7525 (mttm) cc_final: 0.7127 (mttm) REVERT: A 268 MET cc_start: 0.6383 (mtm) cc_final: 0.5211 (mtm) REVERT: A 277 MET cc_start: 0.6685 (mtt) cc_final: 0.5542 (mtt) REVERT: A 293 LYS cc_start: 0.7952 (mtpp) cc_final: 0.7101 (mtpp) REVERT: A 338 ASN cc_start: 0.7382 (p0) cc_final: 0.7058 (p0) REVERT: A 340 ILE cc_start: 0.7217 (mp) cc_final: 0.6994 (mp) REVERT: A 360 LYS cc_start: 0.8625 (tttt) cc_final: 0.8377 (tttt) REVERT: A 396 LYS cc_start: 0.8496 (tppp) cc_final: 0.7910 (tppp) REVERT: A 404 PHE cc_start: 0.7572 (p90) cc_final: 0.6807 (p90) REVERT: A 417 LEU cc_start: 0.7524 (mt) cc_final: 0.7263 (mp) REVERT: A 421 GLU cc_start: 0.8432 (tt0) cc_final: 0.7836 (tt0) REVERT: A 429 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7435 (mtt-85) REVERT: A 431 LYS cc_start: 0.8217 (mtmm) cc_final: 0.7926 (mtpt) REVERT: A 432 GLN cc_start: 0.8602 (tp40) cc_final: 0.8219 (tp-100) REVERT: A 433 HIS cc_start: 0.8474 (m90) cc_final: 0.8074 (m90) REVERT: A 445 ILE cc_start: 0.7982 (pt) cc_final: 0.7715 (pt) REVERT: A 454 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8146 (mmtt) REVERT: A 456 ILE cc_start: 0.8552 (mm) cc_final: 0.7988 (pt) REVERT: A 457 SER cc_start: 0.8055 (m) cc_final: 0.7729 (m) REVERT: A 460 ASP cc_start: 0.7314 (t70) cc_final: 0.7102 (t70) REVERT: A 475 ILE cc_start: 0.8317 (mm) cc_final: 0.8085 (mt) REVERT: A 476 ASN cc_start: 0.7769 (t0) cc_final: 0.7314 (t0) REVERT: A 496 GLU cc_start: 0.7820 (mp0) cc_final: 0.7540 (mp0) REVERT: A 551 GLU cc_start: 0.8611 (pt0) cc_final: 0.8187 (pm20) REVERT: A 559 HIS cc_start: 0.7752 (t70) cc_final: 0.7258 (t-170) REVERT: A 569 ILE cc_start: 0.8378 (tp) cc_final: 0.8007 (tp) REVERT: C 18 GLN cc_start: 0.8004 (tt0) cc_final: 0.7529 (tt0) REVERT: C 25 MET cc_start: 0.8147 (mmp) cc_final: 0.7560 (mmp) REVERT: C 31 ARG cc_start: 0.6795 (ttp-170) cc_final: 0.6473 (ttm170) outliers start: 1 outliers final: 0 residues processed: 385 average time/residue: 0.2779 time to fit residues: 140.8852 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 : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 71 optimal weight: 0.0870 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN ** B 302 ASN ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9358 Z= 0.272 Angle : 0.708 9.775 12680 Z= 0.362 Chirality : 0.049 0.261 1417 Planarity : 0.005 0.086 1669 Dihedral : 7.460 77.172 1426 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.09 % 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: -2.56 (0.24), residues: 1164 helix: -2.40 (0.61), residues: 60 sheet: -1.61 (0.59), residues: 78 loop : -1.85 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP A 200 HIS 0.008 0.001 HIS A 507 PHE 0.026 0.002 PHE B 73 TYR 0.026 0.002 TYR A 117 ARG 0.010 0.001 ARG B 143 *********************** 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 381 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 1.050 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: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6998 (pp30) cc_final: 0.5885 (mm-40) REVERT: B 31 MET cc_start: 0.7566 (mtp) cc_final: 0.6528 (ptp) REVERT: B 32 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7878 (mmtt) REVERT: B 44 ASP cc_start: 0.7438 (t0) cc_final: 0.6743 (t0) REVERT: B 45 MET cc_start: 0.8470 (tmm) cc_final: 0.8146 (tmm) REVERT: B 46 LEU cc_start: 0.8663 (mt) cc_final: 0.8184 (mt) REVERT: B 47 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7455 (ttp80) REVERT: B 55 VAL cc_start: 0.7786 (t) cc_final: 0.7453 (p) REVERT: B 59 ASN cc_start: 0.7417 (m-40) cc_final: 0.6911 (m-40) REVERT: B 61 GLU cc_start: 0.7064 (tm-30) cc_final: 0.3684 (tm-30) REVERT: B 65 LEU