Starting phenix.real_space_refine on Thu Mar 14 18:40:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/03_2024/8hgp_34745.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/03_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_34745/03_2024/8hgp_34745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/03_2024/8hgp_34745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/03_2024/8hgp_34745.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/03_2024/8hgp_34745.pdb" } 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 Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B ARG 558": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 531": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.14, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 2.99 Conformation dependent library (CDL) restraints added in 1.6 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: 1.07 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: 3.33 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: 100.45 - 107.16: 354 107.16 - 113.86: 5134 113.86 - 120.56: 3438 120.56 - 127.26: 3658 127.26 - 133.96: 96 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 2.440 nonbonded pdb=" O VAL B 356 " pdb=" OG SER B 380 " model vdw 2.328 2.440 nonbonded pdb=" NH1 ARG B 103 " pdb=" O LEU B 256 " model vdw 2.392 2.520 nonbonded pdb=" OG SER B 373 " pdb=" O TYR B 409 " model vdw 2.396 2.440 nonbonded pdb=" NH2 ARG B 34 " pdb=" OD1 ASN B 438 " model vdw 2.398 2.520 ... (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 ========== 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 11.160 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.690 Find NCS groups from input model: 0.310 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.530 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 394 time to evaluate : 1.070 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: 0.2372 time to fit residues: 122.9100 Evaluate side-chains 347 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 346 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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: 0.9980 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 55 optimal weight: 0.0030 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 overall best weight: 0.3348 ------------------------------------------------------------------------------- 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 110 ASN A 158 ASN A 408 GLN A 432 GLN A 433 HIS A 486 GLN A 493 ASN C 28 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9358 Z= 0.189 Angle : 0.593 9.625 12680 Z= 0.300 Chirality : 0.046 0.261 1417 Planarity : 0.005 0.061 1669 Dihedral : 9.228 93.038 1426 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.94 % 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: -3.42 (0.21), residues: 1164 helix: -2.71 (0.63), residues: 57 sheet: -2.73 (0.56), residues: 67 loop : -2.48 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 452 HIS 0.004 0.001 HIS A 507 PHE 0.019 0.001 PHE A 180 TYR 0.011 0.001 TYR C 13 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 380 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 379 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.5736 (pp30) cc_final: 0.4544 (mm-40) REVERT: B 31 MET cc_start: 0.7706 (mtp) cc_final: 0.7051 (ptp) REVERT: B 32 LYS cc_start: 0.8093 (mptt) cc_final: 0.7827 (mmtt) REVERT: B 44 ASP cc_start: 0.7132 (t0) cc_final: 0.4801 (t0) REVERT: B 46 LEU cc_start: 0.8732 (mt) cc_final: 0.8438 (mt) REVERT: B 47 ARG cc_start: 0.7620 (ttp80) cc_final: 0.6724 (ttp80) REVERT: B 54 GLN cc_start: 0.7007 (mt0) cc_final: 0.6617 (tp-100) REVERT: B 56 VAL cc_start: 0.8060 (t) cc_final: 0.7639 (t) REVERT: B 59 ASN cc_start: 0.6737 (m-40) cc_final: 0.6287 (m-40) REVERT: B 61 GLU cc_start: 0.6393 (mt-10) cc_final: 0.5636 (mt-10) REVERT: B 65 LEU cc_start: 0.8330 (mt) cc_final: 0.8102 (mt) REVERT: B 73 PHE cc_start: 0.8094 (p90) cc_final: 0.7785 (p90) REVERT: B 74 LEU cc_start: 0.8386 (mt) cc_final: 0.8152 (mt) REVERT: B 75 GLN cc_start: 0.7798 (pt0) cc_final: 0.7514 (pt0) REVERT: B 79 GLU cc_start: 0.6982 (tt0) cc_final: 0.6383 (tt0) REVERT: B 81 GLN cc_start: 0.6689 (mt0) cc_final: 0.6208 (mt0) REVERT: B 92 ARG cc_start: 0.7626 (mtt90) cc_final: 0.7168 (mmm-85) REVERT: B 93 GLN cc_start: 0.8484 (pp30) cc_final: 0.8127 (tm-30) REVERT: B 94 VAL cc_start: 0.8940 (t) cc_final: 0.8725 (t) REVERT: B 105 THR cc_start: 0.7553 (p) cc_final: 0.6649 (t) REVERT: B 106 GLN cc_start: 0.7586 (mt0) cc_final: 0.7033 (mp-120) REVERT: B 116 VAL cc_start: 0.6878 (t) cc_final: 0.6499 (p) REVERT: B 160 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7152 (tp40) REVERT: B 173 PHE cc_start: 0.6816 (m-10) cc_final: 0.6407 (m-10) REVERT: B 185 ASP cc_start: 0.7057 (t0) cc_final: 0.6847 (t0) REVERT: B 193 HIS cc_start: 0.7886 (m90) cc_final: 0.7285 (m90) REVERT: B 211 ASP cc_start: 0.7699 (m-30) cc_final: 0.6398 (p0) REVERT: B 248 LYS cc_start: 0.8614 (mmtt) cc_final: 0.7979 (mmtt) REVERT: B 251 ASP cc_start: 0.7730 (p0) cc_final: 0.7372 (p0) REVERT: B 265 GLU cc_start: 0.6843 (pm20) cc_final: 0.6571 (pm20) REVERT: B 271 LEU cc_start: 0.8376 (mp) cc_final: 0.8059 (mm) REVERT: B 274 TYR cc_start: 0.6657 (t80) cc_final: 0.6230 (t80) REVERT: B 275 ASN cc_start: 0.8182 (t0) cc_final: 0.7518 (t0) REVERT: B 282 MET cc_start: 0.8015 (mtp) cc_final: 0.7428 (mtp) REVERT: B 303 TYR cc_start: 0.7868 (m-80) cc_final: 0.7285 (m-80) REVERT: B 332 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6533 (mp0) REVERT: B 376 PHE cc_start: 0.8122 (m-10) cc_final: 0.7921 (m-80) REVERT: B 377 LEU cc_start: 0.8318 (tp) cc_final: 0.8059 (tt) REVERT: B 411 TYR cc_start: 0.6991 (t80) cc_final: 0.6487 (t80) REVERT: B 420 PRO cc_start: 0.8355 (Cg_endo) cc_final: 0.8144 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7747 (p0) cc_final: 0.7403 (p0) REVERT: B 422 LEU cc_start: 0.8651 (tp) cc_final: 0.7769 (pp) REVERT: B 426 GLN cc_start: 0.7588 (pt0) cc_final: 0.6784 (pp30) REVERT: B 430 VAL cc_start: 0.7377 (p) cc_final: 0.7014 (t) REVERT: B 434 ARG cc_start: 0.7483 (mtt90) cc_final: 0.7236 (mpt-90) REVERT: B 436 LEU cc_start: 0.7901 (mt) cc_final: 0.7413 (mt) REVERT: B 443 LEU cc_start: 0.7827 (tp) cc_final: 0.7365 (mm) REVERT: B 444 THR cc_start: 0.7326 (m) cc_final: 0.7062 (m) REVERT: B 463 SER cc_start: 0.7304 (t) cc_final: 0.6896 (m) REVERT: B 481 PRO cc_start: 0.8282 (Cg_endo) cc_final: 0.7707 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8534 (m100) cc_final: 0.8173 (m100) REVERT: B 483 ASP cc_start: 0.8494 (m-30) cc_final: 0.7836 (t70) REVERT: B 486 PHE cc_start: 0.7895 (m-80) cc_final: 0.7683 (m-80) REVERT: B 488 ASN cc_start: 0.8006 (t0) cc_final: 0.7743 (t0) REVERT: B 494 LEU cc_start: 0.8581 (mt) cc_final: 0.8268 (mt) REVERT: B 517 ARG cc_start: 0.8348 (mtt180) cc_final: 0.7920 (mtm110) REVERT: B 556 ASN cc_start: 0.8013 (t0) cc_final: 0.7439 (t0) REVERT: B 566 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6547 (tm-30) REVERT: B 577 PHE cc_start: 0.8148 (m-80) cc_final: 0.7891 (m-80) REVERT: B 580 GLU cc_start: 0.8501 (tp30) cc_final: 0.8113 (tp30) REVERT: A 29 LYS cc_start: 0.7914 (pttm) cc_final: 0.7451 (pttm) REVERT: A 35 SER cc_start: 0.7977 (t) cc_final: 0.7751 (p) REVERT: A 36 ASN cc_start: 0.8252 (p0) cc_final: 0.7752 (p0) REVERT: A 40 GLN cc_start: 0.6012 (tt0) cc_final: 0.5531 (tt0) REVERT: A 46 ASP cc_start: 0.7477 (t70) cc_final: 0.6704 (t70) REVERT: A 47 HIS cc_start: 0.7948 (t70) cc_final: 0.6746 (t70) REVERT: A 51 LEU cc_start: 0.8770 (tp) cc_final: 0.8540 (tp) REVERT: A 55 PHE cc_start: 0.7912 (m-10) cc_final: 0.7498 (m-10) REVERT: A 62 LEU cc_start: 0.8512 (mt) cc_final: 0.8232 (mm) REVERT: A 74 TYR cc_start: 0.7825 (m-80) cc_final: 0.6911 (m-80) REVERT: A 80 LYS cc_start: 0.8230 (mttm) cc_final: 0.7811 (mttm) REVERT: A 83 GLN cc_start: 0.7836 (mm110) cc_final: 0.7353 (mm110) REVERT: A 93 LEU cc_start: 0.8323 (mp) cc_final: 0.8067 (mt) REVERT: A 110 ASN cc_start: 0.7901 (m110) cc_final: 0.7382 (p0) REVERT: A 114 GLU cc_start: 0.7591 (tt0) cc_final: 0.7064 (tt0) REVERT: A 137 MET cc_start: 0.8316 (mtm) cc_final: 0.7721 (mtm) REVERT: A 143 ILE cc_start: 0.8961 (mt) cc_final: 0.8678 (mm) REVERT: A 162 ILE cc_start: 0.8580 (mm) cc_final: 0.8343 (mm) REVERT: A 163 GLN cc_start: 0.8639 (pt0) cc_final: 0.8064 (tt0) REVERT: A 172 PHE cc_start: 0.7676 (m-10) cc_final: 0.7466 (m-80) REVERT: A 176 MET cc_start: 0.8035 (ptp) cc_final: 0.7539 (ptt) REVERT: A 209 LYS cc_start: 0.8092 (mttt) cc_final: 0.7497 (mtmm) REVERT: A 226 LYS cc_start: 0.7814 (mtpt) cc_final: 0.7196 (mtpt) REVERT: A 233 HIS cc_start: 0.7515 (t-90) cc_final: 0.6956 (t-90) REVERT: A 253 LYS cc_start: 0.8029 (tptm) cc_final: 0.7292 (tptm) REVERT: A 256 ASP cc_start: 0.7006 (t70) cc_final: 0.6617 (t0) REVERT: A 261 LYS cc_start: 0.7448 (mttm) cc_final: 0.6920 (mttm) REVERT: A 262 ASP cc_start: 0.7657 (t0) cc_final: 0.7276 (t0) REVERT: A 268 MET cc_start: 0.6305 (mtm) cc_final: 0.5156 (mtm) REVERT: A 277 MET cc_start: 0.6438 (mtt) cc_final: 0.5459 (mtt) REVERT: A 285 TYR cc_start: 0.5929 (m-10) cc_final: 0.5652 (m-10) REVERT: A 293 LYS cc_start: 0.8033 (mtpp) cc_final: 0.6995 (mmmt) REVERT: A 316 TYR cc_start: 0.7668 (t80) cc_final: 0.7195 (t80) REVERT: A 318 MET cc_start: 0.7839 (tpp) cc_final: 0.7027 (tpp) REVERT: A 338 ASN cc_start: 0.6957 (p0) cc_final: 0.5886 (p0) REVERT: A 340 ILE cc_start: 0.7572 (mp) cc_final: 0.7372 (mp) REVERT: A 345 PHE cc_start: 0.8296 (m-80) cc_final: 0.7982 (m-80) REVERT: A 358 HIS cc_start: 0.8245 (m90) cc_final: 0.7693 (m90) REVERT: A 360 LYS cc_start: 0.8708 (tttt) cc_final: 0.8343 (tttt) REVERT: A 368 ASP cc_start: 0.5124 (m-30) cc_final: 0.4547 (m-30) REVERT: A 369 LEU cc_start: 0.7140 (mt) cc_final: 0.6916 (mm) REVERT: A 396 LYS cc_start: 0.8225 (tppp) cc_final: 0.7801 (tppp) REVERT: A 404 PHE cc_start: 0.7217 (p90) cc_final: 0.6115 (p90) REVERT: A 414 ARG cc_start: 0.6765 (ttm-80) cc_final: 0.6035 (ttt180) REVERT: A 421 GLU cc_start: 