Starting phenix.real_space_refine on Thu Jan 18 21:07:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/01_2024/8hgp_34745.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/01_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_34745/01_2024/8hgp_34745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/01_2024/8hgp_34745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/01_2024/8hgp_34745.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgp_34745/01_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 9 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: 5.57, per 1000 atoms: 0.61 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: 3.74 Conformation dependent library (CDL) restraints added in 1.8 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: 1.08 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: 2.54 Time building geometry restraints manager: 4.03 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 - 21.13: 5668 21.13 - 42.27: 154 42.27 - 63.40: 37 63.40 - 84.53: 18 84.53 - 105.67: 7 Dihedral angle restraints: 5884 sinusoidal: 2521 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 5881 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: 5.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 12.070 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.140 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.480 ------------------------------------------------------------------------------- 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 : 9.595 105.668 3581 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 : 0.975 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: 0.2523 time to fit residues: 131.0076 Evaluate side-chains 347 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 346 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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: 0.6548 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9358 Z= 0.192 Angle : 0.595 9.791 12680 Z= 0.302 Chirality : 0.046 0.260 1417 Planarity : 0.005 0.063 1669 Dihedral : 8.269 72.339 1407 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % 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: -2.73 (0.63), residues: 57 sheet: -2.74 (0.56), residues: 67 loop : -2.48 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.005 0.001 HIS B 490 PHE 0.019 0.001 PHE A 180 TYR 0.011 0.001 TYR B 301 ARG 0.009 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 381 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.5729 (pp30) cc_final: 0.4540 (mm-40) REVERT: B 31 MET cc_start: 0.7710 (mtp) cc_final: 0.7045 (ptp) REVERT: B 32 LYS cc_start: 0.8085 (mptt) cc_final: 0.7815 (mmtt) REVERT: B 44 ASP cc_start: 0.7133 (t0) cc_final: 0.4778 (t0) REVERT: B 46 LEU cc_start: 0.8728 (mt) cc_final: 0.8424 (mt) REVERT: B 47 ARG cc_start: 0.7616 (ttp80) cc_final: 0.6715 (ttp80) REVERT: B 54 GLN cc_start: 0.7003 (mt0) cc_final: 0.6597 (tp-100) REVERT: B 56 VAL cc_start: 0.8057 (t) cc_final: 0.7637 (t) REVERT: B 59 ASN cc_start: 0.6739 (m-40) cc_final: 0.6289 (m-40) REVERT: B 61 GLU cc_start: 0.6407 (mt-10) cc_final: 0.5640 (mt-10) REVERT: B 65 LEU cc_start: 0.8330 (mt) cc_final: 0.8102 (mt) REVERT: B 73 PHE cc_start: 0.8086 (p90) cc_final: 0.7803 (p90) REVERT: B 74 LEU cc_start: 0.8389 (mt) cc_final: 0.8166 (mt) REVERT: B 75 GLN cc_start: 0.7796 (pt0) cc_final: 0.7514 (pt0) REVERT: B 79 GLU cc_start: 0.6972 (tt0) cc_final: 0.6383 (tt0) REVERT: B 81 GLN cc_start: 0.6693 (mt0) cc_final: 0.6206 (mt0) REVERT: B 92 ARG cc_start: 0.7626 (mtt90) cc_final: 0.7179 (mmm-85) REVERT: B 93 GLN cc_start: 0.8485 (pp30) cc_final: 0.7671 (tm-30) REVERT: B 94 VAL cc_start: 0.8936 (t) cc_final: 0.8611 (t) REVERT: B 105 THR cc_start: 0.7551 (p) cc_final: 0.6652 (t) REVERT: B 106 GLN cc_start: 0.7586 (mt0) cc_final: 0.7034 (mp-120) REVERT: B 116 VAL cc_start: 0.6887 (t) cc_final: 0.6504 (p) REVERT: B 160 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7154 (tp40) REVERT: B 173 PHE cc_start: 0.6815 (m-10) cc_final: 0.6402 (m-10) REVERT: B 185 ASP cc_start: 0.7054 (t0) cc_final: 0.6846 (t0) REVERT: B 193 HIS cc_start: 0.7886 (m90) cc_final: 0.7287 (m90) REVERT: B 211 ASP cc_start: 0.7789 (m-30) cc_final: 0.6521 (p0) REVERT: B 227 CYS cc_start: 0.2616 (p) cc_final: 0.2332 (p) REVERT: B 248 LYS cc_start: 0.8613 (mmtt) cc_final: 0.7983 (mmtt) REVERT: B 251 ASP cc_start: 0.7729 (p0) cc_final: 0.7344 (p0) REVERT: B 253 LEU cc_start: 0.7399 (mt) cc_final: 0.6931 (mt) REVERT: B 265 GLU cc_start: 0.6844 (pm20) cc_final: 0.6571 (pm20) REVERT: B 271 LEU cc_start: 0.8374 (mp) cc_final: 0.8051 (mm) REVERT: B 274 TYR cc_start: 0.6655 (t80) cc_final: 0.6220 (t80) REVERT: B 275 ASN cc_start: 0.8185 (t0) cc_final: 0.7490 (t0) REVERT: B 282 MET cc_start: 0.8018 (mtp) cc_final: 0.7375 (mtp) REVERT: B 303 TYR cc_start: 0.7866 (m-80) cc_final: 0.7288 (m-80) REVERT: B 320 GLN cc_start: 0.6476 (mt0) cc_final: 0.6188 (mt0) REVERT: B 332 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6579 (mp0) REVERT: B 377 LEU cc_start: 0.8323 (tp) cc_final: 0.8077 (tt) REVERT: B 411 TYR cc_start: 0.6991 (t80) cc_final: 0.6494 (t80) REVERT: B 420 PRO cc_start: 0.8356 (Cg_endo) cc_final: 0.8150 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7746 (p0) cc_final: 0.7404 (p0) REVERT: B 422 LEU cc_start: 0.8648 (tp) cc_final: 0.7766 (pp) REVERT: B 426 GLN cc_start: 0.7587 (pt0) cc_final: 0.6787 (pp30) REVERT: B 430 VAL cc_start: 0.7367 (p) cc_final: 0.7034 (t) REVERT: B 434 ARG cc_start: 0.7477 (mtt90) cc_final: 0.7195 (mpt-90) REVERT: B 436 LEU cc_start: 0.7905 (mt) cc_final: 0.7356 (mt) REVERT: B 443 LEU cc_start: 0.7827 (tp) cc_final: 0.7362 (mm) REVERT: B 444 THR cc_start: 0.7321 (m) cc_final: 0.6994 (m) REVERT: B 463 SER cc_start: 0.7304 (t) cc_final: 0.6900 (m) REVERT: B 481 PRO cc_start: 0.8281 (Cg_endo) cc_final: 0.7698 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8534 (m100) cc_final: 0.8179 (m100) REVERT: B 483 ASP cc_start: 0.8492 (m-30) cc_final: 0.7835 (t70) REVERT: B 488 ASN cc_start: 0.8014 (t0) cc_final: 0.7744 (t0) REVERT: B 494 LEU cc_start: 0.8579 (mt) cc_final: 0.8266 (mt) REVERT: B 517 ARG cc_start: 0.8348 (mtt180) cc_final: 0.7918 (mtm110) REVERT: B 556 ASN cc_start: 0.8013 (t0) cc_final: 0.7436 (t0) REVERT: B 566 GLU cc_start: 0.7527 (mm-30) cc_final: 0.6544 (tm-30) REVERT: B 577 PHE cc_start: 0.8147 (m-80) cc_final: 0.7889 (m-80) REVERT: B 580 GLU cc_start: 0.8501 (tp30) cc_final: 0.8110 (tp30) REVERT: A 29 LYS cc_start: 0.7933 (pttm) cc_final: 0.7464 (pttm) REVERT: A 35 SER cc_start: 0.7970 (t) cc_final: 0.7744 (p) REVERT: A 36 ASN cc_start: 0.8250 (p0) cc_final: 0.7752 (p0) REVERT: A 40 GLN cc_start: 0.6002 (tt0) cc_final: 0.5524 (tt0) REVERT: A 46 ASP cc_start: 0.7475 (t70) cc_final: 0.6696 (t70) REVERT: A 47 HIS cc_start: 0.7942 (t70) cc_final: 0.6739 (t70) REVERT: A 51 LEU cc_start: 0.8763 (tp) cc_final: 0.8530 (tp) REVERT: A 55 PHE cc_start: 0.7913 (m-10) cc_final: 0.7503 (m-10) REVERT: A 62 LEU cc_start: 0.8514 (mt) cc_final: 0.8230 (mm) REVERT: A 74 TYR cc_start: 0.7820 (m-80) cc_final: 0.6908 (m-80) REVERT: A 80 LYS cc_start: 0.8230 (mttm) cc_final: 0.7829 (mttm) REVERT: A 83 GLN cc_start: 0.7830 (mm110) cc_final: 0.7361 (mm110) REVERT: A 93 LEU cc_start: 0.8322 (mp) cc_final: 0.8068 (mt) REVERT: A 110 ASN cc_start: 0.7897 (m110) cc_final: 0.7376 (p0) REVERT: A 114 GLU cc_start: 0.7594 (tt0) cc_final: 0.7070 (tt0) REVERT: A 143 ILE cc_start: 0.8958 (mt) cc_final: 0.8680 (mm) REVERT: A 163 GLN cc_start: 0.8641 (pt0) cc_final: 0.8096 (tt0) REVERT: A 172 PHE cc_start: 0.7671 (m-10) cc_final: 0.7466 (m-80) REVERT: A 176 MET cc_start: 0.8034 (ptp) cc_final: 0.7545 (ptt) REVERT: A 209 LYS cc_start: 0.8090 (mttt) cc_final: 0.7484 (mtmm) REVERT: A 226 LYS cc_start: 0.7813 (mtpt) cc_final: 0.7195 (mtpt) REVERT: A 233 HIS cc_start: 0.7509 (t-90) cc_final: 0.6952 (t-90) REVERT: A 253 LYS cc_start: 0.8035 (tptm) cc_final: 0.7298 (tptm) REVERT: A 256 ASP cc_start: 0.7001 (t70) cc_final: 0.6620 (t0) REVERT: A 261 LYS cc_start: 0.7446 (mttm) cc_final: 0.6920 (mttm) REVERT: A 262 ASP cc_start: 0.7657 (t0) cc_final: 0.7275 (t0) REVERT: A 268 MET cc_start: 0.6302 (mtm) cc_final: 0.5152 (mtm) REVERT: A 277 MET cc_start: 0.6436 (mtt) cc_final: 0.5459 (mtt) REVERT: A 285 TYR cc_start: 0.5931 (m-10) cc_final: 0.5653 (m-10) REVERT: A 293 LYS cc_start: 0.8033 (mtpp) cc_final: 0.6994 (mmmt) REVERT: A 316 TYR cc_start: 0.7654 (t80) cc_final: 0.7188 (t80) REVERT: A 318 MET cc_start: 0.7836 (tpp) cc_final: 0.7022 (tpp) REVERT: A 338 ASN cc_start: 0.6924 (p0) cc_final: 0.5851 (p0) REVERT: A 345 PHE cc_start: 0.8298 (m-80) cc_final: 0.7980 (m-80) REVERT: A 358 HIS cc_start: 0.8243 (m90) cc_final: 0.7692 (m90) REVERT: A 360 LYS cc_start: 0.8718 (tttt) cc_final: 0.8353 (tttt) REVERT: A 368 ASP cc_start: 0.5132 (m-30) cc_final: 0.4550 (m-30) REVERT: A 369 LEU cc_start: 0.7142 (mt) cc_final: 0.6914 (mm) REVERT: A 396 LYS cc_start: 0.8223 (tppp) cc_final: 0.7800 (tppp) REVERT: A 404 PHE cc_start: 0.7135 (p90) cc_final: 0.6129 (p90) REVERT: A 414 ARG cc_start: 0.6760 (ttm-80) cc_final: 0.6032 (ttt180) REVERT: A 421 GLU cc_start: 0.8705 (tt0) cc_final: 0.8005 (tt0) REVERT: A 429 ARG cc_start: 0.7320 (mtt180) cc_final: 0.7074 (mtt-85) REVERT: A 430 THR cc_start: 0.7442 (m) cc_final: 0.6614 (m) REVERT: A 432 GLN cc_start: 0.8646 (tp40) cc_final: 0.8169 (tp-100) REVERT: A 433 HIS cc_start: 0.8444 (m90) cc_final: 0.8107 (m90) REVERT: A 476 ASN cc_start: 0.7637 (t0) cc_final: 0.7273 (t0) REVERT: A 489 LYS cc_start: 0.7816 (ttmm) cc_final: 0.7580 (mtpp) REVERT: A 496 GLU cc_start: 0.7732 (mp0) cc_final: 0.7426 (mp0) REVERT: A 521 ARG cc_start: 0.7897 (ptt180) cc_final: 0.7577 (tmm-80) REVERT: A 551 GLU cc_start: 0.8638 (pt0) cc_final: 0.8253 (pm20) REVERT: C 5 LYS cc_start: 0.8094 (mttt) cc_final: 0.7824 (tppp) REVERT: C 18 GLN cc_start: 0.7731 (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: 0.8044 (mmp) cc_final: 0.7328 (mmp) REVERT: C 29 TYR cc_start: 0.5216 (t80) cc_final: 0.4144 (t80) outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.2546 time to fit residues: 127.7783 Evaluate side-chains 355 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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: 0.8980 chunk 32 optimal weight: 0.0040 chunk 87 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 0.0470 chunk 114 optimal weight: 0.0970 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 chunk 84 optimal weight: 2.9990 overall best weight: 0.1266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 267 HIS ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9358 Z= 0.144 Angle : 0.554 9.494 12680 Z= 0.280 Chirality : 0.045 0.257 1417 Planarity : 0.004 0.048 1669 Dihedral : 7.348 56.569 1407 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.10 % Allowed : 1.57 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.02 (0.22), residues: 1164 helix: -1.59 (0.84), residues: 42 sheet: -1.91 (0.62), residues: 69 loop : -2.28 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 415 HIS 0.004 0.001 HIS A 145 PHE 0.019 0.001 PHE B 486 TYR 0.034 0.001 TYR A 117 ARG 0.007 0.000 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 364 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 363 time to evaluate : 1.017 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: 0.5782 (pp30) cc_final: 0.4621 (mm-40) REVERT: B 31 MET cc_start: 0.7691 (mtp) cc_final: 0.7004 (ptp) REVERT: B 44 ASP cc_start: 0.7177 (t0) cc_final: 0.6732 (t0) REVERT: B 46 LEU cc_start: 0.8722 (mt) cc_final: 0.8400 (mt) REVERT: B 54 GLN cc_start: 0.6964 (mt0) cc_final: 0.6592 (tp-100) REVERT: B 56 VAL cc_start: 0.8053 (t) cc_final: 0.7719 (m) REVERT: B 59 ASN cc_start: 0.6673 (m-40) cc_final: 0.6344 (m-40) REVERT: B 61 GLU cc_start: 0.6286 (mt-10) cc_final: 0.5415 (mt-10) REVERT: B 65 LEU cc_start: 0.8220 (mt) cc_final: 0.8009 (mt) REVERT: B 75 GLN cc_start: 0.7770 (pt0) cc_final: 0.7502 (pt0) REVERT: B 79 GLU cc_start: 0.6968 (tt0) cc_final: 0.6332 (tt0) REVERT: B 81 GLN cc_start: 0.6737 (mt0) cc_final: 0.6338 (mt0) REVERT: B 93 GLN cc_start: 0.8500 (pp30) cc_final: 0.8138 (tm-30) REVERT: B 100 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7112 (mmm-85) REVERT: B 105 THR cc_start: 0.7549 (p) cc_final: 0.6690 (t) REVERT: B 106 GLN cc_start: 0.7603 (mt0) cc_final: 0.7032 (mp-120) REVERT: B 155 ILE cc_start: 0.7961 (mt) cc_final: 0.7722 (mm) REVERT: B 158 ASN cc_start: 0.7701 (m-40) cc_final: 0.7397 (m110) REVERT: B 173 PHE cc_start: 0.6830 (m-10) cc_final: 0.6406 (m-10) REVERT: B 185 ASP cc_start: 0.7038 (t0) cc_final: 0.6636 (t0) REVERT: B 193 HIS cc_start: 0.7875 (m90) cc_final: 0.7242 (m90) REVERT: B 211 ASP cc_start: 0.7492 (m-30) cc_final: 0.6386 (p0) REVERT: B 248 LYS cc_start: 0.8577 (mmtt) cc_final: 0.7962 (mmtt) REVERT: B 251 ASP cc_start: 0.7749 (p0) cc_final: 0.7359 (p0) REVERT: B 265 GLU cc_start: 0.6930 (pm20) cc_final: 0.6348 (pm20) REVERT: B 267 HIS cc_start: 0.7522 (m170) cc_final: 0.7140 (m170) REVERT: B 274 TYR cc_start: 0.6708 (t80) cc_final: 0.5872 (t80) REVERT: B 275 ASN cc_start: 0.8193 (t0) cc_final: 0.7416 (t0) REVERT: B 282 MET cc_start: 0.8132 (mtp) cc_final: 0.7577 (mtp) REVERT: B 288 ARG cc_start: 0.7840 (mmt-90) cc_final: 0.7561 (mtt90) REVERT: B 303 TYR cc_start: 0.7857 (m-80) cc_final: 0.7168 (m-80) REVERT: B 323 THR cc_start: 0.7359 (t) cc_final: 0.6976 (p) REVERT: B 332 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7082 (mt-10) REVERT: B 377 LEU cc_start: 0.8298 (tp) cc_final: 0.8056 (tt) REVERT: B 411 TYR cc_start: 0.7124 (t80) cc_final: 0.6348 (t80) REVERT: B 420 PRO cc_start: 0.8466 (Cg_endo) cc_final: 0.8144 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7718 (p0) cc_final: 0.7447 (p0) REVERT: B 422 LEU cc_start: 0.8638 (tp) cc_final: 0.8339 (mt) REVERT: B 426 GLN cc_start: 0.7680 (pt0) cc_final: 0.6808 (pp30) REVERT: B 436 LEU cc_start: 0.7832 (mt) cc_final: 0.7627 (mt) REVERT: B 443 LEU cc_start: 0.7795 (tp) cc_final: 0.7324 (mm) REVERT: B 444 THR cc_start: 0.7157 (m) cc_final: 0.6567 (m) REVERT: B 451 SER cc_start: 0.8281 (m) cc_final: 0.7753 (m) REVERT: B 452 TRP cc_start: 0.7847 (p90) cc_final: 0.7454 (p90) REVERT: B 481 PRO cc_start: 0.8231 (Cg_endo) cc_final: 0.7699 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8654 (m100) cc_final: 0.8240 (m100) REVERT: B 483 ASP cc_start: 0.8525 (m-30) cc_final: 0.7833 (t70) REVERT: B 486 PHE cc_start: 0.7899 (m-80) cc_final: 0.7622 (m-10) REVERT: B 487 ARG cc_start: 0.7856 (mmm-85) cc_final: 0.6841 (ttm-80) REVERT: B 494 LEU cc_start: 0.8563 (mt) cc_final: 0.8351 (mt) REVERT: B 517 ARG cc_start: 0.8363 (mtt180) cc_final: 0.8125 (mtt180) REVERT: B 556 ASN cc_start: 0.7954 (t0) cc_final: 0.7399 (t0) REVERT: B 566 GLU cc_start: 0.7482 (mm-30) cc_final: 0.6496 (tm-30) REVERT: B 577 PHE cc_start: 0.8156 (m-80) cc_final: 0.7892 (m-80) REVERT: B 580 GLU cc_start: 0.8443 (tp30) cc_final: 0.8095 (tp30) REVERT: A 29 LYS cc_start: 0.7858 (pttm) cc_final: 0.7388 (pttt) REVERT: A 35 SER cc_start: 0.8021 (t) cc_final: 0.7740 (p) REVERT: A 40 GLN cc_start: 0.5915 (tt0) cc_final: 0.5306 (tt0) REVERT: A 45 GLU cc_start: 0.8234 (mp0) cc_final: 0.7961 (mp0) REVERT: A 46 ASP cc_start: 0.7316 (t70) cc_final: 0.6801 (t70) REVERT: A 47 HIS cc_start: 0.7873 (t70) cc_final: 0.6783 (t70) REVERT: A 51 LEU cc_start: 0.8771 (tp) cc_final: 0.8521 (tp) REVERT: A 55 PHE cc_start: 0.7840 (m-10) cc_final: 0.7494 (m-10) REVERT: A 61 VAL cc_start: 0.8195 (m) cc_final: 0.7880 (p) REVERT: A 65 LEU cc_start: 0.7794 (tp) cc_final: 0.7360 (tt) REVERT: A 74 TYR cc_start: 0.7900 (m-80) cc_final: 0.6924 (m-80) REVERT: A 82 ILE cc_start: 0.8031 (mt) cc_final: 0.7804 (mp) REVERT: A 83 GLN cc_start: 0.7729 (mm110) cc_final: 0.6981 (mm110) REVERT: A 103 ASN cc_start: 0.7131 (m-40) cc_final: 0.6205 (m-40) REVERT: A 107 ILE cc_start: 0.8412 (mm) cc_final: 0.8191 (mm) REVERT: A 110 ASN cc_start: 0.7817 (m110) cc_final: 0.7309 (p0) REVERT: A 114 GLU cc_start: 0.7306 (tt0) cc_final: 0.7011 (tt0) REVERT: A 132 LEU cc_start: 0.7733 (mm) cc_final: 0.7174 (mm) REVERT: A 143 ILE cc_start: 0.8878 (mt) cc_final: 0.8547 (mm) REVERT: A 163 GLN cc_start: 0.8651 (pt0) cc_final: 0.8098 (tt0) REVERT: A 172 PHE cc_start: 0.7658 (m-10) cc_final: 0.7367 (m-80) REVERT: A 176 MET cc_start: 0.8058 (ptp) cc_final: 0.7652 (ptt) REVERT: A 209 LYS cc_start: 0.8051 (mttt) cc_final: 0.7461 (mtmt) REVERT: A 226 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7293 (mtpt) REVERT: A 229 SER cc_start: 0.8288 (p) cc_final: 0.7895 (t) REVERT: A 233 HIS cc_start: 0.7675 (t-90) cc_final: 0.7127 (t-90) REVERT: A 252 ARG cc_start: 0.7107 (mtp85) cc_final: 0.6857 (mtp85) REVERT: A 253 LYS cc_start: 0.8070 (tptm) cc_final: 0.7432 (tptm) REVERT: A 254 PHE cc_start: 0.7393 (m-10) cc_final: 0.6036 (m-80) REVERT: A 255 ARG cc_start: 0.6829 (ttt-90) cc_final: 0.6422 (ttp80) REVERT: A 262 ASP cc_start: 0.7610 (t0) cc_final: 0.7205 (t0) REVERT: A 268 MET cc_start: 0.6301 (mtm) cc_final: 0.5177 (mtm) REVERT: A 277 MET cc_start: 0.6435 (mtt) cc_final: 0.5454 (mtt) REVERT: A 290 THR cc_start: 0.6820 (t) cc_final: 0.6488 (t) REVERT: A 293 LYS cc_start: 0.7729 (mtpp) cc_final: 0.7187 (tppt) REVERT: A 316 TYR cc_start: 0.7654 (t80) cc_final: 0.7211 (t80) REVERT: A 318 MET cc_start: 0.7732 (tpp) cc_final: 0.6957 (tpp) REVERT: A 358 HIS cc_start: 0.8281 (m90) cc_final: 0.7749 (m90) REVERT: A 360 LYS cc_start: 0.8707 (tttt) cc_final: 0.8342 (tttt) REVERT: A 368 ASP cc_start: 0.4893 (m-30) cc_final: 0.4371 (m-30) REVERT: A 396 LYS cc_start: 0.8228 (tppp) cc_final: 0.7773 (tppp) REVERT: A 421 GLU cc_start: 0.8660 (tt0) cc_final: 0.7988 (tt0) REVERT: A 429 ARG cc_start: 0.7590 (mtt180) cc_final: 0.7025 (mtt-85) REVERT: A 430 THR cc_start: 0.7365 (m) cc_final: 0.6928 (t) REVERT: A 431 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7756 (mtpt) REVERT: A 432 GLN cc_start: 0.8618 (tp40) cc_final: 0.8226 (tp-100) REVERT: A 433 HIS cc_start: 0.8403 (m90) cc_final: 0.8146 (m90) REVERT: A 476 ASN cc_start: 0.7643 (t0) cc_final: 0.7216 (t0) REVERT: A 489 LYS cc_start: 0.7719 (ttmm) cc_final: 0.7483 (mmmm) REVERT: A 496 GLU cc_start: 0.7727 (mp0) cc_final: 0.7499 (mp0) REVERT: A 551 GLU cc_start: 0.8707 (pt0) cc_final: 0.8273 (pm20) REVERT: C 5 LYS cc_start: 0.8107 (mttt) cc_final: 0.7842 (tppp) REVERT: C 22 LEU cc_start: 0.7618 (mt) cc_final: 0.7366 (mt) REVERT: C 25 MET cc_start: 0.8028 (mmp) cc_final: 0.7368 (mmp) REVERT: C 29 TYR cc_start: 0.5335 (t80) cc_final: 0.4162 (t80) outliers start: 1 outliers final: 1 residues processed: 364 average time/residue: 0.2569 time to fit residues: 123.1822 Evaluate side-chains 348 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 347 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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: 2.9990 chunk 79 optimal weight: 0.0870 chunk 54 optimal weight: 0.0470 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 70 optimal weight: 0.4980 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 0.0370 chunk 55 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.1734 ------------------------------------------------------------------------------- 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 329 GLN ** 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 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9358 Z= 0.151 Angle : 0.543 9.535 12680 Z= 0.273 Chirality : 0.045 0.258 1417 Planarity : 0.004 0.043 1669 Dihedral : 6.510 56.138 1407 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.22), residues: 1164 helix: -1.34 (0.86), residues: 42 sheet: -1.69 (0.63), residues: 69 loop : -2.13 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 164 HIS 0.002 0.001 HIS A 304 PHE 0.017 0.001 PHE A 180 TYR 0.023 0.001 TYR A 117 ARG 0.011 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 1.085 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: 0.5895 (pp30) cc_final: 0.4710 (mm-40) REVERT: B 31 MET cc_start: 0.7709 (mtp) cc_final: 0.7015 (ptp) REVERT: B 44 ASP cc_start: 0.7205 (t0) cc_final: 0.6729 (t0) REVERT: B 46 LEU cc_start: 0.8745 (mt) cc_final: 0.8480 (mt) REVERT: B 54 GLN cc_start: 0.7058 (mt0) cc_final: 0.6612 (tp40) REVERT: B 56 VAL cc_start: 0.8015 (t) cc_final: 0.7680 (m) REVERT: B 59 ASN cc_start: 0.6682 (m-40) cc_final: 0.6315 (m-40) REVERT: B 61 GLU cc_start: 0.6098 (mt-10) cc_final: 0.5319 (mt-10) REVERT: B 65 LEU cc_start: 0.8178 (mt) cc_final: 0.7932 (mt) REVERT: B 73 PHE cc_start: 0.8132 (p90) cc_final: 0.7732 (p90) REVERT: B 74 LEU cc_start: 0.8415 (mt) cc_final: 0.8212 (mt) REVERT: B 75 GLN cc_start: 0.7758 (pt0) cc_final: 0.7407 (pt0) REVERT: B 79 GLU cc_start: 0.7004 (tt0) cc_final: 0.6218 (tt0) REVERT: B 81 GLN cc_start: 0.6746 (mt0) cc_final: 0.6218 (mt0) REVERT: B 93 GLN cc_start: 0.8517 (pp30) cc_final: 0.8066 (tm-30) REVERT: B 100 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7228 (mmm-85) REVERT: B 103 ARG cc_start: 0.7415 (ttm110) cc_final: 0.6990 (ttm110) REVERT: B 105 THR cc_start: 0.7547 (p) cc_final: 0.6722 (t) REVERT: B 106 GLN cc_start: 0.7543 (mt0) cc_final: 0.6993 (mp-120) REVERT: B 116 VAL cc_start: 0.6961 (t) cc_final: 0.6444 (p) REVERT: B 153 VAL cc_start: 0.7815 (t) cc_final: 0.7558 (t) REVERT: B 155 ILE cc_start: 0.7976 (mt) cc_final: 0.7520 (mt) REVERT: B 158 ASN cc_start: 0.7689 (m-40) cc_final: 0.7399 (m110) REVERT: B 173 PHE cc_start: 0.6896 (m-10) cc_final: 0.6522 (m-10) REVERT: B 185 ASP cc_start: 0.7072 (t0) cc_final: 0.6643 (t0) REVERT: B 193 HIS cc_start: 0.7864 (m90) cc_final: 0.7254 (m90) REVERT: B 211 ASP cc_start: 0.7691 (m-30) cc_final: 0.6088 (p0) REVERT: B 248 LYS cc_start: 0.8575 (mmtt) cc_final: 0.7943 (mmtt) REVERT: B 251 ASP cc_start: 0.7751 (p0) cc_final: 0.7369 (p0) REVERT: B 265 GLU cc_start: 0.6711 (pm20) cc_final: 0.6364 (pm20) REVERT: B 274 TYR cc_start: 0.6621 (t80) cc_final: 0.5849 (t80) REVERT: B 275 ASN cc_start: 0.8166 (t0) cc_final: 0.7521 (t0) REVERT: B 282 MET cc_start: 0.8185 (mtp) cc_final: 0.7927 (mtp) REVERT: B 284 ASN cc_start: 0.7978 (t0) cc_final: 0.7594 (t0) REVERT: B 288 ARG cc_start: 0.7881 (mmt-90) cc_final: 0.7633 (mtt90) REVERT: B 303 TYR cc_start: 0.7873 (m-80) cc_final: 0.7271 (m-80) REVERT: B 320 GLN cc_start: 0.6426 (mt0) cc_final: 0.5782 (mt0) REVERT: B 323 THR cc_start: 0.7450 (t) cc_final: 0.7110 (p) REVERT: B 332 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7028 (mt-10) REVERT: B 364 PHE cc_start: 0.8474 (m-80) cc_final: 0.7744 (m-80) REVERT: B 398 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7835 (mm-40) REVERT: B 411 TYR cc_start: 0.7222 (t80) cc_final: 0.6495 (t80) REVERT: B 426 GLN cc_start: 0.7690 (pt0) cc_final: 0.6823 (pp30) REVERT: B 430 VAL cc_start: 0.7707 (p) cc_final: 0.7328 (t) REVERT: B 432 ARG cc_start: 0.6992 (mmt-90) cc_final: 0.6634 (tpp-160) REVERT: B 436 LEU cc_start: 0.7872 (mt) cc_final: 0.7294 (mt) REVERT: B 444 THR cc_start: 0.7217 (m) cc_final: 0.6804 (m) REVERT: B 451 SER cc_start: 0.8302 (m) cc_final: 0.7707 (m) REVERT: B 452 TRP cc_start: 0.7899 (p90) cc_final: 0.7450 (p90) REVERT: B 467 LEU cc_start: 0.7146 (tp) cc_final: 0.6877 (tp) REVERT: B 481 PRO cc_start: 0.8280 (Cg_endo) cc_final: 0.7746 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8652 (m100) cc_final: 0.8338 (m100) REVERT: B 488 ASN cc_start: 0.7809 (t0) cc_final: 0.7326 (t0) REVERT: B 494 LEU cc_start: 0.8602 (mt) cc_final: 0.8308 (mt) REVERT: B 517 ARG cc_start: 0.8335 (mtt180) cc_final: 0.8103 (mtt180) REVERT: B 527 GLN cc_start: 0.7143 (pm20) cc_final: 0.6139 (pm20) REVERT: B 556 ASN cc_start: 0.7973 (t0) cc_final: 0.7418 (t0) REVERT: B 566 GLU cc_start: 0.7561 (mm-30) cc_final: 0.6439 (tm-30) REVERT: B 577 PHE cc_start: 0.8176 (m-80) cc_final: 0.7899 (m-80) REVERT: B 580 GLU cc_start: 0.8454 (tp30) cc_final: 0.8099 (tp30) REVERT: A 29 LYS