cc_start: 0.8190 (mt) cc_final: 0.7760 (mt) REVERT: B 75 GLN cc_start: 0.8027 (pt0) cc_final: 0.7752 (pt0) REVERT: B 81 GLN cc_start: 0.6612 (mt0) cc_final: 0.6254 (mt0) REVERT: B 93 GLN cc_start: 0.8499 (pp30) cc_final: 0.7666 (tm-30) REVERT: B 100 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7551 (ttp80) REVERT: B 105 THR cc_start: 0.7879 (p) cc_final: 0.7635 (t) REVERT: B 106 GLN cc_start: 0.7745 (mt0) cc_final: 0.7360 (mp10) REVERT: B 109 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7681 (mm-30) REVERT: B 139 GLU cc_start: 0.7399 (mp0) cc_final: 0.7090 (mp0) REVERT: B 143 ARG cc_start: 0.7588 (mtt180) cc_final: 0.7333 (ttm110) REVERT: B 160 GLN cc_start: 0.6948 (tp-100) cc_final: 0.6664 (tp-100) REVERT: B 164 GLN cc_start: 0.7750 (pm20) cc_final: 0.7409 (mm-40) REVERT: B 185 ASP cc_start: 0.7101 (t0) cc_final: 0.6765 (t0) REVERT: B 208 SER cc_start: 0.7883 (m) cc_final: 0.7674 (t) REVERT: B 248 LYS cc_start: 0.8665 (mmtt) cc_final: 0.8017 (mmtt) REVERT: B 253 LEU cc_start: 0.7724 (mt) cc_final: 0.7268 (mt) REVERT: B 265 GLU cc_start: 0.7024 (pm20) cc_final: 0.6357 (pm20) REVERT: B 274 TYR cc_start: 0.6720 (t80) cc_final: 0.6395 (t80) REVERT: B 275 ASN cc_start: 0.8043 (t0) cc_final: 0.7775 (t0) REVERT: B 282 MET cc_start: 0.8399 (mtp) cc_final: 0.7916 (mtp) REVERT: B 288 ARG cc_start: 0.8071 (mmt90) cc_final: 0.7635 (mtt90) REVERT: B 303 TYR cc_start: 0.8262 (m-80) cc_final: 0.7660 (m-80) REVERT: B 311 CYS cc_start: 0.4169 (p) cc_final: 0.3431 (m) REVERT: B 319 ASN cc_start: 0.7758 (m-40) cc_final: 0.7521 (m-40) REVERT: B 323 THR cc_start: 0.7606 (t) cc_final: 0.7272 (p) REVERT: B 332 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7087 (mt-10) REVERT: B 364 PHE cc_start: 0.8841 (m-80) cc_final: 0.8143 (m-80) REVERT: B 398 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7995 (mm-40) REVERT: B 407 THR cc_start: 0.7838 (p) cc_final: 0.7078 (m) REVERT: B 411 TYR cc_start: 0.7297 (t80) cc_final: 0.6470 (t80) REVERT: B 426 GLN cc_start: 0.7830 (pt0) cc_final: 0.7164 (pp30) REVERT: B 444 THR cc_start: 0.7454 (m) cc_final: 0.7139 (m) REVERT: B 452 TRP cc_start: 0.7987 (p90) cc_final: 0.7377 (p90) REVERT: B 481 PRO cc_start: 0.8158 (Cg_endo) cc_final: 0.7655 (Cg_exo) REVERT: B 483 ASP cc_start: 0.8557 (m-30) cc_final: 0.7924 (t0) REVERT: B 487 ARG cc_start: 0.7734 (mmm-85) cc_final: 0.7235 (mtt90) REVERT: B 488 ASN cc_start: 0.7878 (t0) cc_final: 0.7476 (t0) REVERT: B 491 GLN cc_start: 0.5953 (mt0) cc_final: 0.5584 (mt0) REVERT: B 493 LEU cc_start: 0.8289 (tp) cc_final: 0.7936 (tp) REVERT: B 517 ARG cc_start: 0.8485 (mtt180) cc_final: 0.8177 (mtt180) REVERT: B 527 GLN cc_start: 0.7082 (pm20) cc_final: 0.6188 (pm20) REVERT: B 556 ASN cc_start: 0.8273 (t0) cc_final: 0.7660 (t0) REVERT: B 577 PHE cc_start: 0.8492 (m-80) cc_final: 0.8005 (m-80) REVERT: B 580 GLU cc_start: 0.8341 (tp30) cc_final: 0.7997 (tp30) REVERT: A 28 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7552 (ptpp) REVERT: A 29 LYS cc_start: 0.8169 (pttm) cc_final: 0.7558 (pttm) REVERT: A 45 GLU cc_start: 0.8495 (mp0) cc_final: 0.8147 (mp0) REVERT: A 46 ASP cc_start: 0.7380 (t70) cc_final: 0.6887 (t70) REVERT: A 47 HIS cc_start: 0.8093 (t70) cc_final: 0.7001 (t70) REVERT: A 51 LEU cc_start: 0.9103 (tp) cc_final: 0.8706 (tp) REVERT: A 54 MET cc_start: 0.8352 (tpt) cc_final: 0.7991 (tpt) REVERT: A 55 PHE cc_start: 0.8026 (m-10) cc_final: 0.7807 (m-10) REVERT: A 74 TYR cc_start: 0.8252 (m-80) cc_final: 0.7120 (m-80) REVERT: A 77 SER cc_start: 0.8172 (m) cc_final: 0.7197 (p) REVERT: A 80 LYS cc_start: 0.8373 (mttm) cc_final: 0.8081 (mttm) REVERT: A 83 GLN cc_start: 0.7902 (mm110) cc_final: 0.7419 (mm110) REVERT: A 85 VAL cc_start: 0.8148 (t) cc_final: 0.7901 (p) REVERT: A 98 ARG cc_start: 0.7406 (ttt90) cc_final: 0.7140 (tpp80) REVERT: A 102 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7043 (mt-10) REVERT: A 119 LEU cc_start: 0.7074 (tp) cc_final: 0.6634 (tp) REVERT: A 132 LEU cc_start: 0.7576 (mm) cc_final: 0.6966 (mt) REVERT: A 143 ILE cc_start: 0.9055 (mt) cc_final: 0.8617 (mm) REVERT: A 163 GLN cc_start: 0.8162 (pt0) cc_final: 0.7855 (tt0) REVERT: A 176 MET cc_start: 0.8666 (ptp) cc_final: 0.8186 (ptt) REVERT: A 178 MET cc_start: 0.8123 (pmm) cc_final: 0.7918 (pmm) REVERT: A 196 ASN cc_start: 0.8899 (m-40) cc_final: 0.8553 (m110) REVERT: A 209 LYS cc_start: 0.8229 (mttt) cc_final: 0.7665 (mtmm) REVERT: A 252 ARG cc_start: 0.7475 (mtp85) cc_final: 0.7172 (mtp85) REVERT: A 254 PHE cc_start: 0.7371 (m-10) cc_final: 0.7159 (m-10) REVERT: A 255 ARG cc_start: 0.6878 (ttt-90) cc_final: 0.6479 (ttp80) REVERT: A 257 GLU cc_start: 0.8600 (mm-30) cc_final: 0.7935 (mm-30) REVERT: A 261 LYS cc_start: 0.7551 (mttm) cc_final: 0.7209 (ptmt) REVERT: A 262 ASP cc_start: 0.8274 (t0) cc_final: 0.7941 (t0) REVERT: A 268 MET cc_start: 0.6515 (mtm) cc_final: 0.5267 (mtm) REVERT: A 277 MET cc_start: 0.6709 (mtt) cc_final: 0.5562 (mtt) REVERT: A 290 THR cc_start: 0.7293 (t) cc_final: 0.6930 (t) REVERT: A 293 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7106 (mtpp) REVERT: A 307 CYS cc_start: 0.6434 (m) cc_final: 0.6209 (m) REVERT: A 316 TYR cc_start: 0.7803 (t80) cc_final: 0.7385 (t80) REVERT: A 338 ASN cc_start: 0.7468 (p0) cc_final: 0.6202 (p0) REVERT: A 340 ILE cc_start: 0.7220 (mp) cc_final: 0.6859 (mp) REVERT: A 345 PHE cc_start: 0.8471 (m-80) cc_final: 0.8108 (m-80) REVERT: A 360 LYS cc_start: 0.8650 (tttt) cc_final: 0.8333 (tttt) REVERT: A 396 LYS cc_start: 0.8523 (tppp) cc_final: 0.7900 (tppp) REVERT: A 404 PHE cc_start: 0.7446 (p90) cc_final: 0.6763 (p90) REVERT: A 408 GLN cc_start: 0.6803 (mp10) cc_final: 0.6533 (mp10) REVERT: A 417 LEU cc_start: 0.7567 (mt) cc_final: 0.7336 (mp) REVERT: A 421 GLU cc_start: 0.8489 (tt0) cc_final: 0.7875 (tt0) REVERT: A 429 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7433 (mtt-85) REVERT: A 431 LYS cc_start: 0.8212 (mtmm) cc_final: 0.7941 (mtpt) REVERT: A 432 GLN cc_start: 0.8623 (tp40) cc_final: 0.8234 (tp-100) REVERT: A 433 HIS cc_start: 0.8492 (m90) cc_final: 0.8020 (m90) REVERT: A 445 ILE cc_start: 0.7982 (pt) cc_final: 0.7677 (pt) REVERT: A 454 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8200 (mmtt) REVERT: A 456 ILE cc_start: 0.8573 (mm) cc_final: 0.8049 (pt) REVERT: A 457 SER cc_start: 0.8078 (m) cc_final: 0.7759 (m) REVERT: A 475 ILE cc_start: 0.8291 (mm) cc_final: 0.8059 (mt) REVERT: A 476 ASN cc_start: 0.7759 (t0) cc_final: 0.7308 (t0) REVERT: A 487 LYS cc_start: 0.7680 (mtmm) cc_final: 0.7442 (mtmm) REVERT: A 496 GLU cc_start: 0.7816 (mp0) cc_final: 0.7527 (mp0) REVERT: A 551 GLU cc_start: 0.8565 (pt0) cc_final: 0.8109 (pm20) REVERT: A 559 HIS cc_start: 0.7757 (t70) cc_final: 0.7267 (t-170) REVERT: C 18 GLN cc_start: 0.7968 (tt0) cc_final: 0.7316 (tt0) REVERT: C 25 MET cc_start: 0.8056 (mmp) cc_final: 0.7557 (mmp) REVERT: C 31 ARG cc_start: 0.6955 (ttp-170) cc_final: 0.6633 (ttp-110) outliers start: 1 outliers final: 0 residues processed: 380 average time/residue: 0.2687 time to fit residues: 133.2114 Evaluate side-chains 353 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 0.0470 chunk 110 optimal weight: 0.0030 chunk 67 optimal weight: 0.9980 overall best weight: 0.4488 ------------------------------------------------------------------------------- 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 237 HIS ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9358 Z= 0.212 Angle : 0.665 9.297 12680 Z= 0.334 Chirality : 0.048 0.261 1417 Planarity : 0.005 0.074 1669 Dihedral : 7.202 75.496 1426 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % 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: -2.50 (0.24), residues: 1164 helix: -2.59 (0.58), residues: 66 sheet: -1.69 (0.60), residues: 78 loop : -1.77 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP A 200 HIS 0.007 0.001 HIS B 249 PHE 0.024 0.002 PHE B 73 TYR 0.019 0.002 TYR A 113 ARG 0.007 0.001 ARG A 451 *********************** 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 378 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 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: B 31 MET cc_start: 0.7578 (mtp) cc_final: 0.6768 (ptp) REVERT: B 32 LYS cc_start: 0.8379 (mmtp) cc_final: 0.7816 (mmtt) REVERT: B 44 ASP cc_start: 0.7557 (t0) cc_final: 0.6700 (t0) REVERT: B 45 MET cc_start: 0.8446 (tmm) cc_final: 0.8110 (tmm) REVERT: B 46 LEU cc_start: 0.8705 (mt) cc_final: 0.8220 (mt) REVERT: B 47 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7420 (ttp80) REVERT: B 55 VAL cc_start: 0.7821 (t) cc_final: 0.6904 (p) REVERT: B 59 ASN cc_start: 0.7529 (m-40) cc_final: 0.6937 (m-40) REVERT: B 61 GLU cc_start: 0.6939 (tm-30) cc_final: 0.3876 (tm-30) REVERT: B 75 GLN cc_start: 0.7995 (pt0) cc_final: 0.7725 (pt0) REVERT: B 93 GLN cc_start: 0.8515 (pp30) cc_final: 0.7535 (tt0) REVERT: B 100 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7747 (mmm-85) REVERT: B 105 THR cc_start: 0.7885 (p) cc_final: 0.7610 (t) REVERT: B 106 GLN cc_start: 0.7785 (mt0) cc_final: 0.7374 (mp10) REVERT: B 139 GLU cc_start: 0.7392 (mp0) cc_final: 0.7171 (mp0) REVERT: B 155 ILE cc_start: 0.7854 (mm) cc_final: 0.7388 (mm) REVERT: B 157 ARG cc_start: 0.7583 (mtm-85) cc_final: 0.7338 (mtm-85) REVERT: B 164 GLN cc_start: 0.7652 (pm20) cc_final: 0.7216 (mm-40) REVERT: B 172 ILE cc_start: 0.7603 (mt) cc_final: 0.7331 (mt) REVERT: B 173 PHE cc_start: 0.7421 (m-10) cc_final: 0.6887 (m-10) REVERT: B 208 SER cc_start: 0.7909 (m) cc_final: 0.7709 (t) REVERT: B 213 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7248 (tm-30) REVERT: B 217 ARG cc_start: 0.7211 (mtp-110) cc_final: 0.6719 (mtt180) REVERT: B 248 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8005 (mmtt) REVERT: B 265 GLU cc_start: 0.7196 (pm20) cc_final: 0.6386 (pm20) REVERT: B 274 TYR cc_start: 0.6724 (t80) cc_final: 0.6204 (t80) REVERT: B 282 MET cc_start: 0.8349 (mtp) cc_final: 0.7958 (mtp) REVERT: B 288 ARG cc_start: 0.7994 (mmt90) cc_final: 0.7712 (mtt90) REVERT: B 303 TYR cc_start: 0.8050 (m-80) cc_final: 0.7668 (m-80) REVERT: B 311 CYS cc_start: 0.4070 (p) cc_final: 0.3523 (m) REVERT: B 319 ASN cc_start: 0.7723 (m-40) cc_final: 0.7475 (m-40) REVERT: B 332 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7041 (mt-10) REVERT: B 364 PHE cc_start: 0.8804 (m-80) cc_final: 0.8156 (m-80) REVERT: B 398 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7996 (mm-40) REVERT: B 407 THR cc_start: 0.7877 (p) cc_final: 0.7105 (m) REVERT: B 411 TYR cc_start: 0.7242 (t80) cc_final: 0.6422 (t80) REVERT: B 426 GLN cc_start: 0.7858 (pt0) cc_final: 0.7224 (pp30) REVERT: B 432 ARG cc_start: 0.7509 (ttm110) cc_final: 0.7136 (ttm110) REVERT: B 444 THR cc_start: 0.7406 (m) cc_final: 0.7095 (m) REVERT: B 452 TRP cc_start: 0.7956 (p90) cc_final: 0.7331 (p90) REVERT: B 481 PRO cc_start: 0.8144 (Cg_endo) cc_final: 0.7616 (Cg_exo) REVERT: B 487 ARG cc_start: 0.7745 (mmm-85) cc_final: 0.7129 (mtt90) REVERT: B 488 ASN cc_start: 0.7916 (t0) cc_final: 0.7617 (t0) REVERT: B 491 GLN cc_start: 0.5958 (mt0) cc_final: 