0.8668 (tt0) cc_final: 0.7965 (tt0) REVERT: A 429 ARG cc_start: 0.7316 (mtt180) cc_final: 0.7075 (mtt-85) REVERT: A 430 THR cc_start: 0.7439 (m) cc_final: 0.6612 (m) REVERT: A 432 GLN cc_start: 0.8647 (tp40) cc_final: 0.8168 (tp-100) REVERT: A 433 HIS cc_start: 0.8445 (m90) cc_final: 0.8110 (m90) REVERT: A 476 ASN cc_start: 0.7634 (t0) cc_final: 0.7282 (t0) REVERT: A 489 LYS cc_start: 0.7828 (ttmm) cc_final: 0.7596 (mtpp) REVERT: A 496 GLU cc_start: 0.7733 (mp0) cc_final: 0.7427 (mp0) REVERT: A 521 ARG cc_start: 0.7890 (ptt180) cc_final: 0.7573 (tmm-80) REVERT: A 551 GLU cc_start: 0.8700 (pt0) cc_final: 0.8328 (pm20) REVERT: C 5 LYS cc_start: 0.8093 (mttt) cc_final: 0.7826 (tppp) REVERT: C 18 GLN cc_start: 0.7732 (tt0) cc_final: 0.7262 (pm20) REVERT: C 22 LEU cc_start: 0.7632 (mt) cc_final: 0.7313 (mt) REVERT: C 25 MET cc_start: 0.8055 (mmp) cc_final: 0.7337 (mmp) REVERT: C 29 TYR cc_start: 0.5215 (t80) cc_final: 0.4141 (t80) outliers start: 1 outliers final: 1 residues processed: 380 average time/residue: 0.2494 time to fit residues: 124.1212 Evaluate side-chains 344 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 343 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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: 0.1980 chunk 32 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 0.0970 chunk 114 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 267 HIS B 302 ASN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 145 HIS ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.3004 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= 0.202 Angle : 0.604 9.492 12680 Z= 0.306 Chirality : 0.046 0.275 1417 Planarity : 0.004 0.046 1669 Dihedral : 8.134 83.784 1426 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.94 % 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: -2.90 (0.23), residues: 1164 helix: -1.47 (0.85), residues: 42 sheet: -2.09 (0.55), residues: 84 loop : -2.16 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 415 HIS 0.004 0.001 HIS A 304 PHE 0.016 0.001 PHE A 180 TYR 0.032 0.001 TYR A 117 ARG 0.011 0.001 ARG A 149 *********************** 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 377 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 376 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6178 (pp30) cc_final: 0.5098 (mm-40) REVERT: B 30 ASP cc_start: 0.7089 (t0) cc_final: 0.6809 (t0) REVERT: B 31 MET cc_start: 0.7657 (mtp) cc_final: 0.7135 (ptp) REVERT: B 44 ASP cc_start: 0.7259 (t0) cc_final: 0.6544 (t0) REVERT: B 46 LEU cc_start: 0.8796 (mt) cc_final: 0.8485 (mt) REVERT: B 47 ARG cc_start: 0.7694 (ttp80) cc_final: 0.7312 (ttp80) REVERT: B 54 GLN cc_start: 0.7191 (mt0) cc_final: 0.6659 (tp40) REVERT: B 55 VAL cc_start: 0.7387 (t) cc_final: 0.6627 (t) REVERT: B 56 VAL cc_start: 0.7899 (t) cc_final: 0.7600 (m) REVERT: B 65 LEU cc_start: 0.8170 (mt) cc_final: 0.7931 (mt) REVERT: B 73 PHE cc_start: 0.8174 (p90) cc_final: 0.7827 (p90) REVERT: B 75 GLN cc_start: 0.7791 (pt0) cc_final: 0.7432 (pt0) REVERT: B 79 GLU cc_start: 0.6977 (tt0) cc_final: 0.6279 (tt0) REVERT: B 81 GLN cc_start: 0.6787 (mt0) cc_final: 0.6299 (mt0) REVERT: B 93 GLN cc_start: 0.8548 (pp30) cc_final: 0.8226 (tm-30) REVERT: B 100 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7287 (mmm-85) REVERT: B 105 THR cc_start: 0.7670 (p) cc_final: 0.6882 (t) REVERT: B 106 GLN cc_start: 0.7639 (mt0) cc_final: 0.7282 (mp-120) REVERT: B 112 TYR cc_start: 0.7329 (m-80) cc_final: 0.6961 (m-80) REVERT: B 138 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.6985 (tpt170) REVERT: B 139 GLU cc_start: 0.7282 (mp0) cc_final: 0.6921 (mp0) REVERT: B 158 ASN cc_start: 0.7739 (m-40) cc_final: 0.7539 (m110) REVERT: B 173 PHE cc_start: 0.7026 (m-10) cc_final: 0.6675 (m-10) REVERT: B 185 ASP cc_start: 0.7086 (t0) cc_final: 0.6592 (t0) REVERT: B 188 ARG cc_start: 0.6937 (mtm180) cc_final: 0.6729 (tpp80) REVERT: B 193 HIS cc_start: 0.7868 (m90) cc_final: 0.7287 (m90) REVERT: B 248 LYS cc_start: 0.8622 (mmtt) cc_final: 0.7987 (mmtt) REVERT: B 251 ASP cc_start: 0.7767 (p0) cc_final: 0.7379 (p0) REVERT: B 265 GLU cc_start: 0.6915 (pm20) cc_final: 0.6419 (pm20) REVERT: B 274 TYR cc_start: 0.6834 (t80) cc_final: 0.6137 (t80) REVERT: B 275 ASN cc_start: 0.8165 (t0) cc_final: 0.7601 (t0) REVERT: B 282 MET cc_start: 0.8188 (mtp) cc_final: 0.7938 (mtp) REVERT: B 288 ARG cc_start: 0.7837 (mmt-90) cc_final: 0.7606 (mtt90) REVERT: B 303 TYR cc_start: 0.7904 (m-80) cc_final: 0.7362 (m-80) REVERT: B 311 CYS cc_start: 0.3917 (p) cc_final: 0.3227 (m) REVERT: B 319 ASN cc_start: 0.7609 (m-40) cc_final: 0.7321 (m-40) REVERT: B 323 THR cc_start: 0.7336 (t) cc_final: 0.6999 (p) REVERT: B 332 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6535 (mp0) REVERT: B 364 PHE cc_start: 0.8638 (m-80) cc_final: 0.7874 (m-80) REVERT: B 377 LEU cc_start: 0.8341 (tp) cc_final: 0.8017 (tt) REVERT: B 398 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7910 (mm-40) REVERT: B 411 TYR cc_start: 0.7222 (t80) cc_final: 0.6357 (t80) REVERT: B 420 PRO cc_start: 0.8487 (Cg_endo) cc_final: 0.7962 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7654 (p0) cc_final: 0.7328 (p0) REVERT: B 422 LEU cc_start: 0.8658 (tp) cc_final: 0.8280 (mt) REVERT: B 426 GLN cc_start: 0.7696 (pt0) cc_final: 0.6838 (pp30) REVERT: B 430 VAL cc_start: 0.7666 (p) cc_final: 0.7351 (t) REVERT: B 432 ARG cc_start: 0.7065 (mmt-90) cc_final: 0.6799 (mmt-90) REVERT: B 434 ARG cc_start: 0.7329 (mtt90) cc_final: 0.7091 (mpt-90) REVERT: B 436 LEU cc_start: 0.7879 (mt) cc_final: 0.7324 (mt) REVERT: B 443 LEU cc_start: 0.7851 (tp) cc_final: 0.7302 (mm) REVERT: B 444 THR cc_start: 0.7374 (m) cc_final: 0.6825 (m) REVERT: B 451 SER cc_start: 0.8339 (m) cc_final: 0.7696 (m) REVERT: B 452 TRP cc_start: 0.7915 (p90) cc_final: 0.7505 (p90) REVERT: B 467 LEU cc_start: 0.7225 (tp) cc_final: 0.6938 (tp) REVERT: B 481 PRO cc_start: 0.8275 (Cg_endo) cc_final: 0.7702 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8607 (m100) cc_final: 0.8363 (m100) REVERT: B 486 PHE cc_start: 0.8136 (m-80) cc_final: 0.7750 (m-80) REVERT: B 487 ARG cc_start: 0.7977 (mmt90) cc_final: 0.7071 (ttm-80) REVERT: B 494 LEU cc_start: 0.8743 (mt) cc_final: 0.8429 (mt) REVERT: B 517 ARG cc_start: 0.8409 (mtt180) cc_final: 0.8198 (mtt180) REVERT: B 527 GLN cc_start: 0.7067 (pm20) cc_final: 0.6001 (pm20) REVERT: B 556 ASN cc_start: 0.8065 (t0) cc_final: 0.7516 (t0) REVERT: B 566 GLU cc_start: 0.7597 (mm-30) cc_final: 0.6484 (tm-30) REVERT: B 577 PHE cc_start: 0.8216 (m-80) cc_final: 0.7930 (m-80) REVERT: B 580 GLU cc_start: 0.8432 (tp30) cc_final: 0.8004 (tp30) REVERT: A 29 LYS cc_start: 0.8004 (pttm) cc_final: 0.7439 (pttm) REVERT: A 35 SER cc_start: 0.8406 (t) cc_final: 0.8060 (p) REVERT: A 40 GLN cc_start: 0.6336 (tt0) cc_final: 0.5537 (tt0) REVERT: A 46 ASP cc_start: 0.7413 (t70) cc_final: 0.6832 (t70) REVERT: A 47 HIS cc_start: 0.7995 (t70) cc_final: 0.6883 (t70) REVERT: A 51 LEU cc_start: 0.8899 (tp) cc_final: 0.8630 (tp) REVERT: A 55 PHE cc_start: 0.8019 (m-10) cc_final: 0.7599 (m-10) REVERT: A 61 VAL cc_start: 0.8380 (m) cc_final: 0.8054 (p) REVERT: A 65 LEU cc_start: 0.7739 (tp) cc_final: 0.7453 (tt) REVERT: A 74 TYR cc_start: 0.8004 (m-80) cc_final: 0.7040 (m-80) REVERT: A 80 LYS cc_start: 0.8276 (mttm) cc_final: 0.7899 (mttm) REVERT: A 83 GLN cc_start: 0.7757 (mm110) cc_final: 0.7235 (mm110) REVERT: A 110 ASN cc_start: 0.7860 (m110) cc_final: 0.7536 (p0) REVERT: A 114 GLU cc_start: 0.7641 (tt0) cc_final: 0.7410 (tt0) REVERT: A 132 LEU cc_start: 0.7739 (mm) cc_final: 0.7170 (mm) REVERT: A 137 MET cc_start: 0.8076 (mtm) cc_final: 0.7840 (mtm) REVERT: A 143 ILE cc_start: 0.8898 (mt) cc_final: 0.8534 (mm) REVERT: A 163 GLN cc_start: 0.8459 (pt0) cc_final: 0.8039 (tt0) REVERT: A 176 MET cc_start: 0.8234 (ptp) cc_final: 0.7793 (ptt) REVERT: A 209 LYS cc_start: 0.8161 (mttt) cc_final: 0.7548 (mtmt) REVERT: A 229 SER cc_start: 0.8310 (p) cc_final: 0.7853 (t) REVERT: A 230 ASP cc_start: 0.8274 (m-30) cc_final: 0.7377 (p0) REVERT: A 233 HIS cc_start: 0.7698 (t-90) cc_final: 0.7478 (t-90) REVERT: A 254 PHE cc_start: 0.7394 (m-10) cc_final: 0.7172 (m-80) REVERT: A 255 ARG cc_start: 0.6898 (ttt-90) cc_final: 0.6464 (ttp80) REVERT: A 261 LYS cc_start: 0.7486 (mttm) cc_final: 0.7172 (mttm) REVERT: A 262 ASP cc_start: 0.7751 (t0) cc_final: 0.7429 (t0) REVERT: A 268 MET cc_start: 0.6305 (mtm) cc_final: 0.5206 (mtm) REVERT: A 277 MET cc_start: 0.6533 (mtt) cc_final: 0.5548 (mtt) REVERT: A 290 THR cc_start: 0.6908 (t) cc_final: 0.6512 (t) REVERT: A 293 LYS cc_start: 0.7781 (mtpp) cc_final: 0.7037 (mmmt) REVERT: A 318 MET cc_start: 0.7899 (tpp) cc_final: 0.7525 (tpp) REVERT: A 338 ASN cc_start: 0.7131 (p0) cc_final: 0.6156 (p0) REVERT: A 345 PHE cc_start: 0.8422 (m-80) cc_final: 0.7863 (m-80) REVERT: A 358 HIS cc_start: 0.8390 (m90) cc_final: 0.7737 (m90) REVERT: A 360 LYS cc_start: 0.8720 (tttt) cc_final: 0.8359 (tttt) REVERT: A 368 ASP cc_start: 0.4988 (m-30) cc_final: 0.4549 (m-30) REVERT: A 396 LYS cc_start: 0.8283 (tppp) cc_final: 0.7839 (tppp) REVERT: A 404 PHE cc_start: 0.7297 (p90) cc_final: 0.6223 (p90) REVERT: A 421 GLU cc_start: 0.8674 (tt0) cc_final: 0.7695 (tt0) REVERT: A 430 THR cc_start: 0.7354 (m) cc_final: 0.6544 (m) REVERT: A 431 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7805 (mtmt) REVERT: A 432 GLN cc_start: 0.8635 (tp40) cc_final: 0.8297 (tp-100) REVERT: A 433 HIS cc_start: 0.8454 (m90) cc_final: 0.8125 (m90) REVERT: A 451 ARG cc_start: 0.6990 (mtt90) cc_final: 0.6760 (ptp-170) REVERT: A 456 ILE cc_start: 0.8044 (mm) cc_final: 0.7426 (pt) REVERT: A 457 SER cc_start: 0.7653 (m) cc_final: 0.7233 (m) REVERT: A 476 ASN cc_start: 0.7703 (t0) cc_final: 0.7301 (t0) REVERT: A 487 LYS cc_start: 0.7719 (mtmm) cc_final: 0.7436 (mtmm) REVERT: A 496 GLU cc_start: 0.7714 (mp0) cc_final: 0.7404 (mp0) REVERT: A 551 GLU cc_start: 0.8727 (pt0) cc_final: 0.8316 (pm20) REVERT: C 22 LEU cc_start: 0.7728 (mt) cc_final: 0.7469 (mt) REVERT: C 25 