0.5591 (mt0) REVERT: B 517 ARG cc_start: 0.8487 (mtt180) cc_final: 0.8192 (mtt180) REVERT: B 527 GLN cc_start: 0.7047 (pm20) cc_final: 0.6226 (pm20) REVERT: B 556 ASN cc_start: 0.8256 (t0) cc_final: 0.7645 (t0) REVERT: B 577 PHE cc_start: 0.8507 (m-80) cc_final: 0.7999 (m-80) REVERT: B 580 GLU cc_start: 0.8321 (tp30) cc_final: 0.7969 (tp30) REVERT: A 29 LYS cc_start: 0.8147 (pttm) cc_final: 0.7583 (pttm) REVERT: A 45 GLU cc_start: 0.8482 (mp0) cc_final: 0.8166 (mp0) REVERT: A 46 ASP cc_start: 0.7381 (t70) cc_final: 0.6914 (t70) REVERT: A 47 HIS cc_start: 0.7959 (t70) cc_final: 0.6949 (t70) REVERT: A 51 LEU cc_start: 0.9063 (tp) cc_final: 0.8607 (tp) REVERT: A 54 MET cc_start: 0.8359 (tpt) cc_final: 0.7992 (tpt) REVERT: A 55 PHE cc_start: 0.8054 (m-10) cc_final: 0.7832 (m-10) REVERT: A 74 TYR cc_start: 0.8212 (m-80) cc_final: 0.7090 (m-80) REVERT: A 76 LEU cc_start: 0.8180 (mt) cc_final: 0.7911 (mt) REVERT: A 77 SER cc_start: 0.8143 (m) cc_final: 0.7113 (p) REVERT: A 80 LYS cc_start: 0.8344 (mttm) cc_final: 0.8006 (mttm) REVERT: A 98 ARG cc_start: 0.7407 (ttt90) cc_final: 0.7148 (tpp80) REVERT: A 102 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6997 (mt-10) REVERT: A 114 GLU cc_start: 0.7435 (tt0) cc_final: 0.6688 (tt0) REVERT: A 119 LEU cc_start: 0.7202 (tp) cc_final: 0.6767 (tp) REVERT: A 132 LEU cc_start: 0.7553 (mm) cc_final: 0.6910 (mm) REVERT: A 143 ILE cc_start: 0.9065 (mt) cc_final: 0.8645 (mm) REVERT: A 176 MET cc_start: 0.8650 (ptp) cc_final: 0.8157 (ptt) REVERT: A 196 ASN cc_start: 0.8899 (m-40) cc_final: 0.8561 (m110) REVERT: A 209 LYS cc_start: 0.8167 (mttt) cc_final: 0.7515 (mtmm) REVERT: A 252 ARG cc_start: 0.7489 (mtp85) cc_final: 0.7171 (mtp85) REVERT: A 254 PHE cc_start: 0.7319 (m-10) cc_final: 0.7043 (m-10) REVERT: A 255 ARG cc_start: 0.6785 (ttt-90) cc_final: 0.6418 (ttp80) REVERT: A 257 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7872 (mm-30) REVERT: A 261 LYS cc_start: 0.7493 (mttm) cc_final: 0.7140 (mttm) REVERT: A 268 MET cc_start: 0.6485 (mtm) cc_final: 0.5197 (mtm) REVERT: A 277 MET cc_start: 0.6664 (mtt) cc_final: 0.5517 (mtt) REVERT: A 290 THR cc_start: 0.7252 (t) cc_final: 0.6889 (t) REVERT: A 293 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7731 (mtpp) REVERT: A 316 TYR cc_start: 0.7693 (t80) cc_final: 0.7275 (t80) REVERT: A 338 ASN cc_start: 0.7503 (p0) cc_final: 0.7242 (p0) REVERT: A 340 ILE cc_start: 0.7171 (mp) cc_final: 0.6940 (mp) REVERT: A 344 GLU cc_start: 0.7405 (tt0) cc_final: 0.7179 (tt0) REVERT: A 360 LYS cc_start: 0.8576 (tttt) cc_final: 0.8277 (tttt) REVERT: A 377 ARG cc_start: 0.7940 (ptm-80) cc_final: 0.7419 (ptm-80) REVERT: A 396 LYS cc_start: 0.8432 (tppp) cc_final: 0.7814 (tppp) REVERT: A 404 PHE cc_start: 0.7499 (p90) cc_final: 0.6741 (p90) REVERT: A 408 GLN cc_start: 0.6888 (mp10) cc_final: 0.6616 (mp10) REVERT: A 417 LEU cc_start: 0.7415 (mt) cc_final: 0.7105 (mp) REVERT: A 421 GLU cc_start: 0.8499 (tt0) cc_final: 0.7818 (tt0) REVERT: A 429 ARG cc_start: 0.8120 (mtt180) cc_final: 0.7360 (mtt-85) REVERT: A 432 GLN cc_start: 0.8569 (tp40) cc_final: 0.8191 (tp-100) REVERT: A 433 HIS cc_start: 0.8564 (m90) cc_final: 0.8020 (m90) REVERT: A 445 ILE cc_start: 0.8027 (pt) cc_final: 0.7762 (pt) REVERT: A 454 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8158 (mmtt) REVERT: A 456 ILE cc_start: 0.8555 (mm) cc_final: 0.8050 (pt) REVERT: A 457 SER cc_start: 0.8060 (m) cc_final: 0.7715 (m) REVERT: A 475 ILE cc_start: 0.8189 (mm) cc_final: 0.7979 (mt) REVERT: A 476 ASN cc_start: 0.7674 (t0) cc_final: 0.7230 (t0) REVERT: A 487 LYS cc_start: 0.7697 (mtmm) cc_final: 0.7495 (mtmm) REVERT: A 496 GLU cc_start: 0.7801 (mp0) cc_final: 0.7402 (mp0) REVERT: A 551 GLU cc_start: 0.8545 (pt0) cc_final: 0.8123 (pm20) REVERT: A 559 HIS cc_start: 0.7771 (t70) cc_final: 0.7320 (t-170) REVERT: A 569 ILE cc_start: 0.8017 (tp) cc_final: 0.7817 (tp) REVERT: C 18 GLN cc_start: 0.8035 (tt0) cc_final: 0.7493 (tt0) REVERT: C 25 MET cc_start: 0.7955 (mmp) cc_final: 0.7492 (mmp) REVERT: C 31 ARG cc_start: 0.7048 (ttp-170) cc_final: 0.6551 (ttm170) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.2766 time to fit residues: 135.4866 Evaluate side-chains 348 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 0.1980 chunk 115 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 0.0970 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 0.0070 chunk 98 optimal weight: 0.0770 chunk 28 optimal weight: 0.5980 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 HIS B 329 GLN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN A 83 GLN A 163 GLN A 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9358 Z= 0.180 Angle : 0.666 9.588 12680 Z= 0.335 Chirality : 0.048 0.258 1417 Planarity : 0.005 0.072 1669 Dihedral : 6.913 70.755 1426 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.20 % Allowed : 0.10 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -2.38 (0.24), residues: 1164 helix: -2.41 (0.64), residues: 60 sheet: -1.66 (0.62), residues: 78 loop : -1.69 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 200 HIS 0.006 0.001 HIS B 249 PHE 0.017 0.001 PHE B 73 TYR 0.024 0.002 TYR A 117 ARG 0.008 0.001 ARG B 190 ********************** 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 373 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 371 time to evaluate : 0.995 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: 0.7445 (pp30) cc_final: 0.6947 (pt0) REVERT: B 31 MET cc_start: 0.7437 (mtp) cc_final: 0.6663 (ptp) REVERT: B 44 ASP cc_start: 0.7434 (t0) cc_final: 0.6635 (t0) REVERT: B 45 MET cc_start: 0.8325 (tmm) cc_final: 0.8039 (tmm) REVERT: B 46 LEU cc_start: 0.8670 (mt) cc_final: 0.8220 (mt) REVERT: B 47 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7413 (ttp80) REVERT: B 54 GLN cc_start: 0.6916 (mp10) cc_final: 0.6342 (mp10) REVERT: B 55 VAL cc_start: 0.7745 (t) cc_final: 0.7385 (p) REVERT: B 59 ASN cc_start: 0.7564 (m-40) cc_final: 0.6959 (m-40) REVERT: B 61 GLU cc_start: 0.6885 (tm-30) cc_final: 0.3955 (tm-30) REVERT: B 65 LEU cc_start: 0.8276 (mt) cc_final: 0.7909 (mt) REVERT: B 75 GLN cc_start: 0.8027 (pt0) cc_final: 0.7736 (pt0) REVERT: B 97 GLN cc_start: 0.7694 (mp-120) cc_final: 0.7022 (mp10) REVERT: B 100 ARG cc_start: 0.7885 (ttm-80) cc_final: 0.7196 (ttp80) REVERT: B 106 GLN cc_start: 0.7766 (mt0) cc_final: 0.7385 (mp10) REVERT: B 155 ILE cc_start: 0.7888 (mm) cc_final: 0.7560 (mm) REVERT: B 160 GLN cc_start: 0.6604 (tp40) cc_final: 0.6289 (tp40) REVERT: B 173 PHE cc_start: 0.7378 (m-10) cc_final: 0.6652 (m-10) REVERT: B 185 ASP cc_start: 0.7500 (t0) cc_final: 0.7201 (m-30) REVERT: B 211 ASP cc_start: 0.7958 (m-30) cc_final: 0.7526 (m-30) REVERT: B 213 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7615 (tm-30) REVERT: B 217 ARG cc_start: 0.7256 (mtp-110) cc_final: 0.6762 (mtt180) REVERT: B 237 HIS cc_start: 0.7246 (t-90) cc_final: 0.6926 (t70) REVERT: B 248 LYS cc_start: 0.8670 (mmtt) cc_final: 0.7987 (mmtt) REVERT: B 250 SER cc_start: 0.8365 (p) cc_final: 0.8156 (p) REVERT: B 258 PHE cc_start: 0.7561 (m-80) cc_final: 0.7066 (m-80) REVERT: B 265 GLU cc_start: 0.7157 (pm20) cc_final: 0.6531 (pm20) REVERT: B 266 LEU cc_start: 0.8327 (mm) cc_final: 0.8125 (mm) REVERT: B 267 HIS cc_start: 0.7977 (m170) cc_final: 0.7510 (m170) REVERT: B 274 TYR cc_start: 0.6870 (t80) cc_final: 0.6246 (t80) REVERT: B 282 MET cc_start: 0.8413 (mtp) cc_final: 0.7938 (mtp) REVERT: B 288 ARG cc_start: 0.7993 (mmt90) cc_final: 0.7557 (mtt90) REVERT: B 303 TYR cc_start: 0.8092 (m-80) cc_final: 0.7568 (m-80) REVERT: B 319 ASN cc_start: 0.7687 (m-40) cc_final: 0.7468 (m-40) REVERT: B 329 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: B 332 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7042 (mt-10) REVERT: B 364 PHE cc_start: 0.8817 (m-80) cc_final: 0.8189 (m-80) REVERT: B 368 LYS cc_start: 0.8443 (ttmm) cc_final: 0.8206 (ttmm) REVERT: B 398 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7973 (mm-40) REVERT: B 405 GLU cc_start: 0.6421 (mm-30) cc_final: 0.5787 (mm-30) REVERT: B 407 THR cc_start: 0.7901 (p) cc_final: 0.7011 (m) REVERT: B 411 TYR cc_start: 0.7188 (t80) cc_final: 0.6539 (t80) REVERT: B 426 GLN cc_start: 0.7809 (pt0) cc_final: 0.7185 (pp30) REVERT: B 452 TRP cc_start: 0.7930 (p90) cc_final: 0.7252 (p90) REVERT: B 481 PRO cc_start: 0.8114 (Cg_endo) cc_final: 0.7633 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8473 (m100) cc_final: 0.8265 (m100) REVERT: B 487 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.6765 (ttm-80) REVERT: B 488 ASN cc_start: 0.7966 (t0) cc_final: 0.7634 (t0) REVERT: B 491 GLN cc_start: 0.6046 (mt0) cc_final: 0.5654 (mt0) REVERT: B 493 LEU cc_start: 0.8327 (tp) cc_final: 0.7953 (tp) REVERT: B 494 LEU cc_start: 0.8612 (mt) cc_final: 0.8361 (mt) REVERT: B 517 ARG cc_start: 0.8482 (mtt180) cc_final: 0.8177 (mtt180) REVERT: B 539 GLU cc_start: 0.7593 (tp30) cc_final: 0.7372 (tp30) REVERT: B 556 ASN cc_start: 0.8254 (t0) cc_final: 0.7644 (t0) REVERT: B 577 PHE cc_start: 0.8502 (m-80) cc_final: 0.8001 (m-80) REVERT: B 580 GLU cc_start: 0.8341 (tp30) cc_final: 0.7945 (tp30) REVERT: A 29 LYS cc_start: 0.8080 (pttm) cc_final: 0.7496 (pttm) REVERT: A 45 GLU cc_start: 0.8477 (mp0) cc_final: 0.8149 (mp0) REVERT: A 46 ASP cc_start: 0.7305 (t70) cc_final: 0.6836 (t70) REVERT: A 47 HIS cc_start: 0.7858 (t70) cc_final: 0.6730 (t70) REVERT: A 51 LEU cc_start: 0.9023 (tp) cc_final: 0.8540 (tp) REVERT: A 54 MET cc_start: 0.8333 (tpt) cc_final: 0.7973 (tpt) REVERT: A 55 PHE cc_start: 0.8032 (m-10) cc_final: 0.7769 (m-10) REVERT: A 74 TYR cc_start: 0.8133 (m-80) cc_final: 0.7088 (m-80) REVERT: A 76 LEU cc_start: 0.8142 (mt) cc_final: 0.7842 (mt) REVERT: A 77 SER cc_start: 0.8156 (m) cc_final: 0.7079 (p) REVERT: A 80 LYS cc_start: 0.8355 (mttm) cc_final: 0.8092 (mttm) REVERT: A 98 ARG cc_start: 0.7465 (ttt90) cc_final: 0.7241 (tpp80) REVERT: A 102 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6863 (mt-10) REVERT: A 103 ASN cc_start: 0.7289 (m-40) cc_final: 0.6781 (m-40) REVERT: A 105 GLN cc_start: 0.8063 (mt0) cc_final: 0.7671 (mm110) REVERT: A 107 ILE cc_start: 0.8609 (mm) cc_final: 0.8316 (mm) REVERT: A 111 MET cc_start: 0.7070 (ttt) cc_final: 0.6328 (ttt) REVERT: A 112 TYR cc_start: 0.6424 (m-10) cc_final: 0.6202 (m-10) REVERT: A 114 GLU cc_start: 0.7339 (tt0) cc_final: 0.6726 (tt0) REVERT: A 119 LEU cc_start: 0.7211 (tp) cc_final: 0.6805 (tp) REVERT: A 125 TYR cc_start: 0.6796 (p90) cc_final: 0.6532 (p90) REVERT: A 132 LEU cc_start: 0.7549 (mm) cc_final: 0.6982 (mt) REVERT: A 143 ILE cc_start: 0.8973 (mt) cc_final: 0.8537 (mm) REVERT: A 163 GLN cc_start: 0.8524 (tt0) cc_final: 0.8146 (tt0) REVERT: A 166 ASP cc_start: 0.7917 (p0) cc_final: 0.7595 (p0) REVERT: A 176 MET cc_start: 0.8662 (ptp) cc_final: 0.8145 (ptt) REVERT: A 196 ASN cc_start: 0.8952 (m-40) cc_final: 0.8619 (m110) REVERT: A 209 LYS cc_start: 0.8022 (mttt) cc_final: 0.7436 (mtmm) REVERT: A 212 LYS cc_start: 0.7175 (ttmm) cc_final: 0.6870 (ttmm) REVERT: A 252 ARG cc_start: 0.7470 (mtp85) cc_final: 0.7172 (mtp85) REVERT: A 254 PHE cc_start: 0.7335 (m-10) cc_final: 0.7020 (m-10) REVERT: A 256 ASP cc_start: 0.7495 (t70) cc_final: 0.7116 (t0) REVERT: A 257 GLU cc_start: 0.8543 (mm-30) cc_final: 0.7940 (mm-30) REVERT: A 261 LYS cc_start: 0.7518 (mttm) cc_final: 0.7065 (mttm) REVERT: A 268 MET cc_start: 0.6403 (mtm) cc_final: 0.5087 (mtm) REVERT: A 277 MET cc_start: 0.6624 (mtt) cc_final: 0.5431 (mtt) REVERT: A 293 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7745 (mtpp) REVERT: A 316 TYR cc_start: 0.7612 (t80) cc_final: 0.7219 (t80) REVERT: A 325 LYS cc_start: 0.8175 (mttt) cc_final: 0.7675 (mttt) REVERT: A 338 ASN cc_start: 0.7419 (p0) cc_final: 0.7159 (p0) REVERT: A 340 ILE cc_start: 0.7153 (mp) cc_final: 0.6936 (mp) REVERT: A 360 LYS cc_start: 0.8547 (tttt) cc_final: 0.8259 (tttt) REVERT: A 368 ASP cc_start: 0.5109 (m-30) cc_final: 0.4672 (m-30) REVERT: A 371 ILE cc_start: 0.7377 (mm) cc_final: 0.6955 (mm) REVERT: A 377 ARG cc_start: 0.7946 (ptm-80) cc_final: 0.7507 (ptp-110) REVERT: A 396 LYS cc_start: 0.8443 (tppp) cc_final: 0.7772 (tppp) REVERT: A 404 PHE cc_start: 0.7373 (p90) cc_final: 0.6380 (p90) REVERT: A 421 GLU cc_start: 0.8499 (tt0) cc_final: 0.7795 (tt0) REVERT: A 429 ARG cc_start: 0.8078 (mtt180) cc_final: 0.7231 (mtt-85) REVERT: A 432 GLN cc_start: 0.8582 (tp40) cc_final: 0.8257 (tp-100) REVERT: A 433 HIS cc_start: 0.8467 (m90) cc_final: 0.7999 (m90) REVERT: A 454 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8113 (mmtt) REVERT: A 456 ILE cc_start: 0.8567 (mm) cc_final: 0.8012 (pt) REVERT: A 457 SER cc_start: 0.7979 (m) cc_final: 0.7613 (m) REVERT: A 476 ASN cc_start: 0.7647 (t0) cc_final: 0.7212 (t0) REVERT: A 487 LYS cc_start: 0.7776 (mtmm) cc_final: 0.7505 (mtmm) REVERT: A 496 GLU cc_start: 0.7793 (mp0) cc_final: 0.7403 (mp0) REVERT: A 548 GLU cc_start: 0.7175 (mp0) cc_final: 0.6883 (mp0) REVERT: A 551 GLU cc_start: 0.8522 (pt0) cc_final: 0.8132 (pm20) REVERT: A 559 HIS cc_start: 0.7707 (t70) cc_final: 0.7226 (t-170) REVERT: C 18 GLN cc_start: 0.8041 (tt0) cc_final: 0.7557 (tt0) REVERT: C 25 MET cc_start: 0.7903 (mmp) cc_final: 0.7371 (mmp) REVERT: C 31 ARG cc_start: 0.7051 (ttp-170) cc_final: 0.6655 (ttm170) outliers start: 2 outliers final: 0 residues processed: 371 average time/residue: 0.2726 time to fit residues: 131.7292 Evaluate side-chains 352 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 351 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.0030 chunk 92 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.0470 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 overall best weight: 0.3288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.127283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.101587 restraints weight = 16260.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106890 restraints weight = 9267.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.110684 restraints weight = 5911.915| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9358 Z= 0.199 Angle : 0.679 9.737 12680 Z= 0.339 Chirality : 0.048 0.255 1417 Planarity : 0.005 0.073 1669 Dihedral : 6.815 68.524 1426 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % 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 : 1.67 % 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: -2.21 (0.70), residues: 54 sheet: -1.55 (0.68), residues: 68 loop : -1.67 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 200 HIS 0.006 0.001 HIS B 249 PHE 0.017 0.001 PHE B 73 TYR 0.032 0.002 TYR B 64 ARG 0.007 0.001 ARG B 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3196.98 seconds wall clock time: 58 minutes 18.40 seconds (3498.40 seconds total)