MET cc_start: 0.8086 (mmp) cc_final: 0.7417 (mmp) REVERT: C 29 TYR cc_start: 0.5313 (t80) cc_final: 0.4322 (t80) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.2540 time to fit residues: 124.6124 Evaluate side-chains 361 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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: 0.9980 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 70 optimal weight: 0.1980 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN B 81 GLN ** B 156 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN A 468 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.3910 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= 0.258 Angle : 0.639 9.431 12680 Z= 0.327 Chirality : 0.047 0.284 1417 Planarity : 0.005 0.053 1669 Dihedral : 7.727 79.914 1426 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: -2.71 (0.23), residues: 1164 helix: -1.67 (0.78), residues: 42 sheet: -1.85 (0.54), residues: 84 loop : -2.01 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 477 HIS 0.007 0.001 HIS A 507 PHE 0.014 0.002 PHE C 44 TYR 0.031 0.002 TYR A 117 ARG 0.008 0.001 ARG A 149 *********************** 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 379 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.037 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: 0.6540 (pp30) cc_final: 0.4914 (mm-40) REVERT: B 31 MET cc_start: 0.7254 (mtp) cc_final: 0.6391 (ptp) REVERT: B 32 LYS cc_start: 0.8060 (mptt) cc_final: 0.7758 (mmtt) REVERT: B 44 ASP cc_start: 0.7411 (t0) cc_final: 0.6718 (t0) REVERT: B 46 LEU cc_start: 0.8857 (mt) cc_final: 0.8353 (mt) REVERT: B 47 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7420 (ttp80) REVERT: B 59 ASN cc_start: 0.7228 (m-40) cc_final: 0.6797 (m-40) REVERT: B 61 GLU cc_start: 0.6701 (tm-30) cc_final: 0.4354 (tm-30) REVERT: B 64 TYR cc_start: 0.7927 (m-80) cc_final: 0.7555 (m-80) REVERT: B 65 LEU cc_start: 0.8124 (mt) cc_final: 0.7901 (mt) REVERT: B 75 GLN cc_start: 0.7880 (pt0) cc_final: 0.7592 (pt0) REVERT: B 81 GLN cc_start: 0.6669 (mt0) cc_final: 0.6365 (mt0) REVERT: B 93 GLN cc_start: 0.8542 (pp30) cc_final: 0.8294 (tm-30) REVERT: B 100 ARG cc_start: 0.7921 (tpp80) cc_final: 0.7551 (mmm-85) REVERT: B 103 ARG cc_start: 0.7367 (ttm110) cc_final: 0.7082 (ttm110) REVERT: B 105 THR cc_start: 0.7778 (p) cc_final: 0.7485 (t) REVERT: B 106 GLN cc_start: 0.7596 (mt0) cc_final: 0.7302 (mp10) REVERT: B 112 TYR cc_start: 0.7520 (m-80) cc_final: 0.6935 (m-80) REVERT: B 167 ILE cc_start: 0.8444 (mp) cc_final: 0.7987 (mp) REVERT: B 169 TRP cc_start: 0.8406 (m100) cc_final: 0.6763 (m100) REVERT: B 173 PHE cc_start: 0.7193 (m-10) cc_final: 0.6694 (m-10) REVERT: B 182 THR cc_start: 0.7595 (p) cc_final: 0.7324 (p) REVERT: B 185 ASP cc_start: 0.7078 (t0) cc_final: 0.6752 (t0) REVERT: B 193 HIS cc_start: 0.7789 (m90) cc_final: 0.7237 (m90) REVERT: B 211 ASP cc_start: 0.7548 (m-30) cc_final: 0.7266 (p0) REVERT: B 237 HIS cc_start: 0.7556 (t-90) cc_final: 0.7036 (t-90) REVERT: B 239 GLN cc_start: 0.7917 (mm110) cc_final: 0.7664 (mp10) REVERT: B 248 LYS cc_start: 0.8642 (mmtt) cc_final: 0.7936 (mmtt) REVERT: B 251 ASP cc_start: 0.7683 (p0) cc_final: 0.7360 (p0) REVERT: B 274 TYR cc_start: 0.6718 (t80) cc_final: 0.6111 (t80) REVERT: B 275 ASN cc_start: 0.8175 (t0) cc_final: 0.7791 (t0) REVERT: B 282 MET cc_start: 0.8207 (mtp) cc_final: 0.7884 (mtp) REVERT: B 303 TYR cc_start: 0.8143 (m-80) cc_final: 0.7577 (m-80) REVERT: B 311 CYS cc_start: 0.4055 (p) cc_final: 0.3280 (m) REVERT: B 323 THR cc_start: 0.7516 (t) cc_final: 0.7150 (p) REVERT: B 351 ARG cc_start: 0.7838 (mmp80) cc_final: 0.7632 (tpp-160) REVERT: B 364 PHE cc_start: 0.8657 (m-80) cc_final: 0.7943 (m-80) REVERT: B 397 LEU cc_start: 0.8821 (mt) cc_final: 0.8461 (tt) REVERT: B 398 GLN cc_start: 0.8279 (mm-40) cc_final: 0.8016 (mm-40) REVERT: B 411 TYR cc_start: 0.7391 (t80) cc_final: 0.6565 (t80) REVERT: B 420 PRO cc_start: 0.8501 (Cg_endo) cc_final: 0.8149 (Cg_exo) REVERT: B 426 GLN cc_start: 0.7633 (pt0) cc_final: 0.6871 (pp30) REVERT: B 432 ARG cc_start: 0.7099 (mmt-90) cc_final: 0.6882 (mmt-90) REVERT: B 443 LEU cc_start: 0.7930 (tp) cc_final: 0.7717 (tt) REVERT: B 444 THR cc_start: 0.7528 (m) cc_final: 0.6535 (m) REVERT: B 451 SER cc_start: 0.8417 (m) cc_final: 0.7805 (m) REVERT: B 452 TRP cc_start: 0.7985 (p90) cc_final: 0.7492 (p90) REVERT: B 467 LEU cc_start: 0.7309 (tp) cc_final: 0.6471 (pp) REVERT: B 481 PRO cc_start: 0.8231 (Cg_endo) cc_final: 0.7697 (Cg_exo) REVERT: B 486 PHE cc_start: 0.8399 (m-80) cc_final: 0.8103 (m-80) REVERT: B 487 ARG cc_start: 0.7689 (mmt90) cc_final: 0.7186 (ttm-80) REVERT: B 488 ASN cc_start: 0.7779 (t0) cc_final: 0.7363 (t0) REVERT: B 493 LEU cc_start: 0.8210 (tp) cc_final: 0.7955 (tp) REVERT: B 517 ARG cc_start: 0.8420 (mtt180) cc_final: 0.8204 (mtt180) REVERT: B 527 GLN cc_start: 0.6989 (pm20) cc_final: 0.5836 (pm20) REVERT: B 556 ASN cc_start: 0.8069 (t0) cc_final: 0.7512 (t0) REVERT: B 566 GLU cc_start: 0.7639 (mm-30) cc_final: 0.6460 (tm-30) REVERT: B 577 PHE cc_start: 0.8353 (m-80) cc_final: 0.7991 (m-80) REVERT: B 580 GLU cc_start: 0.8436 (tp30) cc_final: 0.8004 (tp30) REVERT: A 36 ASN cc_start: 0.8442 (p0) cc_final: 0.8066 (p0) REVERT: A 45 GLU cc_start: 0.8390 (mp0) cc_final: 0.8054 (mp0) REVERT: A 46 ASP cc_start: 0.7423 (t70) cc_final: 0.6954 (t70) REVERT: A 47 HIS cc_start: 0.8111 (t70) cc_final: 0.7048 (t70) REVERT: A 51 LEU cc_start: 0.8980 (tp) cc_final: 0.8686 (tp) REVERT: A 55 PHE cc_start: 0.8008 (m-10) cc_final: 0.7720 (m-10) REVERT: A 61 VAL cc_start: 0.8380 (m) cc_final: 0.8055 (p) REVERT: A 74 TYR cc_start: 0.8145 (m-80) cc_final: 0.7092 (m-80) REVERT: A 80 LYS cc_start: 0.8322 (mttm) cc_final: 0.7925 (mttm) REVERT: A 83 GLN cc_start: 0.7847 (mm110) cc_final: 0.7339 (mm110) REVERT: A 88 TYR cc_start: 0.7399 (p90) cc_final: 0.6195 (p90) REVERT: A 90 LEU cc_start: 0.8152 (tp) cc_final: 0.7942 (tt) REVERT: A 103 ASN cc_start: 0.7204 (m-40) cc_final: 0.6917 (m-40) REVERT: A 107 ILE cc_start: 0.8544 (mm) cc_final: 0.8288 (mm) REVERT: A 110 ASN cc_start: 0.7862 (m110) cc_final: 0.7606 (p0) REVERT: A 111 MET cc_start: 0.6977 (ttt) cc_final: 0.6428 (ttt) REVERT: A 132 LEU cc_start: 0.7670 (mm) cc_final: 0.6997 (mm) REVERT: A 137 MET cc_start: 0.8289 (mtm) cc_final: 0.8045 (mtm) REVERT: A 143 ILE cc_start: 0.8954 (mt) cc_final: 0.8442 (mm) REVERT: A 167 ILE cc_start: 0.8277 (mm) cc_final: 0.8057 (mm) REVERT: A 176 MET cc_start: 0.8452 (ptp) cc_final: 0.8113 (ptt) REVERT: A 209 LYS cc_start: 0.8277 (mttt) cc_final: 0.7688 (mtmt) REVERT: A 212 LYS cc_start: 0.7582 (ttmm) cc_final: 0.7224 (ttmm) REVERT: A 226 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7370 (mtpt) REVERT: A 229 SER cc_start: 0.8205 (p) cc_final: 0.7816 (t) REVERT: A 233 HIS cc_start: 0.7756 (t-90) cc_final: 0.7355 (t-90) REVERT: A 252 ARG cc_start: 0.7399 (mtp85) cc_final: 0.7137 (mtp85) REVERT: A 254 PHE cc_start: 0.7412 (m-10) cc_final: 0.7201 (m-80) REVERT: A 255 ARG cc_start: 0.7090 (ttt-90) cc_final: 0.6632 (ttp80) REVERT: A 261 LYS cc_start: 0.7629 (mttm) cc_final: 0.7284 (ptmt) REVERT: A 262 ASP cc_start: 0.7754 (t0) cc_final: 0.7452 (t0) REVERT: A 268 MET cc_start: 0.6412 (mtm) cc_final: 0.5364 (mtm) REVERT: A 277 MET cc_start: 0.6834 (mtt) cc_final: 0.5730 (mtt) REVERT: A 290 THR cc_start: 0.7198 (t) cc_final: 0.6957 (t) REVERT: A 293 LYS cc_start: 0.7887 (mtpp) cc_final: 0.6962 (mtpp) REVERT: A 318 MET cc_start: 0.8031 (tpp) cc_final: 0.7652 (tpp) REVERT: A 360 LYS cc_start: 0.8768 (tttt) cc_final: 0.8421 (tttt) REVERT: A 368 ASP cc_start: 0.5028 (m-30) cc_final: 0.4561 (m-30) REVERT: A 396 LYS cc_start: 0.8426 (tppp) cc_final: 0.7920 (tppp) REVERT: A 404 PHE cc_start: 0.7241 (p90) cc_final: 0.6260 (p90) REVERT: A 421 GLU cc_start: 0.8694 (tt0) cc_final: 0.7109 (tt0) REVERT: A 431 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7990 (mtpt) REVERT: A 432 GLN cc_start: 0.8615 (tp40) cc_final: 0.8160 (tp-100) REVERT: A 433 HIS cc_start: 0.8552 (m90) cc_final: 0.8110 (m90) REVERT: A 451 ARG cc_start: 0.6762 (mtt90) cc_final: 0.5540 (ptp-110) REVERT: A 457 SER cc_start: 0.7953 (m) cc_final: 0.7678 (m) REVERT: A 476 ASN cc_start: 0.7740 (t0) cc_final: 0.7362 (t0) REVERT: A 487 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7663 (mtmm) REVERT: A 489 LYS cc_start: 0.7509 (mmmm) cc_final: 0.7109 (mtpp) REVERT: A 496 GLU cc_start: 0.7763 (mp0) cc_final: 0.7504 (mp0) REVERT: A 521 ARG cc_start: 0.7744 (ptt180) cc_final: 0.6731 (ptt180) REVERT: C 25 MET cc_start: 0.8149 (mmp) cc_final: 0.7489 (mmp) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.2457 time to fit residues: 122.1343 Evaluate side-chains 371 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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: 1.9990 chunk 63 optimal weight: 0.5980 chunk 1 optimal weight: 0.0070 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.3798 ------------------------------------------------------------------------------- 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 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 435 GLN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9358 Z= 0.186 Angle : 0.625 11.470 12680 Z= 0.309 Chirality : 0.046 0.270 1417 Planarity : 0.004 0.053 1669 Dihedral : 7.239 75.950 1426 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.23), residues: 1164 helix: -1.46 (0.82), residues: 42 sheet: -0.95 (0.65), residues: 69 loop : -1.96 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 164 HIS 0.008 0.001 HIS A 183 PHE 0.010 0.001 PHE B 371 TYR 0.040 0.002 TYR A 117 ARG 0.005 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 1.051 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: 0.6377 (pp30) cc_final: 0.5199 (mm-40) REVERT: B 31 MET cc_start: 0.7252 (mtp) cc_final: 0.6494 (ptp) REVERT: B 44 ASP cc_start: 0.7223 (t0) cc_final: 0.6622 (t0) REVERT: B 46 LEU cc_start: 0.8796 (mt) cc_final: 0.8282 (mt) REVERT: B 47 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7405 (ttp80) REVERT: B 59 ASN cc_start: 0.7236 (m-40) cc_final: 0.6796 (m-40) REVERT: B 61 GLU cc_start: 0.6700 (tm-30) cc_final: 0.4622 (tm-30) REVERT: B 65 LEU cc_start: 0.8068 (mt) cc_final: 0.7848 (mt) REVERT: B 75 GLN cc_start: 0.7925 (pt0) cc_final: 0.7615 (pt0) REVERT: B 81 GLN cc_start: 0.6567 (mt0) cc_final: 0.6292 (mt0) REVERT: B 93 GLN cc_start: 0.8535 (pp30) cc_final: 0.8272 (tm-30) REVERT: B 100 ARG cc_start: 0.7865 (tpp80) cc_final: 0.7642 (mmm-85) REVERT: B 103 ARG cc_start: 0.7396 (ttm110) cc_final: 0.7186 (ttm110) REVERT: B 105 THR cc_start: 0.7716 (p) cc_final: 0.7508 (t) REVERT: B 106 GLN cc_start: 0.7581 (mt0) cc_final: 0.7297 (mp10) REVERT: B 112 TYR cc_start: 0.7390 (m-80) cc_final: 0.6865 (m-80) REVERT: B 160 GLN cc_start: 0.6959 (tp40) cc_final: 0.6651 (tp40) REVERT: B 185 ASP cc_start: 0.7182 (t0) cc_final: 0.6874 (t0) REVERT: B 193 HIS cc_start: 0.7754 (m90) cc_final: 0.7174 (m90) REVERT: B 237 HIS cc_start: 0.7443 (t-90) cc_final: 0.7093 (t-90) REVERT: B 239 GLN cc_start: 0.7837 (mm110) cc_final: 0.7627 (mp10) REVERT: B 248 LYS cc_start: 0.8588 (mmtt) cc_final: 0.7911 (mmtt) REVERT: B 251 ASP cc_start: 0.7680 (p0) cc_final: 0.7410 (p0) REVERT: B 253 LEU cc_start: 0.7706 (mt) cc_final: 0.7496 (mt) REVERT: B 274 TYR cc_start: 0.6744 (t80) cc_final: 0.6195 (t80) REVERT: B 275 ASN cc_start: 0.8167 (t0) cc_final: 0.7756 (t0) REVERT: B 282 MET cc_start: 0.8135 (mtp) cc_final: 0.7884 (mtp) REVERT: B 288 ARG cc_start: 0.7892 (mpt-90) cc_final: 0.7662 (mtt90) REVERT: B 303 TYR cc_start: 0.8211 (m-80) cc_final: 0.7641 (m-80) REVERT: B 311 CYS cc_start: 0.3901 (p) cc_final: 0.3188 (m) REVERT: B 323 THR cc_start: 0.7479 (t) cc_final: 0.7102 (p) REVERT: B 332 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6622 (mp0) REVERT: B 364 PHE cc_start: 0.8724 (m-80) cc_final: 0.7965 (m-80) REVERT: B 371 PHE cc_start: 0.7376 (m-10) cc_final: 0.7148 (m-10) REVERT: B 397 LEU cc_start: 0.8835 (mt) cc_final: 0.8451 (tt) REVERT: B 398 GLN cc_start: 0.8282 (mm-40) cc_final: 0.8036 (mm-40) REVERT: B 411 TYR cc_start: 0.7275 (t80) cc_final: 0.6455 (t80) REVERT: B 420 PRO cc_start: 0.8356 (Cg_endo) cc_final: 0.7714 (Cg_exo) REVERT: B 426 GLN cc_start: 0.7640 (pt0) cc_final: 0.6884 (pp30) REVERT: B 432 ARG cc_start: 0.7029 (mmt-90) cc_final: 0.6799 (mmt-90) REVERT: B 436 LEU cc_start: 0.7902 (mt) cc_final: 0.7546 (mp) REVERT: B 444 THR cc_start: 0.7447 (m) cc_final: 0.6356 (m) REVERT: B 451 SER cc_start: 0.8388 (m) cc_final: 0.7757 (m) REVERT: B 452 TRP cc_start: 0.7951 (p90) cc_final: 0.7524 (p90) REVERT: B 467 LEU cc_start: 0.7297 (tp) cc_final: 0.6413 (pp) REVERT: B 481 PRO cc_start: 0.8217 (Cg_endo) cc_final: 0.7637 (Cg_exo) REVERT: B 486 PHE cc_start: 0.8462 (m-80) cc_final: 0.8127 (m-80) REVERT: B 487 ARG cc_start: 0.7733 (mmt90) cc_final: 0.7025 (ttm-80) REVERT: B 488 ASN cc_start: 0.7834 (t0) cc_final: 0.7367 (t0) REVERT: B 493 LEU cc_start: 0.8172 (tp) cc_final: 0.7678 (tp) REVERT: B 517 ARG cc_start: 0.8410 (mtt180) cc_final: 0.8180 (mtt180) REVERT: B 539 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7194 (tp30) REVERT: B 556 ASN cc_start: 0.8112 (t0) cc_final: 0.7540 (t0) REVERT: B 566 GLU cc_start: 0.7606 (mm-30) cc_final: 0.6384 (tm-30) REVERT: B 577 PHE cc_start: 0.8364 (m-80) cc_final: 0.7994 (m-80) REVERT: B 580 GLU cc_start: 0.8400 (tp30) cc_final: 0.7935 (tp30) REVERT: B 592 ASP cc_start: 0.8139 (t0) cc_final: 0.7900 (m-30) REVERT: A 29 LYS cc_start: 0.8034 (pttm) cc_final: 0.7471 (pttm) REVERT: A 36 ASN cc_start: 0.8371 (p0) cc_final: 0.8003 (p0) REVERT: A 40 GLN cc_start: 0.6684 (pt0) cc_final: 0.6085 (pt0) REVERT: A 45 GLU cc_start: 0.8348 (mp0) cc_final: 0.8062 (mp0) REVERT: A 46 ASP cc_start: 0.7350 (t70) cc_final: 0.6848 (t70) REVERT: A 47 HIS cc_start: 0.7963 (t70) cc_final: 0.6886 (t70) REVERT: A 51 LEU cc_start: 0.8929 (tp) cc_final: 0.8644 (tp) REVERT: A 61 VAL cc_start: 0.8380 (m) cc_final: 0.7983 (p) REVERT: A 74 TYR cc_start: 0.8135 (m-80) cc_final: 0.7115 (m-80) REVERT: A 80 LYS cc_start: 0.8313 (mttm) cc_final: 0.7916 (mttm) REVERT: A 83 GLN cc_start: 0.7777 (mm110) cc_final: 0.7278 (mm110) REVERT: A 103 ASN cc_start: 0.7142 (m-40) cc_final: 0.6896 (m-40) REVERT: A 107 ILE cc_start: 0.8519 (mm) cc_final: 0.8205 (mm) REVERT: A 110 ASN cc_start: 0.7794 (m110) cc_final: 0.7514 (p0) REVERT: A 132 LEU cc_start: 0.7592 (mm) cc_final: 0.7044 (mm) REVERT: A 137 MET cc_start: 0.8260 (mtm) cc_final: 0.7846 (mtm) REVERT: A 143 ILE cc_start: 0.8934 (mt) cc_final: 0.8464 (mm) REVERT: A 163 GLN cc_start: 0.8141 (tt0) cc_final: 0.7932 (tt0) REVERT: A 176 MET cc_start: 0.8577 (ptp) cc_final: 0.8126 (ptt) REVERT: A 209 LYS cc_start: 0.8224 (mttt) cc_final: 0.7685 (mtmt) REVERT: A 212 LYS cc_start: 0.7436 (ttmm) cc_final: 0.7236 (ttmm) REVERT: A 226 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7501 (mtpt) REVERT: A 230 ASP cc_start: 0.8249 (m-30) cc_final: 0.7366 (p0) REVERT: A 233 HIS cc_start: 0.7648 (t-90) cc_final: 0.7230 (t-90) REVERT: A 254 PHE cc_start: 0.7373 (m-10) cc_final: 0.7114 (m-80) REVERT: A 261 LYS cc_start: 0.7587 (mttm) cc_final: 0.7158 (mttm) REVERT: A 262 ASP cc_start: 0.7787 (t0) cc_final: 0.7505 (t0) REVERT: A 268 MET cc_start: 0.6403 (mtm) cc_final: 0.5228 (mtm) REVERT: A 277 MET cc_start: 0.6840 (mtt) cc_final: 0.5706 (mtt) REVERT: A 338 ASN cc_start: 0.7592 (p0) cc_final: 0.7078 (p0) REVERT: A 344 GLU cc_start: 0.7406 (tt0) cc_final: 0.7182 (tt0) REVERT: A 360 LYS cc_start: 0.8662 (tttt) cc_final: 0.8322 (tttt) REVERT: A 368 ASP cc_start: 0.5036 (m-30) cc_final: 0.4640 (m-30) REVERT: A 396 LYS cc_start: 0.8453 (tppp) cc_final: 0.7927 (tppp) REVERT: A 404 PHE cc_start: 0.7343 (p90) cc_final: 0.6312 (p90) REVERT: A 416 ASP cc_start: 0.7102 (p0) cc_final: 0.6753 (p0) REVERT: A 421 GLU cc_start: 0.8698 (tt0) cc_final: 0.7680 (tt0) REVERT: A 432 GLN cc_start: 0.8578 (tp40) cc_final: 0.8290 (tp-100) REVERT: A 433 HIS cc_start: 0.8566 (m90) cc_final: 0.8188 (m90) REVERT: A 451 ARG cc_start: 0.6956 (mtt90) cc_final: 0.6456 (ptp-170) REVERT: A 457 SER cc_start: 0.7933 (m) cc_final: 0.7582 (m) REVERT: A 476 ASN cc_start: 0.7733 (t0) cc_final: 0.7295 (t0) REVERT: A 487 LYS cc_start: 0.7870 (mtmm) cc_final: 0.7555 (mtmm) REVERT: A 496 GLU cc_start: 0.7750 (mp0) cc_final: 0.7420 (mp0) REVERT: A 551 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8430 (pm20) REVERT: A 559 HIS cc_start: 0.7710 (t70) cc_final: 0.7230 (t-170) REVERT: C 25 MET cc_start: 0.8091 (mmp) cc_final: 0.7452 (mmp) REVERT: C 31 ARG cc_start: 0.6167 (ttp-170) cc_final: 0.5931 (ttm110) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.2480 time to fit residues: 124.8725 Evaluate side-chains 356 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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: 1.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 112 optimal weight: 0.1980 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9358 Z= 0.266 Angle : 0.674 9.385 12680 Z= 0.344 Chirality : 0.048 0.269 1417 Planarity : 0.005 0.051 1669 Dihedral : 7.327 73.031 1426 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.14 % Favored : 86.86 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % 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: -2.55 (0.24), residues: 1164 helix: -1.76 (0.78), residues: 42 sheet: -1.51 (0.55), residues: 93 loop : -1.90 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 200 HIS 0.007 0.001 HIS A 507 PHE 0.018 0.002 PHE A 172 TYR 0.030 0.002 TYR A 117 ARG 0.006 0.001 ARG A 224 *********************** 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 377 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6822 (pp30) cc_final: 0.5768 (mm-40) REVERT: B 31 MET cc_start: 0.7485 (mtp) cc_final: 0.6561 (ptp) REVERT: B 44 ASP cc_start: 0.7396 (t0) cc_final: 0.6693 (t0) REVERT: B 45 MET cc_start: 0.8548 (tmm) cc_final: 0.8308 (tmm) REVERT: B 46 LEU cc_start: 0.8686 (mt) cc_final: 0.8390 (mt) REVERT: B 47 ARG cc_start: 0.7657 (ttp80) cc_final: 0.7309 (ttp80) REVERT: B 61 GLU cc_start: 0.6769 (tm-30) cc_final: 0.3695 (tm-30) REVERT: B 64 TYR cc_start: 0.7920 (m-80) cc_final: 0.7585 (m-80) REVERT: B 65 LEU cc_start: 0.8032 (mt) cc_final: 0.7798 (mt) REVERT: B 70 SER cc_start: 0.8670 (p) cc_final: 0.8455 (p) REVERT: B 75 GLN cc_start: 0.7912 (pt0) cc_final: 0.7658 (pt0) REVERT: B 78 GLN cc_start: 0.7654 (pm20) cc_final: 0.7423 (pm20) REVERT: B 79 GLU cc_start: 0.6983 (tt0) cc_final: 0.6518 (tt0) REVERT: B 81 GLN cc_start: 0.6530 (mt0) cc_final: 0.6031 (mt0) REVERT: B 93 GLN cc_start: 0.8461 (pp30) cc_final: 0.7509 (tm-30) REVERT: B 103 ARG cc_start: 0.7433 (ttm110) cc_final: 0.7122 (ttm110) REVERT: B 106 GLN cc_start: 0.7638 (mt0) cc_final: 0.7329 (mp10) REVERT: B 139 GLU cc_start: 0.7427 (mp0) cc_final: 0.7122 (mp0) REVERT: B 143 ARG cc_start: 0.6885 (mtt180) cc_final: 0.6541 (mmt90) REVERT: B 168 LEU cc_start: 0.8440 (tp) cc_final: 0.8180 (tp) REVERT: B 185 ASP cc_start: 0.7112 (t0) cc_final: 0.6663 (t0) REVERT: B 213 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7339 (tm-30) REVERT: B 248 LYS cc_start: 0.8642 (mmtt) cc_final: 0.7964 (mmtt) REVERT: B 251 ASP cc_start: 0.7699 (p0) cc_final: 0.7442 (p0) REVERT: B 266 LEU cc_start: 0.8415 (tp) cc_final: 0.8109 (tp) REVERT: B 267 HIS cc_start: 0.7543 (m170) cc_final: 0.7166 (m170) REVERT: B 274 TYR cc_start: 0.6650 (t80) cc_final: 0.6247 (t80) REVERT: B 303 TYR cc_start: 0.8232 (m-80) cc_final: 0.7677 (m-80) REVERT: B 311 CYS cc_start: 0.4023 (p) cc_final: 0.3302 (m) REVERT: B 321 GLU cc_start: 0.7744 (mp0) cc_final: 0.7221 (mp0) REVERT: B 323 THR cc_start: 0.7492 (t) cc_final: 0.7152 (p) REVERT: B 332 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6658 (mp0) REVERT: B 345 LEU cc_start: 0.7984 (mt) cc_final: 0.7678 (mt) REVERT: B 350 LEU cc_start: 0.7989 (mt) cc_final: 0.7690 (mt) REVERT: B 364 PHE cc_start: 0.8777 (m-80) cc_final: 0.8086 (m-80) REVERT: B 371 PHE cc_start: 0.7703 (m-10) cc_final: 0.7229 (m-10) REVERT: B 397 LEU cc_start: 0.8875 (mt) cc_final: 0.8639 (tt) REVERT: B 398 GLN cc_start: 0.8274 (mm-40) cc_final: 0.8023 (mm-40) REVERT: B 411 TYR cc_start: 0.7295 (t80) cc_final: 0.6530 (t80) REVERT: B 420 PRO cc_start: 0.8381 (Cg_endo) cc_final: 0.8117 (Cg_exo) REVERT: B 426 GLN cc_start: 0.7638 (pt0) cc_final: 0.6955 (pp30) REVERT: B 436 LEU cc_start: 0.7899 (mt) cc_final: 0.7531 (mp) REVERT: B 444 THR cc_start: 0.7537 (m) cc_final: 0.6508 (m) REVERT: B 451 SER cc_start: 0.8449 (m) cc_final: 0.7828 (m) REVERT: B 452 TRP cc_start: 0.7974 (p90) cc_final: 0.7455 (p90) REVERT: B 467 LEU cc_start: 0.7367 (tp) cc_final: 0.6501 (pp) REVERT: B 481 PRO cc_start: 0.8116 (Cg_endo) cc_final: 0.7554 (Cg_exo) REVERT: B 484 GLN cc_start: 0.8815 (mt0) cc_final: 0.8473 (mm-40) REVERT: B 490 HIS cc_start: 0.8391 (m-70) cc_final: 0.8171 (m-70) REVERT: B 493 LEU cc_start: 0.8358 (tp) cc_final: 0.8086 (tp) REVERT: B 517 ARG cc_start: 0.8466 (mtt180) cc_final: 0.8196 (ptp90) REVERT: B 527 GLN cc_start: 0.7217 (pm20) cc_final: 0.6066 (pm20) REVERT: B 577 PHE cc_start: 0.8417 (m-80) cc_final: 0.8022 (m-80) REVERT: B 580 GLU cc_start: 0.8351 (tp30) cc_final: 0.7921 (tp30) REVERT: A 29 LYS cc_start: 0.8099 (pttm) cc_final: 0.7530 (pttm) REVERT: A 40 GLN cc_start: 0.6902 (pt0) cc_final: 0.6244 (pt0) REVERT: A 44 PHE cc_start: 0.8342 (m-10) cc_final: 0.8027 (m-10) REVERT: A 45 GLU cc_start: 0.8408 (mp0) cc_final: 0.8066 (mp0) REVERT: A 46 ASP cc_start: 0.7362 (t70) cc_final: 0.6849 (t70) REVERT: A 47 HIS cc_start: 0.8069 (t70) cc_final: 0.6955 (t70) REVERT: A 51 LEU cc_start: 0.9035 (tp) cc_final: 0.8713 (tp) REVERT: A 54 MET cc_start: 0.8269 (tpt) cc_final: 0.8012 (tpt) REVERT: A 55 PHE cc_start: 0.8004 (m-10) cc_final: 0.7775 (m-10) REVERT: A 61 VAL cc_start: 0.8387 (m) cc_final: 0.8105 (p) REVERT: A 74 TYR cc_start: 0.8231 (m-80) cc_final: 0.7153 (m-80) REVERT: A 77 SER cc_start: 0.8174 (m) cc_final: 0.7178 (p) REVERT: A 80 LYS cc_start: 0.8290 (mttm) cc_final: 0.7982 (mttm) REVERT: A 88 TYR cc_start: 0.7226 (p90) cc_final: 0.5650 (p90) REVERT: A 111 MET cc_start: 0.6943 (ttt) cc_final: 0.6322 (ttt) REVERT: A 112 TYR cc_start: 0.6617 (m-80) cc_final: 0.6290 (m-10) REVERT: A 119 LEU cc_start: 0.7162 (tp) cc_final: 0.6882 (tp) REVERT: A 132 LEU cc_start: 0.7489 (mm) cc_final: 0.6827 (mm) REVERT: A 137 MET cc_start: 0.8487 (mtm) cc_final: 0.8165 (mtm) REVERT: A 138 ARG cc_start: 0.8338 (mtt180) cc_final: 0.8070 (mtt-85) REVERT: A 143 ILE cc_start: 0.9025 (mt) cc_final: 0.8574 (mm) REVERT: A 163 GLN cc_start: 0.8327 (tt0) cc_final: 0.7863 (tt0) REVERT: A 176 MET cc_start: 0.8669 (ptp) cc_final: 0.8229 (ptt) REVERT: A 209 LYS cc_start: 0.8321 (mttt) cc_final: 0.7745 (mtmt) REVERT: A 212 LYS cc_start: 0.7662 (ttmm) cc_final: 0.7362 (ttmm) REVERT: A 229 SER cc_start: 0.8055 (p) cc_final: 0.7803 (p) REVERT: A 230 ASP cc_start: 0.8325 (m-30) cc_final: 0.8060 (m-30) REVERT: A 233 HIS cc_start: 0.7630 (t-90) cc_final: 0.7130 (t-90) REVERT: A 254 PHE cc_start: 0.7394 (m-10) cc_final: 0.7158 (m-80) REVERT: A 261 LYS cc_start: 0.7579 (mttm) cc_final: 0.7136 (mttm) REVERT: A 268 MET cc_start: 0.6525 (mtm) cc_final: 0.5425 (mtm) REVERT: A 277 MET cc_start: 0.6964 (mtt) cc_final: 0.5844 (mtt) REVERT: A 293 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7025 (mtpp) REVERT: A 338 ASN cc_start: 0.7633 (p0) cc_final: 0.6147 (p0) REVERT: A 340 ILE cc_start: 0.7370 (mp) cc_final: 0.7137 (mp) REVERT: A 345 PHE cc_start: 0.8539 (m-80) cc_final: 0.8198 (m-80) REVERT: A 360 LYS cc_start: 0.8660 (tttt) cc_final: 0.8314 (tttt) REVERT: A 368 ASP cc_start: 0.5165 (m-30) cc_final: 0.4708 (m-30) REVERT: A 396 LYS cc_start: 0.8533 (tppp) cc_final: 0.7980 (tppp) REVERT: A 404 PHE cc_start: 0.7268 (p90) cc_final: 0.6447 (p90) REVERT: A 417 LEU cc_start: 0.7633 (mt) cc_final: 0.7381 (mm) REVERT: A 421 GLU cc_start: 0.8703 (tt0) cc_final: 0.7650 (tt0) REVERT: A 424 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7371 (mt-10) REVERT: A 432 GLN cc_start: 0.8600 (tp40) cc_final: 0.8229 (tp-100) REVERT: A 433 HIS cc_start: 0.8588 (m90) cc_final: 0.8156 (m90) REVERT: A 445 ILE cc_start: 0.7928 (pt) cc_final: 0.7716 (pt) REVERT: A 454 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8178 (mmtt) REVERT: A 456 ILE cc_start: 0.8447 (mm) cc_final: 0.7909 (pt) REVERT: A 457 SER cc_start: 0.8119 (m) cc_final: 0.7483 (t) REVERT: A 476 ASN cc_start: 0.7780 (t0) cc_final: 0.6728 (t0) REVERT: A 479 LYS cc_start: 0.7954 (mtpt) cc_final: 0.7059 (mtpt) REVERT: A 487 LYS cc_start: 0.7741 (mtmm) cc_final: 0.7489 (mtmm) REVERT: A 496 GLU cc_start: 0.7775 (mp0) cc_final: 0.7391 (mp0) REVERT: A 551 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8497 (pm20) REVERT: A 559 HIS cc_start: 0.7773 (t70) cc_final: 0.7304 (t-170) REVERT: A 569 ILE cc_start: 0.8348 (tp) cc_final: 0.7965 (tp) REVERT: C 25 MET cc_start: 0.8032 (mmp) cc_final: 0.7431 (mmt) REVERT: C 31 ARG cc_start: 0.6579 (ttp-170) cc_final: 0.6356 (ttm170) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.2452 time to fit residues: 121.7394 Evaluate side-chains 366 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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: 0.6980 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 44 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9358 Z= 0.213 Angle : 0.645 9.332 12680 Z= 0.326 Chirality : 0.047 0.265 1417 Planarity : 0.005 0.059 1669 Dihedral : 7.238 72.458 1426 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.24), residues: 1164 helix: -1.65 (0.79), residues: 42 sheet: -1.36 (0.64), residues: 66 loop : -1.81 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 200 HIS 0.017 0.001 HIS A 183 PHE 0.021 0.002 PHE B 73 TYR 0.019 0.001 TYR A 117 ARG 0.009 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 370 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.7528 (mtp) cc_final: 0.6496 (ptp) REVERT: B 44 ASP cc_start: 0.7160 (t0) cc_final: 0.6636 (t0) REVERT: B 45 MET cc_start: 0.8504 (tmm) cc_final: 0.8252 (tmm) REVERT: B 46 LEU cc_start: 0.8642 (mt) cc_final: 0.8379 (mt) REVERT: B 47 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7297 (ttp80) REVERT: B 61 GLU cc_start: 0.6728 (tm-30) cc_final: 0.3307 (tm-30) REVERT: B 64 TYR cc_start: 0.7900 (m-80) cc_final: 0.7633 (m-80) REVERT: B 65 LEU cc_start: 0.8035 (mt) cc_final: 0.7820 (mt) REVERT: B 70 SER cc_start: 0.8656 (p) cc_final: 0.8406 (p) REVERT: B 79 GLU cc_start: 0.6955 (tt0) cc_final: 0.6456 (tt0) REVERT: B 81 GLN cc_start: 0.6450 (mt0) cc_final: 0.6009 (mt0) REVERT: B 93 GLN cc_start: 0.8477 (pp30) cc_final: 0.7682 (tt0) REVERT: B 100 ARG cc_start: 0.7782 (mmm-85) cc_final: 0.7433 (mmm-85) REVERT: B 106 GLN cc_start: 0.7766 (mt0) cc_final: 0.7462 (mp-120) REVERT: B 139 GLU cc_start: 0.7409 (mp0) cc_final: 0.7155 (mp0) REVERT: B 168 LEU cc_start: 0.8391 (tp) cc_final: 0.8129 (tp) REVERT: B 185 ASP cc_start: 0.6934 (t0) cc_final: 0.6632 (t0) REVERT: B 193 HIS cc_start: 0.7661 (m90) cc_final: 0.7207 (m90) REVERT: B 226 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7524 (tpp80) REVERT: B 248 LYS cc_start: 0.8570 (mmtt) cc_final: 0.7930 (mmtt) REVERT: B 251 ASP cc_start: 0.7704 (p0) cc_final: 0.7482 (p0) REVERT: B 253 LEU cc_start: 0.7755 (mt) cc_final: 0.7521 (mt) REVERT: B 265 GLU cc_start: 0.7119 (pm20) cc_final: 0.6198 (pm20) REVERT: B 266 LEU cc_start: 0.8324 (tp) cc_final: 0.7790 (tp) REVERT: B 267 HIS cc_start: 0.7624 (m170) cc_final: 0.6852 (m170) REVERT: B 274 TYR cc_start: 0.6409 (t80) cc_final: 0.6067 (t80) REVERT: B 282 MET cc_start: 0.8451 (mtm) cc_final: 0.8230 (mtm) REVERT: B 288 ARG cc_start: 0.7803 (mpt-90) cc_final: 0.7333 (mmt-90) REVERT: B 303 TYR cc_start: 0.8231 (m-80) cc_final: 0.7648 (m-80) REVERT: B 311 CYS cc_start: 0.4042 (p) cc_final: 0.3403 (m) REVERT: B 321 GLU cc_start: 0.7761 (mp0) cc_final: 0.7158 (mp0) REVERT: B 332 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6655 (mp0) REVERT: B 345 LEU cc_start: 0.8117 (mt) cc_final: 0.7878 (mt) REVERT: B 364 PHE cc_start: 0.8787 (m-80) cc_final: 0.8253 (m-80) REVERT: B 371 PHE cc_start: 0.7664 (m-10) cc_final: 0.7170 (m-10) REVERT: B 376 PHE cc_start: 0.8097 (m-10) cc_final: 0.7757 (m-10) REVERT: B 397 LEU cc_start: 0.8838 (mt) cc_final: 0.8504 (tt) REVERT: B 398 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8077 (mm-40) REVERT: B 405 GLU cc_start: 0.6522 (tp30) cc_final: 0.6072 (tp30) REVERT: B 411 TYR cc_start: 0.7261 (t80) cc_final: 0.6470 (t80) REVERT: B 420 PRO cc_start: 0.8318 (Cg_endo) cc_final: 0.8005 (Cg_exo) REVERT: B 430 VAL cc_start: 0.7865 (t) cc_final: 0.7330 (p) REVERT: B 436 LEU cc_start: 0.7873 (mt) cc_final: 0.7617 (mt) REVERT: B 444 THR cc_start: 0.7483 (m) cc_final: 0.6076 (m) REVERT: B 452 TRP cc_start: 0.7994 (p90) cc_final: 0.7571 (p90) REVERT: B 467 LEU cc_start: 0.7298 (tp) cc_final: 0.6353 (pt) REVERT: B 481 PRO cc_start: 0.8103 (Cg_endo) cc_final: 0.7514 (Cg_exo) REVERT: B 484 GLN cc_start: 0.8786 (mt0) cc_final: 0.8429 (mm-40) REVERT: B 486 PHE cc_start: 0.8480 (m-10) cc_final: 0.7761 (m-10) REVERT: B 487 ARG cc_start: 0.7677 (mmt90) cc_final: 0.7008 (ttm-80) REVERT: B 493 LEU cc_start: 0.8352 (tp) cc_final: 0.8073 (tp) REVERT: B 517 ARG cc_start: 0.8486 (mtt180) cc_final: 0.8273 (mtt180) REVERT: B 527 GLN cc_start: 0.7270 (pm20) cc_final: 0.6646 (pm20) REVERT: B 577 PHE cc_start: 0.8511 (m-80) cc_final: 0.8006 (m-80) REVERT: B 580 GLU cc_start: 0.8337 (tp30) cc_final: 0.7891 (tp30) REVERT: A 29 LYS cc_start: 0.8171 (pttm) cc_final: 0.7612 (pttm) REVERT: A 40 GLN cc_start: 0.6836 (pt0) cc_final: 0.6098 (pt0) REVERT: A 44 PHE cc_start: 0.8377 (m-10) cc_final: 0.7987 (m-10) REVERT: A 45 GLU cc_start: 0.8425 (mp0) cc_final: 0.8103 (mp0) REVERT: A 46 ASP cc_start: 0.7338 (t70) cc_final: 0.6822 (t70) REVERT: A 47 HIS cc_start: 0.7988 (t70) cc_final: 0.6868 (t70) REVERT: A 51 LEU cc_start: 0.8991 (tp) cc_final: 0.8592 (tp) REVERT: A 54 MET cc_start: 0.8286 (tpt) cc_final: 0.8000 (tpt) REVERT: A 61 VAL cc_start: 0.8444 (m) cc_final: 0.8130 (p) REVERT: A 74 TYR cc_start: 0.8228 (m-80) cc_final: 0.7152 (m-80) REVERT: A 77 SER cc_start: 0.8086 (m) cc_final: 0.7154 (p) REVERT: A 80 LYS cc_start: 0.8308 (mttm) cc_final: 0.7999 (mttm) REVERT: A 88 TYR cc_start: 0.7264 (p90) cc_final: 0.5583 (p90) REVERT: A 106 ILE cc_start: 0.7864 (tt) cc_final: 0.7299 (mm) REVERT: A 111 MET cc_start: 0.7083 (ttt) cc_final: 0.6688 (ttt) REVERT: A 112 TYR cc_start: 0.7493 (m-80) cc_final: 0.6772 (m-80) REVERT: A 114 GLU cc_start: 0.7666 (tt0) cc_final: 0.7256 (tt0) REVERT: A 119 LEU cc_start: 0.7248 (tp) cc_final: 0.6910 (tp) REVERT: A 132 LEU cc_start: 0.7451 (mm) cc_final: 0.6777 (mm) REVERT: A 135 LEU cc_start: 0.8352 (tp) cc_final: 0.7886 (tp) REVERT: A 137 MET cc_start: 0.8539 (mtm) cc_final: 0.7866 (mtm) REVERT: A 143 ILE cc_start: 0.8968 (mt) cc_final: 0.8606 (mm) REVERT: A 163 GLN cc_start: 0.8318 (tt0) cc_final: 0.7883 (tt0) REVERT: A 176 MET cc_start: 0.8566 (ptp) cc_final: 0.8052 (ptt) REVERT: A 209 LYS cc_start: 0.8261 (mttt) cc_final: 0.7663 (mtmt) REVERT: A 229 SER cc_start: 0.8081 (p) cc_final: 0.7622 (t) REVERT: A 230 ASP cc_start: 0.8326 (m-30) cc_final: 0.7032 (p0) REVERT: A 254 PHE cc_start: 0.7318 (m-10) cc_final: 0.7016 (m-80) REVERT: A 261 LYS cc_start: 0.7538 (mttm) cc_final: 0.7181 (mttm) REVERT: A 262 ASP cc_start: 0.8164 (t0) cc_final: 0.7497 (t0) REVERT: A 268 MET cc_start: 0.6511 (mtm) cc_final: 0.5418 (mtm) REVERT: A 277 MET cc_start: 0.6942 (mtt) cc_final: 0.5832 (mtt) REVERT: A 293 LYS cc_start: 0.7859 (mtpp) cc_final: 0.6902 (mtpp) REVERT: A 338 ASN cc_start: 0.7619 (p0) cc_final: 0.6179 (p0) REVERT: A 340 ILE cc_start: 0.7383 (mp) cc_final: 0.7165 (mp) REVERT: A 345 PHE cc_start: 0.8531 (m-80) cc_final: 0.7919 (m-80) REVERT: A 360 LYS cc_start: 0.8644 (tttt) cc_final: 0.8312 (tttt) REVERT: A 396 LYS cc_start: 0.8527 (tppp) cc_final: 0.7918 (tppp) REVERT: A 421 GLU cc_start: 0.8571 (tt0) cc_final: 0.7835 (tt0) REVERT: A 424 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7436 (mt-10) REVERT: A 432 GLN cc_start: 0.8576 (tp40) cc_final: 0.8237 (tp-100) REVERT: A 433 HIS cc_start: 0.8543 (m90) cc_final: 0.8106 (m90) REVERT: A 445 ILE cc_start: 0.7972 (pt) cc_final: 0.7674 (pt) REVERT: A 451 ARG cc_start: 0.7419 (ptp-110) cc_final: 0.7151 (mtt-85) REVERT: A 454 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8230 (mmtt) REVERT: A 457 SER cc_start: 0.8075 (m) cc_final: 0.7415 (t) REVERT: A 476 ASN cc_start: 0.7777 (t0) cc_final: 0.6766 (t0) REVERT: A 479 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7062 (mtpt) REVERT: A 496 GLU cc_start: 0.7817 (mp0) cc_final: 0.7399 (mp0) REVERT: A 551 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8527 (mt-10) REVERT: A 559 HIS cc_start: 0.7757 (t70) cc_final: 0.7293 (t-170) REVERT: C 25 MET cc_start: 0.8106 (mmp) cc_final: 0.7725 (mmt) REVERT: C 31 ARG cc_start: 0.6548 (ttp-170) cc_final: 0.6343 (ttm170) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.2440 time to fit residues: 118.4678 Evaluate side-chains 356 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 107 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** B 329 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** B 491 GLN A 32 GLN ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.5348 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= 0.213 Angle : 0.657 12.031 12680 Z= 0.329 Chirality : 0.047 0.263 1417 Planarity : 0.004 0.050 1669 Dihedral : 7.170 69.524 1426 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.46 % Favored : 87.54 % Rotamer: Outliers : 0.10 % Allowed : 0.59 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.24), residues: 1164 helix: -1.80 (0.74), residues: 48 sheet: -1.29 (0.66), residues: 66 loop : -1.82 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 477 HIS 0.009 0.001 HIS A 183 PHE 0.019 0.002 PHE B 73 TYR 0.016 0.001 TYR A 125 ARG 0.007 0.001 ARG A 149 *********************** 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 355 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 354 time to evaluate : 0.795 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 31 MET cc_start: 0.7533 (mtp) cc_final: 0.6670 (ptp) REVERT: B 32 LYS cc_start: 0.8189 (mmtp) cc_final: 0.7809 (mmtt) REVERT: B 44 ASP cc_start: 0.7322 (t0) cc_final: 0.6702 (t0) REVERT: B 45 MET cc_start: 0.8492 (tmm) cc_final: 0.8249 (tmm) REVERT: B 46 LEU cc_start: 0.8640 (mt) cc_final: 0.8382 (mt) REVERT: B 47 ARG cc_start: 0.7597 (ttp80) cc_final: 0.7264 (ttp80) REVERT: B 61 GLU cc_start: 0.6804 (tm-30) cc_final: 0.3287 (tm-30) REVERT: B 65 LEU cc_start: 0.8015 (mt) cc_final: 0.7755 (mt) REVERT: B 70 SER cc_start: 0.8676 (p) cc_final: 0.8447 (p) REVERT: B 79 GLU cc_start: 0.7016 (tt0) cc_final: 0.6724 (tt0) REVERT: B 81 GLN cc_start: 0.6429 (mt0) cc_final: 0.6099 (mt0) REVERT: B 93 GLN cc_start: 0.8475 (pp30) cc_final: 0.7244 (tt0) REVERT: B 100 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7434 (mmm-85) REVERT: B 106 GLN cc_start: 0.7791 (mt0) cc_final: 0.7475 (mp-120) REVERT: B 139 GLU cc_start: 0.7388 (mp0) cc_final: 0.7104 (mp0) REVERT: B 143 ARG cc_start: 0.7110 (mtt180) cc_final: 0.6704 (mtt180) REVERT: B 153 VAL cc_start: 0.7910 (t) cc_final: 0.6723 (t) REVERT: B 168 LEU cc_start: 0.8430 (tp) cc_final: 0.8186 (tp) REVERT: B 169 TRP cc_start: 0.8394 (m100) cc_final: 0.6585 (m100) REVERT: B 185 ASP cc_start: 0.7014 (t0) cc_final: 0.6809 (t0) REVERT: B 193 HIS cc_start: 0.7628 (m90) cc_final: 0.7182 (m90) REVERT: B 248 LYS cc_start: 0.8587 (mmtt) cc_final: 0.7931 (mmtt) REVERT: B 251 ASP cc_start: 0.7721 (p0) cc_final: 0.7460 (p0) REVERT: B 253 LEU cc_start: 0.7734 (mt) cc_final: 0.7503 (mt) REVERT: B 265 GLU cc_start: 0.7050 (pm20) cc_final: 0.6306 (pm20) REVERT: B 266 LEU cc_start: 0.8336 (tp) cc_final: 0.8135 (mm) REVERT: B 274 TYR cc_start: 0.6309 (t80) cc_final: 0.6061 (t80) REVERT: B 282 MET cc_start: 0.8389 (mtm) cc_final: 0.8124 (mtm) REVERT: B 288 ARG cc_start: 0.7789 (mpt-90) cc_final: 0.7506 (mpt-90) REVERT: B 303 TYR cc_start: 0.8142 (m-80) cc_final: 0.7775 (m-80) REVERT: B 311 CYS cc_start: 0.4018 (p) cc_final: 0.3398 (m) REVERT: B 323 THR cc_start: 0.7709 (t) cc_final: 0.7358 (p) REVERT: B 332 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6813 (mp0) REVERT: B 345 LEU cc_start: 0.8165 (mt) cc_final: 0.7851 (mt) REVERT: B 364 PHE cc_start: 0.8820 (m-80) cc_final: 0.8228 (m-80) REVERT: B 376 PHE cc_start: 0.8138 (m-10) cc_final: 0.7772 (m-10) REVERT: B 397 LEU cc_start: 0.8838 (mt) cc_final: 0.8496 (tt) REVERT: B 398 GLN cc_start: 0.8281 (mm-40) cc_final: 0.8063 (mm-40) REVERT: B 411 TYR cc_start: 0.7271 (t80) cc_final: 0.6480 (t80) REVERT: B 432 ARG cc_start: 0.7027 (mmt-90) cc_final: 0.6663 (tpp-160) REVERT: B 434 ARG cc_start: 0.7434 (mtt90) cc_final: 0.6943 (mmt180) REVERT: B 436 LEU cc_start: 0.7903 (mt) cc_final: 0.7638 (mt) REVERT: B 444 THR cc_start: 0.7487 (m) cc_final: 0.6073 (m) REVERT: B 452 TRP cc_start: 0.7992 (p90) cc_final: 0.7540 (p90) REVERT: B 463 SER cc_start: 0.7573 (t) cc_final: 0.7277 (p) REVERT: B 467 LEU cc_start: 0.7253 (tp) cc_final: 0.6338 (pt) REVERT: B 481 PRO cc_start: 0.8105 (Cg_endo) cc_final: 0.7567 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8444 (m100) cc_final: 0.8155 (m100) REVERT: B 484 GLN cc_start: 0.8800 (mt0) cc_final: 0.8383 (mm-40) REVERT: B 486 PHE cc_start: 0.8325 (m-10) cc_final: 0.8106 (m-10) REVERT: B 487 ARG cc_start: 0.7816 (mmt90) cc_final: 0.7032 (ttm-80) REVERT: B 493 LEU cc_start: 0.8356 (tp) cc_final: 0.7721 (tp) REVERT: B 517 ARG cc_start: 0.8503 (mtt180) cc_final: 0.8273 (mtt180) REVERT: B 577 PHE cc_start: 0.8517 (m-80) cc_final: 0.8090 (m-80) REVERT: B 580 GLU cc_start: 0.8341 (tp30) cc_final: 0.7970 (tp30) REVERT: A 29 LYS cc_start: 0.8104 (pttm) cc_final: 0.7543 (pttm) REVERT: A 40 GLN cc_start: 0.6808 (pt0) cc_final: 0.6094 (pt0) REVERT: A 44 PHE cc_start: 0.8365 (m-10) cc_final: 0.8039 (m-10) REVERT: A 45 GLU cc_start: 0.8429 (mp0) cc_final: 0.8127 (mp0) REVERT: A 46 ASP cc_start: 0.7386 (t70) cc_final: 0.6930 (t70) REVERT: A 47 HIS cc_start: 0.7957 (t70) cc_final: 0.6853 (t70) REVERT: A 51 LEU cc_start: 0.9063 (tp) cc_final: 0.8660 (tp) REVERT: A 54 MET cc_start: 0.8300 (tpt) cc_final: 0.8003 (tpt) REVERT: A 55 PHE cc_start: 0.8090 (m-10) cc_final: 0.7830 (m-10) REVERT: A 61 VAL cc_start: 0.8449 (m) cc_final: 0.8140 (p) REVERT: A 74 TYR cc_start: 0.8265 (m-80) cc_final: 0.7155 (m-80) REVERT: A 77 SER cc_start: 0.8091 (m) cc_final: 0.7827 (p) REVERT: A 88 TYR cc_start: 0.7154 (p90) cc_final: 0.5594 (p90) REVERT: A 111 MET cc_start: 0.7272 (ttt) cc_final: 0.6839 (ttt) REVERT: A 112 TYR cc_start: 0.7459 (m-80) cc_final: 0.6667 (m-80) REVERT: A 114 GLU cc_start: 0.7793 (tt0) cc_final: 0.7214 (tt0) REVERT: A 119 LEU cc_start: 0.7320 (tp) cc_final: 0.7035 (tp) REVERT: A 132 LEU cc_start: 0.7125 (mm) cc_final: 0.6407 (mm) REVERT: A 137 MET cc_start: 0.8646 (mtm) cc_final: 0.8229 (mtm) REVERT: A 163 GLN cc_start: 0.8294 (tt0) cc_final: 0.7735 (tt0) REVERT: A 165 ARG cc_start: 0.7402 (mtp-110) cc_final: 0.7193 (mtp-110) REVERT: A 172 PHE cc_start: 0.8122 (m-80) cc_final: 0.7783 (m-10) REVERT: A 173 LEU cc_start: 0.8089 (mt) cc_final: 0.7835 (mm) REVERT: A 176 MET cc_start: 0.8607 (ptp) cc_final: 0.7937 (ptp) REVERT: A 196 ASN cc_start: 0.8871 (m-40) cc_final: 0.8564 (m110) REVERT: A 209 LYS cc_start: 0.8220 (mttt) cc_final: 0.7642 (mtmt) REVERT: A 212 LYS cc_start: 0.7385 (ttmm) cc_final: 0.7014 (ttmm) REVERT: A 229 SER cc_start: 0.7932 (p) cc_final: 0.7472 (t) REVERT: A 230 ASP cc_start: 0.8225 (m-30) cc_final: 0.6956 (p0) REVERT: A 254 PHE cc_start: 0.7383 (m-10) cc_final: 0.7060 (m-10) REVERT: A 255 ARG cc_start: 0.6504 (tpt170) cc_final: 0.6003 (tpt170) REVERT: A 257 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8176 (mm-30) REVERT: A 261 LYS cc_start: 0.7521 (mttm) cc_final: 0.6954 (mttm) REVERT: A 262 ASP cc_start: 0.8102 (t0) cc_final: 0.7502 (t0) REVERT: A 268 MET cc_start: 0.6532 (mtm) cc_final: 0.5423 (mtm) REVERT: A 277 MET cc_start: 0.6916 (mtt) cc_final: 0.5855 (mtt) REVERT: A 293 LYS cc_start: 0.7948 (mtpp) cc_final: 0.7049 (mtpp) REVERT: A 338 ASN cc_start: 0.7642 (p0) cc_final: 0.6212 (p0) REVERT: A 345 PHE cc_start: 0.8519 (m-80) cc_final: 0.7823 (m-80) REVERT: A 360 LYS cc_start: 0.8606 (tttt) cc_final: 0.8258 (tttt) REVERT: A 396 LYS cc_start: 0.8414 (tppp) cc_final: 0.7794 (tppp) REVERT: A 404 PHE cc_start: 0.7397 (p90) cc_final: 0.6627 (p90) REVERT: A 407 ILE cc_start: 0.7640 (mm) cc_final: 0.7243 (tp) REVERT: A 417 LEU cc_start: 0.7792 (mp) cc_final: 0.7435 (mp) REVERT: A 421 GLU cc_start: 0.8621 (tt0) cc_final: 0.7974 (tt0) REVERT: A 424 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7469 (mt-10) REVERT: A 431 LYS cc_start: 0.8108 (mtmm) cc_final: 0.7875 (mtmm) REVERT: A 432 GLN cc_start: 0.8471 (tp40) cc_final: 0.8245 (tp-100) REVERT: A 433 HIS cc_start: 0.8452 (m90) cc_final: 0.8045 (m90) REVERT: A 454 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8238 (mmtt) REVERT: A 457 SER cc_start: 0.8057 (m) cc_final: 0.7734 (m) REVERT: A 476 ASN cc_start: 0.7778 (t0) cc_final: 0.6762 (t0) REVERT: A 479 LYS cc_start: 0.7923 (mtpt) cc_final: 0.7066 (mtpt) REVERT: A 496 GLU cc_start: 0.7824 (mp0) cc_final: 0.7398 (mp0) REVERT: A 559 HIS cc_start: 0.7772 (t70) cc_final: 0.7268 (t-170) REVERT: C 25 MET cc_start: 0.8021 (mmp) cc_final: 0.7721 (mmt) REVERT: C 31 ARG cc_start: 0.6508 (ttp-170) cc_final: 0.6303 (ttm170) outliers start: 1 outliers final: 0 residues processed: 354 average time/residue: 0.2455 time to fit residues: 114.0622 Evaluate side-chains 352 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 94 optimal weight: 0.4980 chunk 98 optimal weight: 0.0770 chunk 103 optimal weight: 0.2980 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.3536 ------------------------------------------------------------------------------- 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 ** 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 40 GLN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN A 557 GLN A 565 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9358 Z= 0.179 Angle : 0.640 11.171 12680 Z= 0.318 Chirality : 0.046 0.260 1417 Planarity : 0.005 0.085 1669 Dihedral : 6.914 65.778 1426 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.24), residues: 1164 helix: -2.37 (0.63), residues: 61 sheet: -1.09 (0.69), residues: 66 loop : -1.79 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 164 HIS 0.007 0.001 HIS A 183 PHE 0.016 0.001 PHE B 73 TYR 0.017 0.001 TYR A 125 ARG 0.008 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 354 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 1.010 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: 0.7192 (pp30) cc_final: 0.6669 (pp30) REVERT: B 31 MET cc_start: 0.7484 (mtp) cc_final: 0.6689 (ptp) REVERT: B 32 LYS cc_start: 0.8143 (mmtp) cc_final: 0.7855 (mmtt) REVERT: B 44 ASP cc_start: 0.7285 (t0) cc_final: 0.6699 (t0) REVERT: B 45 MET cc_start: 0.8443 (tmm) cc_final: 0.8194 (tmm) REVERT: B 46 LEU cc_start: 0.8708 (mt) cc_final: 0.8448 (mt) REVERT: B 47 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7259 (ttp80) REVERT: B 54 GLN cc_start: 0.7174 (mp-120) cc_final: 0.6847 (mp10) REVERT: B 61 GLU cc_start: 0.6813 (tm-30) cc_final: 0.3441 (tm-30) REVERT: B 65 LEU cc_start: 0.8040 (mt) cc_final: 0.7772 (mt) REVERT: B 75 GLN cc_start: 0.7934 (pt0) cc_final: 0.7719 (pt0) REVERT: B 79 GLU cc_start: 0.7067 (tt0) cc_final: 0.6722 (tt0) REVERT: B 81 GLN cc_start: 0.6487 (mt0) cc_final: 0.6144 (mt0) REVERT: B 93 GLN cc_start: 0.8516 (pp30) cc_final: 0.7419 (tm-30) REVERT: B 100 ARG cc_start: 0.7774 (mmm-85) cc_final: 0.7254 (mmm-85) REVERT: B 106 GLN cc_start: 0.7771 (mt0) cc_final: 0.7486 (mp-120) REVERT: B 139 GLU cc_start: 0.7390 (mp0) cc_final: 0.6984 (mp0) REVERT: B 143 ARG cc_start: 0.7056 (mtt180) cc_final: 0.6695 (mtt180) REVERT: B 153 VAL cc_start: 0.7843 (t) cc_final: 0.6522 (t) REVERT: B 168 LEU cc_start: 0.8419 (tp) cc_final: 0.8181 (tp) REVERT: B 169 TRP cc_start: 0.8378 (m100) cc_final: 0.6498 (m100) REVERT: B 193 HIS cc_start: 0.7614 (m90) cc_final: 0.7179 (m90) REVERT: B 213 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7279 (tm-30) REVERT: B 248 LYS cc_start: 0.8575 (mmtt) cc_final: 0.7883 (mmtt) REVERT: B 251 ASP cc_start: 0.7759 (p0) cc_final: 0.7271 (p0) REVERT: B 253 LEU cc_start: 0.7725 (mt) cc_final: 0.7480 (mt) REVERT: B 258 PHE cc_start: 0.7452 (m-80) cc_final: 0.7031 (m-80) REVERT: B 265 GLU cc_start: 0.7132 (pm20) cc_final: 0.6369 (pm20) REVERT: B 266 LEU cc_start: 0.8376 (tp) cc_final: 0.7792 (mm) REVERT: B 274 TYR cc_start: 0.6563 (t80) cc_final: 0.6237 (t80) REVERT: B 282 MET cc_start: 0.8439 (mtm) cc_final: 0.8148 (mtm) REVERT: B 286 GLU cc_start: 0.7842 (mp0) cc_final: 0.7627 (mp0) REVERT: B 303 TYR cc_start: 0.8061 (m-80) cc_final: 0.7617 (m-80) REVERT: B 311 CYS cc_start: 0.4094 (p) cc_final: 0.3501 (m) REVERT: B 345 LEU cc_start: 0.8159 (mt) cc_final: 0.7743 (mt) REVERT: B 351 ARG cc_start: 0.8261 (mmp80) cc_final: 0.7967 (tpp-160) REVERT: B 364 PHE cc_start: 0.8828 (m-80) cc_final: 0.8269 (m-80) REVERT: B 371 PHE cc_start: 0.7583 (m-10) cc_final: 0.7341 (m-10) REVERT: B 376 PHE cc_start: 0.8096 (m-10) cc_final: 0.7725 (m-10) REVERT: B 397 LEU cc_start: 0.8843 (mt) cc_final: 0.8526 (tt) REVERT: B 398 GLN cc_start: 0.8277 (mm-40) cc_final: 0.8065 (mm-40) REVERT: B 411 TYR cc_start: 0.7143 (t80) cc_final: 0.6331 (t80) REVERT: B 426 GLN cc_start: 0.7680 (pt0) cc_final: 0.7024 (pp30) REVERT: B 436 LEU cc_start: 0.7891 (mt) cc_final: 0.7650 (mt) REVERT: B 444 THR cc_start: 0.7461 (m) cc_final: 0.5979 (m) REVERT: B 452 TRP cc_start: 0.7996 (p90) cc_final: 0.7442 (p90) REVERT: B 467 LEU cc_start: 0.7293 (tp) cc_final: 0.6345 (pt) REVERT: B 481 PRO cc_start: 0.8097 (Cg_endo) cc_final: 0.7588 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8415 (m100) cc_final: 0.8179 (m100) REVERT: B 486 PHE cc_start: 0.8372 (m-10) cc_final: 0.8081 (m-10) REVERT: B 487 ARG cc_start: 0.7810 (mmt90) cc_final: 0.7052 (ttm-80) REVERT: B 493 LEU cc_start: 0.8309 (tp) cc_final: 0.7666 (tp) REVERT: B 517 ARG cc_start: 0.8510 (mtt180) cc_final: 0.8223 (mtt180) REVERT: B 527 GLN cc_start: 0.7279 (pm20) cc_final: 0.6334 (pm20) REVERT: B 577 PHE cc_start: 0.8521 (m-80) cc_final: 0.8091 (m-80) REVERT: A 28 LYS cc_start: 0.7813 (mtmm) cc_final: 0.7278 (ptpp) REVERT: A 40 GLN cc_start: 0.6666 (pt0) cc_final: 0.6106 (pt0) REVERT: A 45 GLU cc_start: 0.8428 (mp0) cc_final: 0.8139 (mp0) REVERT: A 46 ASP cc_start: 0.7320 (t70) cc_final: 0.6870 (t70) REVERT: A 47 HIS cc_start: 0.7899 (t70) cc_final: 0.6798 (t70) REVERT: A 51 LEU cc_start: 0.9067 (tp) cc_final: 0.8643 (tp) REVERT: A 54 MET cc_start: 0.8331 (tpt) cc_final: 0.7972 (tpt) REVERT: A 55 PHE cc_start: 0.8085 (m-10) cc_final: 0.7755 (m-10) REVERT: A 61 VAL cc_start: 0.8442 (m) cc_final: 0.8149 (p) REVERT: A 74 TYR cc_start: 0.8246 (m-80) cc_final: 0.7165 (m-80) REVERT: A 76 LEU cc_start: 0.8240 (mt) cc_final: 0.7975 (mt) REVERT: A 77 SER cc_start: 0.7927 (m) cc_final: 0.7513 (p) REVERT: A 80 LYS cc_start: 0.8349 (mttp) cc_final: 0.8084 (mttp) REVERT: A 88 TYR cc_start: 0.7167 (p90) cc_final: 0.5756 (p90) REVERT: A 111 MET cc_start: 0.7352 (ttt) cc_final: 0.6900 (ttt) REVERT: A 112 TYR cc_start: 0.7477 (m-80) cc_final: 0.6675 (m-80) REVERT: A 114 GLU cc_start: 0.7659 (tt0) cc_final: 0.7072 (tt0) REVERT: A 119 LEU cc_start: 0.7399 (tp) cc_final: 0.7123 (tp) REVERT: A 135 LEU cc_start: 0.8363 (tp) cc_final: 0.7905 (tp) REVERT: A 137 MET cc_start: 0.8595 (mtm) cc_final: 0.7992 (mtm) REVERT: A 138 ARG cc_start: 0.8316 (mtt180) cc_final: 0.8094 (mtt-85) REVERT: A 163 GLN cc_start: 0.8261 (tt0) cc_final: 0.7604 (tt0) REVERT: A 165 ARG cc_start: 0.7309 (mtp-110) cc_final: 0.7082 (mtp-110) REVERT: A 172 PHE cc_start: 0.8085 (m-80) cc_final: 0.7750 (m-10) REVERT: A 173 LEU cc_start: 0.8099 (mt) cc_final: 0.7829 (mm) REVERT: A 176 MET cc_start: 0.8571 (ptp) cc_final: 0.7908 (ptp) REVERT: A 196 ASN cc_start: 0.8874 (m-40) cc_final: 0.8568 (m110) REVERT: A 209 LYS cc_start: 0.8111 (mttt) cc_final: 0.7551 (mtmm) REVERT: A 212 LYS cc_start: 0.7283 (ttmm) cc_final: 0.6919 (ttmm) REVERT: A 229 SER cc_start: 0.7938 (p) cc_final: 0.7550 (t) REVERT: A 230 ASP cc_start: 0.8197 (m-30) cc_final: 0.6931 (p0) REVERT: A 254 PHE cc_start: 0.7446 (m-10) cc_final: 0.7129 (m-10) REVERT: A 257 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8149 (mm-30) REVERT: A 261 LYS cc_start: 0.7523 (mttm) cc_final: 0.7119 (ptmt) REVERT: A 262 ASP cc_start: 0.8206 (t0) cc_final: 0.7586 (t0) REVERT: A 268 MET cc_start: 0.6500 (mtm) cc_final: 0.5383 (mtm) REVERT: A 277 MET cc_start: 0.6903 (mtt) cc_final: 0.5754 (mtt) REVERT: A 293 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7124 (mtpp) REVERT: A 325 LYS cc_start: 0.8307 (mttt) cc_final: 0.7848 (mttt) REVERT: A 338 ASN cc_start: 0.7622 (p0) cc_final: 0.7128 (p0) REVERT: A 340 ILE cc_start: 0.7280 (mp) cc_final: 0.6994 (mp) REVERT: A 344 GLU cc_start: 0.7455 (tt0) cc_final: 0.7187 (tt0) REVERT: A 360 LYS cc_start: 0.8583 (tttt) cc_final: 0.8256 (tttt) REVERT: A 396 LYS cc_start: 0.8402 (tppp) cc_final: 0.7738 (tppp) REVERT: A 404 PHE cc_start: 0.7391 (p90) cc_final: 0.6670 (p90) REVERT: A 407 ILE cc_start: 0.7610 (mm) cc_final: 0.7187 (tp) REVERT: A 420 PHE cc_start: 0.8405 (m-80) cc_final: 0.8204 (m-80) REVERT: A 421 GLU cc_start: 0.8604 (tt0) cc_final: 0.7851 (tt0) REVERT: A 424 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 432 GLN cc_start: 0.8447 (tp40) cc_final: 0.8245 (tp-100) REVERT: A 433 HIS cc_start: 0.8483 (m90) cc_final: 0.8145 (m90) REVERT: A 454 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8252 (mmtt) REVERT: A 457 SER cc_start: 0.8047 (m) cc_final: 0.7712 (m) REVERT: A 476 ASN cc_start: 0.7788 (t0) cc_final: 0.6867 (t0) REVERT: A 479 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7099 (mtpt) REVERT: A 489 LYS cc_start: 0.7074 (tptm) cc_final: 0.6721 (mtpp) REVERT: A 496 GLU cc_start: 0.7787 (mp0) cc_final: 0.7470 (mp0) REVERT: A 551 GLU cc_start: 0.8759 (pt0) cc_final: 0.8321 (pm20) REVERT: A 559 HIS cc_start: 0.7718 (t70) cc_final: 0.7241 (t-170) REVERT: C 25 MET cc_start: 0.7983 (mmp) cc_final: 0.7713 (mmt) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.2586 time to fit residues: 119.3841 Evaluate side-chains 350 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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: 0.0270 chunk 115 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 237 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9358 Z= 0.219 Angle : 0.684 10.907 12680 Z= 0.343 Chirality : 0.048 0.260 1417 Planarity : 0.005 0.078 1669 Dihedral : 7.015 65.055 1426 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.29 % Favored : 87.71 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.24), residues: 1164 helix: -2.50 (0.61), residues: 62 sheet: -1.39 (0.63), residues: 76 loop : -1.77 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 477 HIS 0.012 0.001 HIS A 183 PHE 0.016 0.001 PHE B 73 TYR 0.017 0.002 TYR A 125 ARG 0.009 0.001 ARG A 149 ********************** 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 367 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.7228 (pp30) cc_final: 0.6624 (pp30) REVERT: B 31 MET cc_start: 0.7514 (mtp) cc_final: 0.6721 (ptp) REVERT: B 32 LYS cc_start: 0.8106 (mmtp) cc_final: 0.7768 (mmtt) REVERT: B 44 ASP cc_start: 0.7347 (t0) cc_final: 0.6721 (t0) REVERT: B 45 MET cc_start: 0.8493 (tmm) cc_final: 0.8180 (tmm) REVERT: B 46 LEU cc_start: 0.8721 (mt) cc_final: 0.8279 (mt) REVERT: B 47 ARG cc_start: 0.7637 (ttp80) cc_final: 0.7279 (ttp80) REVERT: B 54 GLN cc_start: 0.7249 (mp-120) cc_final: 0.7015 (mp10) REVERT: B 59 ASN cc_start: 0.7206 (m-40) cc_final: 0.6873 (m-40) REVERT: B 61 GLU cc_start: 0.6886 (tm-30) cc_final: 0.3542 (tm-30) REVERT: B 65 LEU cc_start: 0.8048 (mt) cc_final: 0.7835 (mt) REVERT: B 75 GLN cc_start: 0.7959 (pt0) cc_final: 0.7750 (pt0) REVERT: B 79 GLU cc_start: 0.7012 (tt0) cc_final: 0.6790 (tt0) REVERT: B 81 GLN cc_start: 0.6519 (mt0) cc_final: 0.6138 (mt0) REVERT: B 93 GLN cc_start: 0.8488 (pp30) cc_final: 0.7475 (tm-30) REVERT: B 100 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7390 (mmm-85) REVERT: B 139 GLU cc_start: 0.7433 (mp0) cc_final: 0.7047 (mp0) REVERT: B 153 VAL cc_start: 0.7924 (t) cc_final: 0.7527 (t) REVERT: B 156 GLN cc_start: 0.7546 (tm-30) cc_final: 0.7104 (tm-30) REVERT: B 168 LEU cc_start: 0.8443 (tp) cc_final: 0.8194 (tp) REVERT: B 169 TRP cc_start: 0.8373 (m100) cc_final: 0.6760 (m100) REVERT: B 187 ASN cc_start: 0.7750 (m110) cc_final: 0.7500 (m-40) REVERT: B 193 HIS cc_start: 0.7617 (m90) cc_final: 0.7174 (m90) REVERT: B 248 LYS cc_start: 0.8581 (mmtt) cc_final: 0.7896 (mmtt) REVERT: B 251 ASP cc_start: 0.7755 (p0) cc_final: 0.7540 (p0) REVERT: B 253 LEU cc_start: 0.7735 (mt) cc_final: 0.7514 (mt) REVERT: B 265 GLU cc_start: 0.7112 (pm20) cc_final: 0.6446 (pm20) REVERT: B 266 LEU cc_start: 0.8351 (tp) cc_final: 0.8115 (mm) REVERT: B 274 TYR cc_start: 0.6516 (t80) cc_final: 0.6269 (t80) REVERT: B 275 ASN cc_start: 0.8174 (t0) cc_final: 0.7895 (t0) REVERT: B 282 MET cc_start: 0.8396 (mtm) cc_final: 0.8163 (mtm) REVERT: B 303 TYR cc_start: 0.8120 (m-80) cc_final: 0.7640 (m-80) REVERT: B 311 CYS cc_start: 0.4049 (p) cc_final: 0.3434 (m) REVERT: B 323 THR cc_start: 0.7800 (t) cc_final: 0.7575 (p) REVERT: B 329 GLN cc_start: 0.8142 (tp40) cc_final: 0.7897 (tp-100) REVERT: B 345 LEU cc_start: 0.8261 (mt) cc_final: 0.7991 (mt) REVERT: B 364 PHE cc_start: 0.8863 (m-80) cc_final: 0.8298 (m-80) REVERT: B 376 PHE cc_start: 0.8133 (m-10) cc_final: 0.7917 (m-10) REVERT: B 397 LEU cc_start: 0.8856 (mt) cc_final: 0.8519 (tt) REVERT: B 398 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8124 (mm-40) REVERT: B 411 TYR cc_start: 0.7180 (t80) cc_final: 0.6434 (t80) REVERT: B 444 THR cc_start: 0.7494 (m) cc_final: 0.6047 (m) REVERT: B 452 TRP cc_start: 0.7978 (p90) cc_final: 0.7606 (p90) REVERT: B 467 LEU cc_start: 0.7332 (tp) cc_final: 0.6359 (pt) REVERT: B 481 PRO cc_start: 0.8081 (Cg_endo) cc_final: 0.7598 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8402 (m100) cc_final: 0.8143 (m100) REVERT: B 486 PHE cc_start: 0.8359 (m-10) cc_final: 0.8090 (m-10) REVERT: B 487 ARG cc_start: 0.7798 (mmt90) cc_final: 0.7013 (ttm-80) REVERT: B 488 ASN cc_start: 0.8287 (t0) cc_final: 0.7780 (t0) REVERT: B 493 LEU cc_start: 0.8324 (tp) cc_final: 0.7679 (tp) REVERT: B 517 ARG cc_start: 0.8503 (mtt180) cc_final: 0.8235 (mtt180) REVERT: B 520 CYS cc_start: 0.4963 (t) cc_final: 0.4127 (m) REVERT: B 527 GLN cc_start: 0.7219 (pm20) cc_final: 0.6309 (pm20) REVERT: B 577 PHE cc_start: 0.8535 (m-80) cc_final: 0.8090 (m-80) REVERT: A 28 LYS cc_start: 0.7681 (mtmm) cc_final: 0.7090 (ptpp) REVERT: A 40 GLN cc_start: 0.6446 (pt0) cc_final: 0.5945 (pt0) REVERT: A 45 GLU cc_start: 0.8437 (mp0) cc_final: 0.8135 (mp0) REVERT: A 46 ASP cc_start: 0.7333 (t70) cc_final: 0.6886 (t70) REVERT: A 47 HIS cc_start: 0.7927 (t70) cc_final: 0.6767 (t70) REVERT: A 51 LEU cc_start: 0.9067 (tp) cc_final: 0.8620 (tp) REVERT: A 54 MET cc_start: 0.8326 (tpt) cc_final: 0.7979 (tpt) REVERT: A 55 PHE cc_start: 0.8077 (m-10) cc_final: 0.7775 (m-10) REVERT: A 61 VAL cc_start: 0.8402 (m) cc_final: 0.8102 (p) REVERT: A 74 TYR cc_start: 0.8237 (m-80) cc_final: 0.7163 (m-80) REVERT: A 77 SER cc_start: 0.7935 (m) cc_final: 0.7572 (p) REVERT: A 80 LYS cc_start: 0.8403 (mttp) cc_final: 0.8137 (mttp) REVERT: A 88 TYR cc_start: 0.7071 (p90) cc_final: 0.5801 (p90) REVERT: A 90 LEU cc_start: 0.8261 (tp) cc_final: 0.7817 (tp) REVERT: A 111 MET cc_start: 0.7421 (ttt) cc_final: 0.6941 (ttt) REVERT: A 112 TYR cc_start: 0.7431 (m-80) cc_final: 0.6560 (m-80) REVERT: A 114 GLU cc_start: 0.7766 (tt0) cc_final: 0.7286 (tt0) REVERT: A 119 LEU cc_start: 0.7313 (tp) cc_final: 0.7044 (tp) REVERT: A 132 LEU cc_start: 0.7737 (pp) cc_final: 0.7515 (pp) REVERT: A 135 LEU cc_start: 0.8364 (tp) cc_final: 0.7896 (tp) REVERT: A 137 MET cc_start: 0.8638 (mtm) cc_final: 0.8017 (mtm) REVERT: A 163 GLN cc_start: 0.8180 (tt0) cc_final: 0.7682 (tt0) REVERT: A 165 ARG cc_start: 0.7360 (mtp-110) cc_final: 0.7145 (mtp-110) REVERT: A 172 PHE cc_start: 0.8114 (m-80) cc_final: 0.7881 (m-80) REVERT: A 173 LEU cc_start: 0.8099 (mt) cc_final: 0.7833 (mm) REVERT: A 176 MET cc_start: 0.8579 (ptp) cc_final: 0.8022 (ptp) REVERT: A 209 LYS cc_start: 0.8251 (mttt) cc_final: 0.7685 (mtmm) REVERT: A 212 LYS cc_start: 0.7365 (ttmm) cc_final: 0.7018 (ttmm) REVERT: A 230 ASP cc_start: 0.8233 (m-30) cc_final: 0.6932 (p0) REVERT: A 254 PHE cc_start: 0.7410 (m-10) cc_final: 0.7151 (m-10) REVERT: A 256 ASP cc_start: 0.8021 (t70) cc_final: 0.7697 (t70) REVERT: A 257 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8169 (mm-30) REVERT: A 261 LYS cc_start: 0.7536 (mttm) cc_final: 0.6993 (mttm) REVERT: A 262 ASP cc_start: 0.8172 (t0) cc_final: 0.7533 (t0) REVERT: A 268 MET cc_start: 0.6553 (mtm) cc_final: 0.5458 (mtm) REVERT: A 277 MET cc_start: 0.6944 (mtt) cc_final: 0.5814 (mtt) REVERT: A 293 LYS cc_start: 0.7927 (mtpp) cc_final: 0.7021 (mtpp) REVERT: A 325 LYS cc_start: 0.8319 (mttt) cc_final: 0.7861 (mttt) REVERT: A 338 ASN cc_start: 0.7661 (p0) cc_final: 0.6980 (p0) REVERT: A 345 PHE cc_start: 0.8439 (m-80) cc_final: 0.8098 (m-80) REVERT: A 360 LYS cc_start: 0.8586 (tttt) cc_final: 0.8232 (tttt) REVERT: A 370 HIS cc_start: 0.7822 (m90) cc_final: 0.7540 (m90) REVERT: A 377 ARG cc_start: 0.7937 (ptm-80) cc_final: 0.7347 (ptp-110) REVERT: A 396 LYS cc_start: 0.8399 (tppp) cc_final: 0.7718 (tppp) REVERT: A 404 PHE cc_start: 0.7132 (p90) cc_final: 0.6477 (p90) REVERT: A 420 PHE cc_start: 0.8442 (m-80) cc_final: 0.8186 (m-80) REVERT: A 421 GLU cc_start: 0.8561 (tt0) cc_final: 0.7931 (tt0) REVERT: A 424 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7474 (mt-10) REVERT: A 432 GLN cc_start: 0.8576 (tp-100) cc_final: 0.8078 (tp-100) REVERT: A 433 HIS cc_start: 0.8348 (m90) cc_final: 0.7955 (m90) REVERT: A 454 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8297 (mmtt) REVERT: A 457 SER cc_start: 0.8109 (m) cc_final: 0.7761 (m) REVERT: A 476 ASN cc_start: 0.7839 (t0) cc_final: 0.6916 (t0) REVERT: A 479 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7116 (mtpt) REVERT: A 489 LYS cc_start: 0.7059 (tptm) cc_final: 0.6783 (mtpp) REVERT: A 496 GLU cc_start: 0.7795 (mp0) cc_final: 0.7465 (mp0) REVERT: A 551 GLU cc_start: 0.8769 (pt0) cc_final: 0.8319 (pm20) REVERT: A 559 HIS cc_start: 0.7768 (t70) cc_final: 0.7289 (t-170) REVERT: C 25 MET cc_start: 0.8004 (mmp) cc_final: 0.7338 (mmt) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.2563 time to fit residues: 122.8613 Evaluate side-chains 352 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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: 0.0010 chunk 13 optimal weight: 0.0980 chunk 25 optimal weight: 0.1980 chunk 92 optimal weight: 0.0370 chunk 38 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 0.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.101224 restraints weight = 16461.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.106549 restraints weight = 9249.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.110292 restraints weight = 5835.083| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.5597 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= 0.167 Angle : 0.649 10.289 12680 Z= 0.322 Chirality : 0.046 0.262 1417 Planarity : 0.004 0.076 1669 Dihedral : 6.710 61.382 1426 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % 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: -2.37 (0.24), residues: 1164 helix: -2.32 (0.67), residues: 56 sheet: -1.55 (0.57), residues: 88 loop : -1.70 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 516 HIS 0.008 0.001 HIS A 183 PHE 0.015 0.001 PHE A 287 TYR 0.017 0.001 TYR A 125 ARG 0.009 0.001 ARG A 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2965.30 seconds wall clock time: 53 minutes 2.92 seconds (3182.92 seconds total)