cc_start: 0.7855 (pttm) cc_final: 0.7307 (pttm) REVERT: A 36 ASN cc_start: 0.8239 (p0) cc_final: 0.7947 (p0) REVERT: A 40 GLN cc_start: 0.6129 (tt0) cc_final: 0.5429 (tt0) REVERT: A 46 ASP cc_start: 0.7329 (t70) cc_final: 0.6704 (t70) REVERT: A 47 HIS cc_start: 0.7883 (t70) cc_final: 0.6785 (t70) REVERT: A 51 LEU cc_start: 0.8843 (tp) cc_final: 0.8555 (tp) REVERT: A 55 PHE cc_start: 0.7830 (m-10) cc_final: 0.7524 (m-10) REVERT: A 61 VAL cc_start: 0.8438 (m) cc_final: 0.8126 (p) REVERT: A 74 TYR cc_start: 0.7909 (m-80) cc_final: 0.6931 (m-80) REVERT: A 80 LYS cc_start: 0.8281 (mtmm) cc_final: 0.7785 (mtmm) REVERT: A 83 GLN cc_start: 0.7695 (mm110) cc_final: 0.7214 (mm110) REVERT: A 98 ARG cc_start: 0.7489 (ttt90) cc_final: 0.7230 (tpp80) REVERT: A 102 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6974 (mt-10) REVERT: A 107 ILE cc_start: 0.8437 (mm) cc_final: 0.8233 (mm) REVERT: A 110 ASN cc_start: 0.7797 (m110) cc_final: 0.7324 (p0) REVERT: A 132 LEU cc_start: 0.7736 (mm) cc_final: 0.7173 (mm) REVERT: A 143 ILE cc_start: 0.8914 (mt) cc_final: 0.8584 (mm) REVERT: A 163 GLN cc_start: 0.8729 (pt0) cc_final: 0.8100 (tt0) REVERT: A 172 PHE cc_start: 0.7701 (m-10) cc_final: 0.7412 (m-80) REVERT: A 176 MET cc_start: 0.8097 (ptp) cc_final: 0.7732 (ptt) REVERT: A 209 LYS cc_start: 0.8086 (mttt) cc_final: 0.7479 (mtmt) REVERT: A 229 SER cc_start: 0.8263 (p) cc_final: 0.7889 (t) REVERT: A 233 HIS cc_start: 0.7743 (t-90) cc_final: 0.7526 (t-90) REVERT: A 253 LYS cc_start: 0.8068 (tptm) cc_final: 0.7392 (tptm) REVERT: A 254 PHE cc_start: 0.7372 (m-10) cc_final: 0.5966 (m-80) REVERT: A 255 ARG cc_start: 0.6957 (ttt-90) cc_final: 0.6521 (ttp80) REVERT: A 261 LYS cc_start: 0.7199 (ptmt) cc_final: 0.6752 (ptmt) REVERT: A 262 ASP cc_start: 0.7720 (t0) cc_final: 0.7340 (t0) REVERT: A 268 MET cc_start: 0.6259 (mtm) cc_final: 0.5177 (mtm) REVERT: A 277 MET cc_start: 0.6457 (mtt) cc_final: 0.5475 (mtt) REVERT: A 290 THR cc_start: 0.6891 (t) cc_final: 0.6489 (t) REVERT: A 293 LYS cc_start: 0.7765 (mtpp) cc_final: 0.7161 (mmmt) REVERT: A 318 MET cc_start: 0.7731 (tpp) cc_final: 0.7364 (tpp) REVERT: A 338 ASN cc_start: 0.7461 (p0) cc_final: 0.6496 (p0) REVERT: A 345 PHE cc_start: 0.8215 (m-80) cc_final: 0.7844 (m-80) REVERT: A 358 HIS cc_start: 0.8381 (m90) cc_final: 0.7797 (m90) REVERT: A 360 LYS cc_start: 0.8689 (tttt) cc_final: 0.8324 (tttt) REVERT: A 368 ASP cc_start: 0.5112 (m-30) cc_final: 0.3905 (m-30) REVERT: A 396 LYS cc_start: 0.8248 (tppp) cc_final: 0.7793 (tppp) REVERT: A 404 PHE cc_start: 0.7194 (p90) cc_final: 0.5976 (p90) REVERT: A 421 GLU cc_start: 0.8644 (tt0) cc_final: 0.7961 (tt0) REVERT: A 429 ARG cc_start: 0.7628 (mtt180) cc_final: 0.7062 (mtt-85) REVERT: A 430 THR cc_start: 0.7437 (m) cc_final: 0.6113 (t) REVERT: A 431 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7855 (mtmt) REVERT: A 432 GLN cc_start: 0.8611 (tp40) cc_final: 0.8273 (tp-100) REVERT: A 433 HIS cc_start: 0.8440 (m90) cc_final: 0.8143 (m90) REVERT: A 456 ILE cc_start: 0.7952 (mm) cc_final: 0.7277 (pt) REVERT: A 457 SER cc_start: 0.7459 (m) cc_final: 0.6987 (m) REVERT: A 476 ASN cc_start: 0.7569 (t0) cc_final: 0.7154 (t0) REVERT: A 496 GLU cc_start: 0.7706 (mp0) cc_final: 0.7475 (mp0) REVERT: A 519 GLU cc_start: 0.7081 (tt0) cc_final: 0.6776 (tt0) REVERT: A 521 ARG cc_start: 0.7684 (ptt180) cc_final: 0.7188 (tmm-80) REVERT: A 551 GLU cc_start: 0.8707 (pt0) cc_final: 0.8263 (pm20) REVERT: C 5 LYS cc_start: 0.7998 (mttt) cc_final: 0.7755 (tppp) REVERT: C 22 LEU cc_start: 0.7552 (mt) cc_final: 0.7295 (mt) REVERT: C 25 MET cc_start: 0.8058 (mmp) cc_final: 0.7421 (mmp) REVERT: C 29 TYR cc_start: 0.5364 (t80) cc_final: 0.4325 (t80) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.2672 time to fit residues: 125.7598 Evaluate side-chains 352 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 239 GLN B 257 HIS ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 435 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9358 Z= 0.257 Angle : 0.666 12.733 12680 Z= 0.339 Chirality : 0.048 0.289 1417 Planarity : 0.005 0.076 1669 Dihedral : 6.418 57.767 1407 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % 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: -2.57 (0.23), residues: 1164 helix: -1.43 (0.82), residues: 42 sheet: -1.80 (0.56), residues: 84 loop : -1.91 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 477 HIS 0.008 0.001 HIS A 507 PHE 0.014 0.002 PHE B 486 TYR 0.035 0.002 TYR A 117 ARG 0.008 0.001 ARG A 222 *********************** 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 373 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6722 (pp30) cc_final: 0.5115 (mm-40) REVERT: B 31 MET cc_start: 0.7424 (mtp) cc_final: 0.6964 (ptp) REVERT: B 44 ASP cc_start: 0.7428 (t0) cc_final: 0.6698 (t0) REVERT: B 46 LEU cc_start: 0.8856 (mt) cc_final: 0.8376 (mt) REVERT: B 47 ARG cc_start: 0.7819 (ttp80) cc_final: 0.7406 (ttp80) REVERT: B 54 GLN cc_start: 0.7194 (mt0) cc_final: 0.6987 (mp10) REVERT: B 70 SER cc_start: 0.8482 (p) cc_final: 0.8226 (p) REVERT: B 75 GLN cc_start: 0.7862 (pt0) cc_final: 0.7532 (pt0) REVERT: B 80 VAL cc_start: 0.7761 (t) cc_final: 0.7469 (p) REVERT: B 81 GLN cc_start: 0.6833 (mt0) cc_final: 0.6507 (mt0) REVERT: B 85 LEU cc_start: 0.8188 (tp) cc_final: 0.7911 (tp) REVERT: B 93 GLN cc_start: 0.8545 (pp30) cc_final: 0.7713 (tm-30) REVERT: B 94 VAL cc_start: 0.8921 (t) cc_final: 0.8549 (p) REVERT: B 100 ARG cc_start: 0.7906 (ttm-80) cc_final: 0.7516 (mmm-85) REVERT: B 103 ARG cc_start: 0.7420 (ttm110) cc_final: 0.6919 (ttm110) REVERT: B 105 THR cc_start: 0.7789 (p) cc_final: 0.7198 (t) REVERT: B 106 GLN cc_start: 0.7598 (mt0) cc_final: 0.7255 (mp10) REVERT: B 112 TYR cc_start: 0.7499 (m-80) cc_final: 0.6934 (m-80) REVERT: B 153 VAL cc_start: 0.7985 (t) cc_final: 0.7611 (t) REVERT: B 160 GLN cc_start: 0.6928 (tp-100) cc_final: 0.6667 (tp-100) REVERT: B 169 TRP cc_start: 0.8437 (m100) cc_final: 0.6694 (m100) REVERT: B 173 PHE cc_start: 0.7082 (m-10) cc_final: 0.6746 (m-10) REVERT: B 182 THR cc_start: 0.7535 (p) cc_final: 0.7291 (p) REVERT: B 185 ASP cc_start: 0.7102 (t0) cc_final: 0.6779 (t0) REVERT: B 193 HIS cc_start: 0.7785 (m90) cc_final: 0.7171 (m90) REVERT: B 226 ARG cc_start: 0.7051 (mmm160) cc_final: 0.6721 (mmp80) REVERT: B 248 LYS cc_start: 0.8647 (mmtt) cc_final: 0.7945 (mmtt) REVERT: B 251 ASP cc_start: 0.7696 (p0) cc_final: 0.7198 (p0) REVERT: B 274 TYR cc_start: 0.6749 (t80) cc_final: 0.6320 (t80) REVERT: B 275 ASN cc_start: 0.8159 (t0) cc_final: 0.7674 (t0) REVERT: B 282 MET cc_start: 0.8169 (mtp) cc_final: 0.7910 (mtp) REVERT: B 303 TYR cc_start: 0.8138 (m-80) cc_final: 0.7569 (m-80) REVERT: B 311 CYS cc_start: 0.4115 (p) cc_final: 0.3345 (m) REVERT: B 320 GLN cc_start: 0.6628 (mt0) cc_final: 0.5997 (mt0) REVERT: B 332 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7057 (mt-10) REVERT: B 364 PHE cc_start: 0.8630 (m-80) cc_final: 0.7929 (m-80) REVERT: B 398 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7938 (mm-40) REVERT: B 411 TYR cc_start: 0.7352 (t80) cc_final: 0.6543 (t80) REVERT: B 422 LEU cc_start: 0.8280 (mt) cc_final: 0.7774 (mt) REVERT: B 430 VAL cc_start: 0.7734 (p) cc_final: 0.7490 (t) REVERT: B 443 LEU cc_start: 0.7987 (tt) cc_final: 0.7765 (tt) REVERT: B 444 THR cc_start: 0.7499 (m) cc_final: 0.6354 (m) REVERT: B 451 SER cc_start: 0.8412 (m) cc_final: 0.7805 (m) REVERT: B 452 TRP cc_start: 0.8006 (p90) cc_final: 0.7496 (p90) REVERT: B 455 LEU cc_start: 0.7387 (mt) cc_final: 0.7171 (mt) REVERT: B 467 LEU cc_start: 0.7289 (tp) cc_final: 0.6443 (pp) REVERT: B 481 PRO cc_start: 0.8200 (Cg_endo) cc_final: 0.7682 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8641 (m100) cc_final: 0.8364 (m100) REVERT: B 486 PHE cc_start: 0.8349 (m-10) cc_final: 0.7838 (m-10) REVERT: B 487 ARG cc_start: 0.7951 (mmm-85) cc_final: 0.7623 (mtt90) REVERT: B 488 ASN cc_start: 0.7836 (t0) cc_final: 0.6874 (t0) REVERT: B 491 GLN cc_start: 0.6035 (mt0) cc_final: 0.5603 (mt0) REVERT: B 517 ARG cc_start: 0.8415 (mtt180) cc_final: 0.8204 (mtt180) REVERT: B 527 GLN cc_start: 0.7168 (pm20) cc_final: 0.6051 (pm20) REVERT: B 556 ASN cc_start: 0.8124 (t0) cc_final: 0.7551 (t0) REVERT: B 566 GLU cc_start: 0.7629 (mm-30) cc_final: 0.6461 (tm-30) REVERT: B 577 PHE cc_start: 0.8359 (m-80) cc_final: 0.8019 (m-80) REVERT: B 580 GLU cc_start: 0.8416 (tp30) cc_final: 0.7956 (tp30) REVERT: B 592 ASP cc_start: 0.7838 (t0) cc_final: 0.7636 (m-30) REVERT: A 36 ASN cc_start: 0.8445 (p0) cc_final: 0.8008 (p0) REVERT: A 46 ASP cc_start: 0.7394 (t70) cc_final: 0.6831 (t70) REVERT: A 47 HIS cc_start: 0.8055 (t70) cc_final: 0.6927 (t70) REVERT: A 51 LEU cc_start: 0.8986 (tp) cc_final: 0.8698 (tp) REVERT: A 55 PHE cc_start: 0.7988 (m-10) cc_final: 0.7783 (m-10) REVERT: A 61 VAL cc_start: 0.8388 (m) cc_final: 0.8092 (p) REVERT: A 74 TYR cc_start: 0.8123 (m-80) cc_final: 0.7094 (m-80) REVERT: A 88 TYR cc_start: 0.7345 (p90) cc_final: 0.5956 (p90) REVERT: A 98 ARG cc_start: 0.7452 (ttt90) cc_final: 0.7107 (tpp80) REVERT: A 110 ASN cc_start: 0.7897 (m110) cc_final: 0.7652 (p0) REVERT: A 111 MET cc_start: 0.6957 (ttt) cc_final: 0.6333 (ttt) REVERT: A 132 LEU cc_start: 0.7502 (mm) cc_final: 0.6960 (mm) REVERT: A 143 ILE cc_start: 0.9040 (mt) cc_final: 0.8587 (mm) REVERT: A 163 GLN cc_start: 0.8386 (pt0) cc_final: 0.8140 (tt0) REVERT: A 178 MET cc_start: 0.8246 (pmm) cc_final: 0.8030 (pmm) REVERT: A 209 LYS cc_start: 0.8284 (mttt) cc_final: 0.7687 (mtmt) REVERT: A 229 SER cc_start: 0.8224 (p) cc_final: 0.7902 (t) REVERT: A 252 ARG cc_start: 0.7469 (mtp85) cc_final: 0.7258 (mtp85) REVERT: A 261 LYS cc_start: 0.7282 (ptmt) cc_final: 0.6788 (ptmt) REVERT: A 262 ASP cc_start: 0.7838 (t0) cc_final: 0.7413 (t0) REVERT: A 268 MET cc_start: 0.6349 (mtm) cc_final: 0.5327 (mtm) REVERT: A 277 MET cc_start: 0.6767 (mtt) cc_final: 0.5757 (mtt) REVERT: A 293 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7289 (tppt) REVERT: A 338 ASN cc_start: 0.7662 (p0) cc_final: 0.7385 (p0) REVERT: A 340 ILE cc_start: 0.7487 (mp) cc_final: 0.7251 (mp) REVERT: A 360 LYS cc_start: 0.8675 (tttt) cc_final: 0.8342 (tttt) REVERT: A 396 LYS cc_start: 0.8415 (tppp) cc_final: 0.7931 (tppp) REVERT: A 404 PHE cc_start: 0.7425 (p90) cc_final: 0.6633 (p90) REVERT: A 421 GLU cc_start: 0.8700 (tt0) cc_final: 0.7725 (tt0) REVERT: A 430 THR cc_start: 0.7402 (m) cc_final: 0.6585 (m) REVERT: A 431 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7949 (mtmm) REVERT: A 432 GLN cc_start: 0.8586 (tp40) cc_final: 0.8176 (tp-100) REVERT: A 433 HIS cc_start: 0.8535 (m90) cc_final: 0.8121 (m90) REVERT: A 436 PHE cc_start: 0.7998 (m-80) cc_final: 0.7791 (m-80) REVERT: A 451 ARG cc_start: 0.6722 (mtt90) cc_final: 0.6467 (ptp-170) REVERT: A 456 ILE cc_start: 0.8263 (mm) cc_final: 0.7713 (pt) REVERT: A 457 SER cc_start: 0.7997 (m) cc_final: 0.7617 (m) REVERT: A 476 ASN cc_start: 0.7753 (t0) cc_final: 0.7334 (t0) REVERT: A 487 LYS cc_start: 0.7863 (mtmm) cc_final: 0.7554 (mtmm) REVERT: A 496 GLU cc_start: 0.7747 (mp0) cc_final: 0.7476 (mp0) REVERT: C 25 MET cc_start: 0.8131 (mmp) cc_final: 0.7508 (mmp) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.2575 time to fit residues: 125.1914 Evaluate side-chains 360 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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: 0.5980 chunk 100 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 65 optimal weight: 0.3980 chunk 27 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN ** B 329 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9358 Z= 0.170 Angle : 0.586 9.366 12680 Z= 0.297 Chirality : 0.046 0.272 1417 Planarity : 0.005 0.062 1669 Dihedral : 6.021 58.064 1407 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.24), residues: 1164 helix: -1.32 (0.83), residues: 42 sheet: -1.27 (0.66), residues: 64 loop : -1.86 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 164 HIS 0.006 0.001 HIS A 183 PHE 0.021 0.001 PHE B 108 TYR 0.022 0.001 TYR A 117 ARG 0.010 0.001 ARG C 31 *********************** 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 367 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 1.032 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: 0.6424 (pp30) cc_final: 0.5092 (tm-30) REVERT: B 31 MET cc_start: 0.7393 (mtp) cc_final: 0.6520 (ptp) REVERT: B 44 ASP cc_start: 0.7196 (t0) cc_final: 0.6932 (t0) REVERT: B 45 MET cc_start: 0.8370 (tmm) cc_final: 0.8137 (tmm) REVERT: B 46 LEU cc_start: 0.8785 (mt) cc_final: 0.8266 (mt) REVERT: B 59 ASN cc_start: 0.7171 (m-40) cc_final: 0.6670 (m-40) REVERT: B 61 GLU cc_start: 0.6514 (tm-30) cc_final: 0.4477 (tm-30) REVERT: B 64 TYR cc_start: 0.7916 (m-80) cc_final: 0.7538 (m-80) REVERT: B 65 LEU cc_start: 0.8125 (mt) cc_final: 0.7722 (mt) REVERT: B 68 ASN cc_start: 0.8580 (m-40) cc_final: 0.8380 (m-40) REVERT: B 75 GLN cc_start: 0.7846 (pt0) cc_final: 0.7509 (pt0) REVERT: B 78 GLN cc_start: 0.7582 (pm20) cc_final: 0.7205 (pm20) REVERT: B 79 GLU cc_start: 0.6962 (tt0) cc_final: 0.6164 (tt0) REVERT: B 81 GLN cc_start: 0.6592 (mt0) cc_final: 0.6055 (mt0) REVERT: B 100 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.7419 (mmm-85) REVERT: B 103 ARG cc_start: 0.7395 (ttm110) cc_final: 0.7031 (ttm110) REVERT: B 105 THR cc_start: 0.7724 (p) cc_final: 0.7207 (t) REVERT: B 106 GLN cc_start: 0.7486 (mt0) cc_final: 0.7229 (mp10) REVERT: B 112 TYR cc_start: 0.7444 (m-80) cc_final: 0.6851 (m-80) REVERT: B 160 GLN cc_start: 0.6736 (tp-100) cc_final: 0.6527 (tp40) REVERT: B 169 TRP cc_start: 0.8389 (m100) cc_final: 0.7596 (m100) REVERT: B 173 PHE cc_start: 0.6993 (m-10) cc_final: 0.6751 (m-10) REVERT: B 193 HIS cc_start: 0.7781 (m90) cc_final: 0.7221 (m90) REVERT: B 237 HIS cc_start: 0.7489 (t-90) cc_final: 0.7031 (t-90) REVERT: B 248 LYS cc_start: 0.8605 (mmtt) cc_final: 0.7880 (mmtt) REVERT: B 251 ASP cc_start: 0.7720 (p0) cc_final: 0.7211 (p0) REVERT: B 274 TYR cc_start: 0.6657 (t80) cc_final: 0.5780 (t80) REVERT: B 275 ASN cc_start: 0.8150 (t0) cc_final: 0.7659 (t0) REVERT: B 282 MET cc_start: 0.8176 (mtp) cc_final: 0.7932 (mtp) REVERT: B 288 ARG cc_start: 0.7912 (mmt-90) cc_final: 0.7652 (mmt-90) REVERT: B 303 TYR cc_start: 0.8104 (m-80) cc_final: 0.7609 (m-80) REVERT: B 311 CYS cc_start: 0.3920 (p) cc_final: 0.3163 (m) REVERT: B 320 GLN cc_start: 0.6661 (mt0) cc_final: 0.6041 (mt0) REVERT: B 323 THR cc_start: 0.7707 (t) cc_final: 0.7313 (p) REVERT: B 332 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7085 (mt-10) REVERT: B 364 PHE cc_start: 0.8633 (m-80) cc_final: 0.7967 (m-80) REVERT: B 398 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8016 (mm-40) REVERT: B 411 TYR cc_start: 0.7268 (t80) cc_final: 0.6489 (t80) REVERT: B 421 ASP cc_start: 0.7653 (p0) cc_final: 0.7366 (p0) REVERT: B 422 LEU cc_start: 0.8265 (mt) cc_final: 0.7820 (mt) REVERT: B 426 GLN cc_start: 0.7677 (pt0) cc_final: 0.6920 (pp30) REVERT: B 432 ARG cc_start: 0.7127 (mmt-90) cc_final: 0.6347 (tpp-160) REVERT: B 436 LEU cc_start: 0.7904 (mt) cc_final: 0.7411 (mp) REVERT: B 444 THR cc_start: 0.7401 (m) cc_final: 0.6124 (m) REVERT: B 451 SER cc_start: 0.8393 (m) cc_final: 0.7733 (m) REVERT: B 452 TRP cc_start: 0.8007 (p90) cc_final: 0.7533 (p90) REVERT: B 467 LEU cc_start: 0.7238 (tp) cc_final: 0.6361 (pp) REVERT: B 481 PRO cc_start: 0.8201 (Cg_endo) cc_final: 0.7757 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8639 (m100) cc_final: 0.8434 (m100) REVERT: B 487 ARG cc_start: 0.7916 (mmm-85) cc_final: 0.7508 (mtt90) REVERT: B 488 ASN cc_start: 0.7895 (t0) cc_final: 0.6956 (t0) REVERT: B 491 GLN cc_start: 0.6065 (mt0) cc_final: 0.5632 (mt0) REVERT: B 517 ARG cc_start: 0.8427 (mtt180) cc_final: 0.8159 (mtt180) REVERT: B 556 ASN cc_start: 0.8130 (t0) cc_final: 0.7552 (t0) REVERT: B 566 GLU cc_start: 0.7593 (mm-30) cc_final: 0.6386 (tm-30) REVERT: B 577 PHE cc_start: 0.8368 (m-80) cc_final: 0.8009 (m-80) REVERT: B 580 GLU cc_start: 0.8420 (tp30) cc_final: 0.7947 (tp30) REVERT: A 29 LYS cc_start: 0.8000 (pttm) cc_final: 0.7614 (pttm) REVERT: A 40 GLN cc_start: 0.6707 (pt0) cc_final: 0.6094 (pt0) REVERT: A 44 PHE cc_start: 0.8289 (m-80) cc_final: 0.7883 (m-10) REVERT: A 45 GLU cc_start: 0.8358 (mp0) cc_final: 0.8061 (mp0) REVERT: A 46 ASP cc_start: 0.7433 (t70) cc_final: 0.6980 (t70) REVERT: A 47 HIS cc_start: 0.7933 (t70) cc_final: 0.6858 (t70) REVERT: A 51 LEU cc_start: 0.8902 (tp) cc_final: 0.8630 (tp) REVERT: A 55 PHE cc_start: 0.7928 (m-10) cc_final: 0.7698 (m-10) REVERT: A 61 VAL cc_start: 0.8405 (m) cc_final: 0.8069 (p) REVERT: A 74 TYR cc_start: 0.8098 (m-80) cc_final: 0.7093 (m-80) REVERT: A 83 GLN cc_start: 0.7735 (mm110) cc_final: 0.7264 (mm110) REVERT: A 98 ARG cc_start: 0.7453 (ttt90) cc_final: 0.6987 (tpp80) REVERT: A 102 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6979 (mt-10) REVERT: A 103 ASN cc_start: 0.7098 (m-40) cc_final: 0.6864 (m-40) REVERT: A 107 ILE cc_start: 0.8505 (mm) cc_final: 0.8242 (mm) REVERT: A 110 ASN cc_start: 0.7832 (m110) cc_final: 0.7539 (p0) REVERT: A 112 TYR cc_start: 0.6499 (m-80) cc_final: 0.6266 (m-10) REVERT: A 132 LEU cc_start: 0.7503 (mm) cc_final: 0.6980 (mm) REVERT: A 137 MET cc_start: 0.8160 (mtm) cc_final: 0.7902 (mtm) REVERT: A 143 ILE cc_start: 0.8987 (mt) cc_final: 0.8531 (mm) REVERT: A 167 ILE cc_start: 0.8323 (mm) cc_final: 0.8086 (mm) REVERT: A 178 MET cc_start: 0.8208 (pmm) cc_final: 0.7982 (pmm) REVERT: A 209 LYS cc_start: 0.8226 (mttt) cc_final: 0.7645 (mtmt) REVERT: A 230 ASP cc_start: 0.8291 (m-30) cc_final: 0.7256 (p0) REVERT: A 252 ARG cc_start: 0.7441 (mtp85) cc_final: 0.7209 (ttp-110) REVERT: A 253 LYS cc_start: 0.8062 (tptm) cc_final: 0.7378 (tptm) REVERT: A 254 PHE cc_start: 0.7359 (m-10) cc_final: 0.5526 (m-80) REVERT: A 261 LYS cc_start: 0.7241 (ptmt) cc_final: 0.6726 (ptmt) REVERT: A 268 MET cc_start: 0.6296 (mtm) cc_final: 0.5241 (mtm) REVERT: A 277 MET cc_start: 0.6839 (mtt) cc_final: 0.5764 (mtt) REVERT: A 293 LYS cc_start: 0.7897 (mtpp) cc_final: 0.7014 (mtpp) REVERT: A 338 ASN cc_start: 0.7712 (p0) cc_final: 0.7206 (p0) REVERT: A 340 ILE cc_start: 0.7450 (mp) cc_final: 0.7166 (mp) REVERT: A 344 GLU cc_start: 0.7373 (tt0) cc_final: 0.7167 (tt0) REVERT: A 360 LYS cc_start: 0.8717 (tttt) cc_final: 0.8375 (tttt) REVERT: A 396 LYS cc_start: 0.8389 (tppp) cc_final: 0.7849 (tppp) REVERT: A 404 PHE cc_start: 0.7355 (p90) cc_final: 0.6566 (p90) REVERT: A 421 GLU cc_start: 0.8709 (tt0) cc_final: 0.7702 (tt0) REVERT: A 430 THR cc_start: 0.7454 (m) cc_final: 0.6636 (m) REVERT: A 432 GLN cc_start: 0.8624 (tp40) cc_final: 0.8194 (tp-100) REVERT: A 433 HIS cc_start: 0.8508 (m90) cc_final: 0.8138 (m90) REVERT: A 457 SER cc_start: 0.7889 (m) cc_final: 0.7574 (m) REVERT: A 475 ILE cc_start: 0.8285 (mm) cc_final: 0.8029 (mt) REVERT: A 476 ASN cc_start: 0.7634 (t0) cc_final: 0.7222 (t0) REVERT: A 487 LYS cc_start: 0.7817 (mtmm) cc_final: 0.7527 (mtmm) REVERT: A 496 GLU cc_start: 0.7765 (mp0) cc_final: 0.7414 (mp0) REVERT: A 551 GLU cc_start: 0.8666 (pt0) cc_final: 0.8280 (pm20) REVERT: A 559 HIS cc_start: 0.7714 (t70) cc_final: 0.7242 (t-170) REVERT: C 10 MET cc_start: 0.6302 (mmp) cc_final: 0.5482 (mmp) REVERT: C 25 MET cc_start: 0.8068 (mmp) cc_final: 0.7433 (mmp) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.2585 time to fit residues: 123.9216 Evaluate side-chains 340 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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: 0.3980 chunk 63 optimal weight: 0.0970 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 111 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 329 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 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9358 Z= 0.191 Angle : 0.611 11.277 12680 Z= 0.309 Chirality : 0.046 0.269 1417 Planarity : 0.005 0.069 1669 Dihedral : 6.015 57.788 1407 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.24), residues: 1164 helix: -1.36 (0.82), residues: 42 sheet: -1.65 (0.61), residues: 74 loop : -1.83 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 200 HIS 0.009 0.001 HIS B 237 PHE 0.029 0.001 PHE B 73 TYR 0.035 0.002 TYR C 21 ARG 0.014 0.001 ARG B 143 *********************** 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 364 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 1.021 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: 0.6454 (pp30) cc_final: 0.5429 (mm-40) REVERT: B 31 MET cc_start: 0.7392 (mtp) cc_final: 0.6448 (ptp) REVERT: B 40 GLU cc_start: 0.8564 (mp0) cc_final: 0.8342 (pm20) REVERT: B 44 ASP cc_start: 0.7288 (t0) cc_final: 0.6555 (t0) REVERT: B 45 MET cc_start: 0.8390 (tmm) cc_final: 0.8105 (tmm) REVERT: B 46 LEU cc_start: 0.8631 (mt) cc_final: 0.8223 (mt) REVERT: B 47 ARG cc_start: 0.7635 (ttp80) cc_final: 0.7248 (ttp80) REVERT: B 60 LEU cc_start: 0.7534 (tp) cc_final: 0.7334 (tt) REVERT: B 61 GLU cc_start: 0.6515 (tm-30) cc_final: 0.3566 (tm-30) REVERT: B 75 GLN cc_start: 0.7878 (pt0) cc_final: 0.7560 (pt0) REVERT: B 78 GLN cc_start: 0.7541 (pm20) cc_final: 0.7254 (pm20) REVERT: B 79 GLU cc_start: 0.6991 (tt0) cc_final: 0.6279 (tt0) REVERT: B 81 GLN cc_start: 0.6607 (mt0) cc_final: 0.6020 (mt0) REVERT: B 100 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7552 (mmm-85) REVERT: B 103 ARG cc_start: 0.7367 (ttm110) cc_final: 0.7036 (ttm110) REVERT: B 105 THR cc_start: 0.7700 (p) cc_final: 0.7178 (t) REVERT: B 106 GLN cc_start: 0.7624 (mt0) cc_final: 0.7278 (mp10) REVERT: B 112 TYR cc_start: 0.7241 (m-80) cc_final: 0.6731 (m-80) REVERT: B 168 LEU cc_start: 0.8330 (tp) cc_final: 0.8101 (tp) REVERT: B 185 ASP cc_start: 0.7354 (t0) cc_final: 0.6262 (t0) REVERT: B 193 HIS cc_start: 0.7885 (m90) cc_final: 0.7310 (m90) REVERT: B 213 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7119 (tm-30) REVERT: B 248 LYS cc_start: 0.8543 (mmtt) cc_final: 0.7884 (mmtt) REVERT: B 251 ASP cc_start: 0.7723 (p0) cc_final: 0.7361 (p0) REVERT: B 274 TYR cc_start: 0.6623 (t80) cc_final: 0.6044 (t80) REVERT: B 282 MET cc_start: 0.8210 (mtp) cc_final: 0.7900 (mtp) REVERT: B 303 TYR cc_start: 0.8001 (m-80) cc_final: 0.7543 (m-80) REVERT: B 311 CYS cc_start: 0.3933 (p) cc_final: 0.3112 (m) REVERT: B 320 GLN cc_start: 0.6678 (mt0) cc_final: 0.6053 (mt0) REVERT: B 323 THR cc_start: 0.7667 (t) cc_final: 0.7296 (p) REVERT: B 332 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7080 (mt-10) REVERT: B 364 PHE cc_start: 0.8733 (m-80) cc_final: 0.8031 (m-80) REVERT: B 398 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8044 (mm-40) REVERT: B 411 TYR cc_start: 0.7335 (t80) cc_final: 0.6453 (t80) REVERT: B 426 GLN cc_start: 0.7652 (pt0) cc_final: 0.6911 (pp30) REVERT: B 432 ARG cc_start: 0.7222 (mmt-90) cc_final: 0.6309 (tpp-160) REVERT: B 436 LEU cc_start: 0.7900 (mt) cc_final: 0.7420 (mp) REVERT: B 444 THR cc_start: 0.7428 (m) cc_final: 0.6245 (m) REVERT: B 451 SER cc_start: 0.8416 (m) cc_final: 0.7730 (m) REVERT: B 452 TRP cc_start: 0.8014 (p90) cc_final: 0.7492 (p90) REVERT: B 467 LEU cc_start: 0.7224 (tp) cc_final: 0.6358 (pp) REVERT: B 481 PRO cc_start: 0.8195 (Cg_endo) cc_final: 0.7754 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8630 (m100) cc_final: 0.8411 (m100) REVERT: B 483 ASP cc_start: 0.8505 (m-30) cc_final: 0.8212 (m-30) REVERT: B 484 GLN cc_start: 0.8781 (mt0) cc_final: 0.8536 (mm-40) REVERT: B 487 ARG cc_start: 0.7892 (mmm-85) cc_final: 0.7281 (mtt90) REVERT: B 517 ARG cc_start: 0.8419 (mtt180) cc_final: 0.8185 (mtt180) REVERT: B 527 GLN cc_start: 0.7349 (pm20) cc_final: 0.5990 (pm20) REVERT: B 566 GLU cc_start: 0.7616 (mm-30) cc_final: 0.6325 (tm-30) REVERT: B 577 PHE cc_start: 0.8388 (m-80) cc_final: 0.8018 (m-80) REVERT: B 580 GLU cc_start: 0.8425 (tp30) cc_final: 0.7951 (tp30) REVERT: A 29 LYS cc_start: 0.8075 (pttm) cc_final: 0.7689 (pttm) REVERT: A 40 GLN cc_start: 0.6436 (pt0) cc_final: 0.5166 (pt0) REVERT: A 44 PHE cc_start: 0.8330 (m-80) cc_final: 0.7922 (m-10) REVERT: A 45 GLU cc_start: 0.8371 (mp0) cc_final: 0.8052 (mp0) REVERT: A 46 ASP cc_start: 0.7307 (t70) cc_final: 0.6874 (t70) REVERT: A 47 HIS cc_start: 0.7956 (t70) cc_final: 0.6875 (t70) REVERT: A 51 LEU cc_start: 0.8962 (tp) cc_final: 0.8637 (tp) REVERT: A 61 VAL cc_start: 0.8402 (m) cc_final: 0.8069 (p) REVERT: A 74 TYR cc_start: 0.8129 (m-80) cc_final: 0.7105 (m-80) REVERT: A 90 LEU cc_start: 0.7981 (tt) cc_final: 0.7758 (tp) REVERT: A 98 ARG cc_start: 0.7440 (ttt90) cc_final: 0.6982 (tpp80) REVERT: A 102 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6947 (mt-10) REVERT: A 110 ASN cc_start: 0.7823 (m110) cc_final: 0.7557 (p0) REVERT: A 112 TYR cc_start: 0.6570 (m-80) cc_final: 0.6313 (m-10) REVERT: A 119 LEU cc_start: 0.7192 (tp) cc_final: 0.6772 (tp) REVERT: A 122 LEU cc_start: 0.7821 (mp) cc_final: 0.7414 (mm) REVERT: A 132 LEU cc_start: 0.7452 (mm) cc_final: 0.6855 (mm) REVERT: A 135 LEU cc_start: 0.8334 (tp) cc_final: 0.7796 (tt) REVERT: A 137 MET cc_start: 0.8047 (mtm) cc_final: 0.7709 (mtm) REVERT: A 143 ILE cc_start: 0.9008 (mt) cc_final: 0.8513 (mm) REVERT: A 165 ARG cc_start: 0.7479 (mtp180) cc_final: 0.7250 (mtp-110) REVERT: A 172 PHE cc_start: 0.8282 (m-80) cc_final: 0.8080 (m-80) REVERT: A 178 MET cc_start: 0.8200 (pmm) cc_final: 0.7979 (pmm) REVERT: A 209 LYS cc_start: 0.8303 (mttt) cc_final: 0.7625 (mtmm) REVERT: A 230 ASP cc_start: 0.8220 (m-30) cc_final: 0.7304 (p0) REVERT: A 254 PHE cc_start: 0.7351 (m-10) cc_final: 0.7079 (m-80) REVERT: A 261 LYS cc_start: 0.7248 (ptmt) cc_final: 0.6838 (ptmt) REVERT: A 262 ASP cc_start: 0.7925 (t70) cc_final: 0.7349 (t0) REVERT: A 268 MET cc_start: 0.6325 (mtm) cc_final: 0.5276 (mtm) REVERT: A 277 MET cc_start: 0.6872 (mtt) cc_final: 0.5785 (mtt) REVERT: A 293 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7057 (mtpp) REVERT: A 338 ASN cc_start: 0.7733 (p0) cc_final: 0.7218 (p0) REVERT: A 340 ILE cc_start: 0.7419 (mp) cc_final: 0.7168 (mp) REVERT: A 344 GLU cc_start: 0.7329 (tt0) cc_final: 0.7115 (tt0) REVERT: A 360 LYS cc_start: 0.8659 (tttt) cc_final: 0.8321 (tttt) REVERT: A 396 LYS cc_start: 0.8479 (tppp) cc_final: 0.7875 (tppp) REVERT: A 404 PHE cc_start: 0.7470 (p90) cc_final: 0.6657 (p90) REVERT: A 421 GLU cc_start: 0.8530 (tt0) cc_final: 0.7817 (tt0) REVERT: A 430 THR cc_start: 0.7476 (m) cc_final: 0.6656 (m) REVERT: A 432 GLN cc_start: 0.8560 (tp40) cc_final: 0.8213 (tp-100) REVERT: A 433 HIS cc_start: 0.8554 (m90) cc_final: 0.8174 (m90) REVERT: A 451 ARG cc_start: 0.7449 (ptp-110) cc_final: 0.7199 (ptp90) REVERT: A 456 ILE cc_start: 0.8342 (mm) cc_final: 0.7692 (pt) REVERT: A 457 SER cc_start: 0.7977 (m) cc_final: 0.7199 (t) REVERT: A 475 ILE cc_start: 0.8271 (mm) cc_final: 0.8020 (mt) REVERT: A 476 ASN cc_start: 0.7662 (t0) cc_final: 0.7246 (t0) REVERT: A 487 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7515 (mtmm) REVERT: A 496 GLU cc_start: 0.7759 (mp0) cc_final: 0.7414 (mp0) REVERT: A 551 GLU cc_start: 0.8637 (pt0) cc_final: 0.8167 (pm20) REVERT: A 559 HIS cc_start: 0.7713 (t70) cc_final: 0.7233 (t-170) REVERT: C 25 MET cc_start: 0.8029 (mmp) cc_final: 0.7435 (mmp) REVERT: C 29 TYR cc_start: 0.5649 (t80) cc_final: 0.4234 (t80) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.2535 time to fit residues: 120.5605 Evaluate side-chains 343 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 0.0030 chunk 87 optimal weight: 1.9990 chunk 101 optimal weight: 0.0970 chunk 107 optimal weight: 0.0070 chunk 97 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 overall best weight: 0.3606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9358 Z= 0.192 Angle : 0.642 16.109 12680 Z= 0.322 Chirality : 0.046 0.267 1417 Planarity : 0.005 0.058 1669 Dihedral : 6.083 57.389 1407 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.24), residues: 1164 helix: -1.35 (0.83), residues: 42 sheet: -1.54 (0.58), residues: 79 loop : -1.78 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 200 HIS 0.005 0.001 HIS B 267 PHE 0.023 0.001 PHE B 73 TYR 0.030 0.002 TYR C 21 ARG 0.014 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 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: 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: 0.6522 (pp30) cc_final: 0.5228 (mm-40) REVERT: B 31 MET cc_start: 0.7437 (mtp) cc_final: 0.6559 (ptp) REVERT: B 40 GLU cc_start: 0.8562 (mp0) cc_final: 0.8343 (pm20) REVERT: B 44 ASP cc_start: 0.7269 (t0) cc_final: 0.6570 (t0) REVERT: B 45 MET cc_start: 0.8389 (tmm) cc_final: 0.8109 (tmm) REVERT: B 46 LEU cc_start: 0.8609 (mt) cc_final: 0.8227 (mt) REVERT: B 47 ARG cc_start: 0.7589 (ttp80) cc_final: 0.7239 (ttp80) REVERT: B 60 LEU cc_start: 0.7524 (tp) cc_final: 0.7318 (tt) REVERT: B 61 GLU cc_start: 0.6540 (tm-30) cc_final: 0.3554 (tm-30) REVERT: B 65 LEU cc_start: 0.8082 (mt) cc_final: 0.7660 (mt) REVERT: B 75 GLN cc_start: 0.7842 (pt0) cc_final: 0.7540 (pt0) REVERT: B 78 GLN cc_start: 0.7595 (pm20) cc_final: 0.7344 (pm20) REVERT: B 79 GLU cc_start: 0.6978 (tt0) cc_final: 0.6241 (tt0) REVERT: B 81 GLN cc_start: 0.6573 (mt0) cc_final: 0.6042 (mt0) REVERT: B 100 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7579 (mmm-85) REVERT: B 105 THR cc_start: 0.7693 (p) cc_final: 0.7201 (t) REVERT: B 106 GLN cc_start: 0.7644 (mt0) cc_final: 0.7285 (mp10) REVERT: B 112 TYR cc_start: 0.7187 (m-80) cc_final: 0.6692 (m-80) REVERT: B 139 GLU cc_start: 0.7351 (mp0) cc_final: 0.7140 (mp0) REVERT: B 160 GLN cc_start: 0.7082 (tp40) cc_final: 0.6797 (tp40) REVERT: B 164 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7760 (mp-120) REVERT: B 168 LEU cc_start: 0.8336 (tp) cc_final: 0.8113 (tp) REVERT: B 185 ASP cc_start: 0.6985 (t0) cc_final: 0.6749 (t0) REVERT: B 193 HIS cc_start: 0.7684 (m90) cc_final: 0.7144 (m90) REVERT: B 213 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7168 (tm-30) REVERT: B 248 LYS cc_start: 0.8529 (mmtt) cc_final: 0.7875 (mmtt) REVERT: B 251 ASP cc_start: 0.7755 (p0) cc_final: 0.7347 (p0) REVERT: B 274 TYR cc_start: 0.6688 (t80) cc_final: 0.5998 (t80) REVERT: B 282 MET cc_start: 0.8201 (mtp) cc_final: 0.7913 (mtp) REVERT: B 286 GLU cc_start: 0.8071 (pp20) cc_final: 0.7283 (tm-30) REVERT: B 303 TYR cc_start: 0.8082 (m-80) cc_final: 0.7577 (m-80) REVERT: B 311 CYS cc_start: 0.3970 (p) cc_final: 0.3144 (m) REVERT: B 320 GLN cc_start: 0.6686 (mt0) cc_final: 0.6066 (mt0) REVERT: B 323 THR cc_start: 0.7665 (t) cc_final: 0.7311 (p) REVERT: B 351 ARG cc_start: 0.8062 (mmp80) cc_final: 0.7769 (tpp-160) REVERT: B 364 PHE cc_start: 0.8772 (m-80) cc_final: 0.8078 (m-80) REVERT: B 398 GLN cc_start: 0.8262 (mm-40) cc_final: 0.8000 (mm-40) REVERT: B 411 TYR cc_start: 0.7315 (t80) cc_final: 0.6422 (t80) REVERT: B 426 GLN cc_start: 0.7670 (pt0) cc_final: 0.6932 (pp30) REVERT: B 436 LEU cc_start: 0.7946 (mt) cc_final: 0.7119 (mp) REVERT: B 444 THR cc_start: 0.7420 (m) cc_final: 0.6213 (m) REVERT: B 451 SER cc_start: 0.8420 (m) cc_final: 0.7735 (m) REVERT: B 452 TRP cc_start: 0.8012 (p90) cc_final: 0.7510 (p90) REVERT: B 463 SER cc_start: 0.7692 (t) cc_final: 0.7120 (m) REVERT: B 467 LEU cc_start: 0.7236 (tp) cc_final: 0.6408 (pp) REVERT: B 481 PRO cc_start: 0.8191 (Cg_endo) cc_final: 0.7751 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8617 (m100) cc_final: 0.8401 (m100) REVERT: B 483 ASP cc_start: 0.8502 (m-30) cc_final: 0.8219 (m-30) REVERT: B 484 GLN cc_start: 0.8776 (mt0) cc_final: 0.8538 (mm-40) REVERT: B 487 ARG cc_start: 0.7938 (mmm-85) cc_final: 0.7556 (mtt90) REVERT: B 517 ARG cc_start: 0.8446 (mtt180) cc_final: 0.8201 (mtt180) REVERT: B 527 GLN cc_start: 0.7392 (pm20) cc_final: 0.6050 (pm20) REVERT: B 556 ASN cc_start: 0.7534 (m-40) cc_final: 0.7254 (t0) REVERT: B 566 GLU cc_start: 0.7610 (mm-30) cc_final: 0.6326 (tm-30) REVERT: B 577 PHE cc_start: 0.8396 (m-80) cc_final: 0.8019 (m-80) REVERT: B 580 GLU cc_start: 0.8421 (tp30) cc_final: 0.7932 (tp30) REVERT: A 29 LYS cc_start: 0.8081 (pttm) cc_final: 0.7789 (pttm) REVERT: A 40 GLN cc_start: 0.6600 (pt0) cc_final: 0.5136 (pt0) REVERT: A 44 PHE cc_start: 0.8349 (m-10) cc_final: 0.7975 (m-10) REVERT: A 45 GLU cc_start: 0.8404 (mp0) cc_final: 0.8093 (mp0) REVERT: A 46 ASP cc_start: 0.7330 (t70) cc_final: 0.6877 (t70) REVERT: A 47 HIS cc_start: 0.7940 (t70) cc_final: 0.6850 (t70) REVERT: A 51 LEU cc_start: 0.8945 (tp) cc_final: 0.8647 (tp) REVERT: A 55 PHE cc_start: 0.8003 (m-10) cc_final: 0.7737 (m-10) REVERT: A 61 VAL cc_start: 0.8458 (m) cc_final: 0.8135 (p) REVERT: A 74 TYR cc_start: 0.8141 (m-80) cc_final: 0.7108 (m-80) REVERT: A 102 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6936 (mt-10) REVERT: A 106 ILE cc_start: 0.7823 (tt) cc_final: 0.7295 (mm) REVERT: A 110 ASN cc_start: 0.7816 (m110) cc_final: 0.7590 (p0) REVERT: A 112 TYR cc_start: 0.7470 (m-80) cc_final: 0.6882 (m-80) REVERT: A 119 LEU cc_start: 0.7163 (tp) cc_final: 0.6802 (tp) REVERT: A 122 LEU cc_start: 0.7816 (mp) cc_final: 0.7422 (mm) REVERT: A 132 LEU cc_start: 0.7383 (mm) cc_final: 0.6811 (mm) REVERT: A 163 GLN cc_start: 0.8408 (tt0) cc_final: 0.7790 (tt0) REVERT: A 209 LYS cc_start: 0.8313 (mttt) cc_final: 0.7741 (mtmm) REVERT: A 230 ASP cc_start: 0.8238 (m-30) cc_final: 0.7221 (p0) REVERT: A 252 ARG cc_start: 0.7627 (mtp85) cc_final: 0.7058 (ttp-110) REVERT: A 254 PHE cc_start: 0.7377 (m-10) cc_final: 0.7070 (m-80) REVERT: A 261 LYS cc_start: 0.7278 (ptmt) cc_final: 0.6787 (ptmt) REVERT: A 262 ASP cc_start: 0.7908 (t70) cc_final: 0.7330 (t0) REVERT: A 268 MET cc_start: 0.6302 (mtm) cc_final: 0.5272 (mtm) REVERT: A 277 MET cc_start: 0.6916 (mtt) cc_final: 0.5817 (mtt) REVERT: A 293 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7120 (mtpp) REVERT: A 325 LYS cc_start: 0.8294 (mttt) cc_final: 0.7775 (mttt) REVERT: A 338 ASN cc_start: 0.7730 (p0) cc_final: 0.7237 (p0) REVERT: A 340 ILE cc_start: 0.7433 (mp) cc_final: 0.7149 (mp) REVERT: A 344 GLU cc_start: 0.7399 (tt0) cc_final: 0.7146 (tt0) REVERT: A 351 ILE cc_start: 0.7416 (tt) cc_final: 0.6875 (mp) REVERT: A 360 LYS cc_start: 0.8691 (tttt) cc_final: 0.8355 (tttt) REVERT: A 396 LYS cc_start: 0.8464 (tppp) cc_final: 0.7865 (tppp) REVERT: A 404 PHE cc_start: 0.7359 (p90) cc_final: 0.6636 (p90) REVERT: A 421 GLU cc_start: 0.8533 (tt0) cc_final: 0.7826 (tt0) REVERT: A 430 THR cc_start: 0.7438 (m) cc_final: 0.6626 (m) REVERT: A 432 GLN cc_start: 0.8574 (tp40) cc_final: 0.8214 (tp-100) REVERT: A 433 HIS cc_start: 0.8587 (m90) cc_final: 0.8156 (m90) REVERT: A 454 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8141 (mmtt) REVERT: A 457 SER cc_start: 0.8003 (m) cc_final: 0.7292 (t) REVERT: A 476 ASN cc_start: 0.7626 (t0) cc_final: 0.7211 (t0) REVERT: A 487 LYS cc_start: 0.7779 (mtmm) cc_final: 0.7510 (mtmm) REVERT: A 496 GLU cc_start: 0.7765 (mp0) cc_final: 0.7404 (mp0) REVERT: A 551 GLU cc_start: 0.8571 (pt0) cc_final: 0.8121 (pm20) REVERT: A 559 HIS cc_start: 0.7716 (t70) cc_final: 0.7226 (t-170) REVERT: C 18 GLN cc_start: 0.7825 (tt0) cc_final: 0.7380 (tt0) REVERT: C 25 MET cc_start: 0.7958 (mmp) cc_final: 0.7414 (mmp) REVERT: C 29 TYR cc_start: 0.5674 (t80) cc_final: 0.4240 (t80) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.2682 time to fit residues: 127.8573 Evaluate side-chains 338 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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: 0.0370 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 0.0670 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 94 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 0.0170 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 overall best weight: 0.1032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** 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 435 GLN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9358 Z= 0.152 Angle : 0.606 10.922 12680 Z= 0.301 Chirality : 0.045 0.258 1417 Planarity : 0.004 0.054 1669 Dihedral : 5.790 56.677 1407 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % 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: -2.41 (0.24), residues: 1164 helix: -2.10 (0.70), residues: 54 sheet: -1.49 (0.59), residues: 79 loop : -1.77 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 164 HIS 0.009 0.001 HIS B 267 PHE 0.018 0.001 PHE B 73 TYR 0.020 0.001 TYR A 113 ARG 0.012 0.001 ARG B 143 *********************** 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 351 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 1.048 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: 0.7436 (mtp) cc_final: 0.6533 (ptp) REVERT: B 40 GLU cc_start: 0.8534 (mp0) cc_final: 0.8311 (pm20) REVERT: B 44 ASP cc_start: 0.7232 (t0) cc_final: 0.6448 (t0) REVERT: B 45 MET cc_start: 0.8289 (tmm) cc_final: 0.8057 (tmm) REVERT: B 46 LEU cc_start: 0.8596 (mt) cc_final: 0.8254 (mt) REVERT: B 47 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7082 (ttp80) REVERT: B 61 GLU cc_start: 0.6563 (tm-30) cc_final: 0.3246 (tm-30) REVERT: B 65 LEU cc_start: 0.8031 (mt) cc_final: 0.7749 (mt) REVERT: B 75 GLN cc_start: 0.7847 (pt0) cc_final: 0.7031 (pp30) REVERT: B 78 GLN cc_start: 0.7673 (pm20) cc_final: 0.7375 (pm20) REVERT: B 79 GLU cc_start: 0.7019 (tt0) cc_final: 0.6611 (tt0) REVERT: B 81 GLN cc_start: 0.6498 (mt0) cc_final: 0.6177 (mt0) REVERT: B 100 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7514 (mmm-85) REVERT: B 106 GLN cc_start: 0.7699 (mt0) cc_final: 0.7425 (mp10) REVERT: B 112 TYR cc_start: 0.7283 (m-80) cc_final: 0.6703 (m-80) REVERT: B 139 GLU cc_start: 0.7230 (mp0) cc_final: 0.6965 (mp0) REVERT: B 160 GLN cc_start: 0.6951 (tp40) cc_final: 0.6706 (tp-100) REVERT: B 164 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7682 (mp-120) REVERT: B 168 LEU cc_start: 0.8353 (tp) cc_final: 0.8150 (tp) REVERT: B 185 ASP cc_start: 0.6943 (t0) cc_final: 0.6629 (t0) REVERT: B 193 HIS cc_start: 0.7660 (m90) cc_final: 0.7158 (m90) REVERT: B 237 HIS cc_start: 0.7272 (t-90) cc_final: 0.7061 (t70) REVERT: B 248 LYS cc_start: 0.8505 (mmtt) cc_final: 0.7833 (mmtt) REVERT: B 251 ASP cc_start: 0.7765 (p0) cc_final: 0.7333 (p0) REVERT: B 265 GLU cc_start: 0.6770 (pm20) cc_final: 0.6403 (pm20) REVERT: B 274 TYR cc_start: 0.6588 (t80) cc_final: 0.5986 (t80) REVERT: B 282 MET cc_start: 0.8208 (mtp) cc_final: 0.7893 (mtp) REVERT: B 286 GLU cc_start: 0.8097 (pp20) cc_final: 0.7253 (tm-30) REVERT: B 303 TYR cc_start: 0.7913 (m-80) cc_final: 0.7526 (m-80) REVERT: B 311 CYS cc_start: 0.3984 (p) cc_final: 0.3205 (m) REVERT: B 320 GLN cc_start: 0.6638 (mt0) cc_final: 0.6030 (mt0) REVERT: B 323 THR cc_start: 0.7669 (t) cc_final: 0.7327 (p) REVERT: B 351 ARG cc_start: 0.7980 (mmp80) cc_final: 0.7711 (tpp-160) REVERT: B 364 PHE cc_start: 0.8771 (m-80) cc_final: 0.8102 (m-80) REVERT: B 398 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7931 (mp10) REVERT: B 411 TYR cc_start: 0.7199 (t80) cc_final: 0.6434 (t80) REVERT: B 426 GLN cc_start: 0.7704 (pt0) cc_final: 0.6954 (pp30) REVERT: B 429 GLN cc_start: 0.6591 (mt0) cc_final: 0.6166 (mm-40) REVERT: B 436 LEU cc_start: 0.7943 (mt) cc_final: 0.7633 (mt) REVERT: B 444 THR cc_start: 0.7333 (m) cc_final: 0.6079 (m) REVERT: B 451 SER cc_start: 0.8393 (m) cc_final: 0.7679 (m) REVERT: B 452 TRP cc_start: 0.7964 (p90) cc_final: 0.7315 (p90) REVERT: B 467 LEU cc_start: 0.7126 (tp) cc_final: 0.6328 (pp) REVERT: B 481 PRO cc_start: 0.8216 (Cg_endo) cc_final: 0.7878 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8629 (m100) cc_final: 0.8325 (m100) REVERT: B 483 ASP cc_start: 0.8468 (m-30) cc_final: 0.8240 (m-30) REVERT: B 484 GLN cc_start: 0.8728 (mt0) cc_final: 0.8452 (mp10) REVERT: B 486 PHE cc_start: 0.7917 (m-10) cc_final: 0.7103 (m-10) REVERT: B 487 ARG cc_start: 0.7997 (mmm-85) cc_final: 0.7390 (mtt90) REVERT: B 488 ASN cc_start: 0.8260 (t0) cc_final: 0.7796 (t0) REVERT: B 517 ARG cc_start: 0.8383 (mtt180) cc_final: 0.8092 (mtt180) REVERT: B 566 GLU cc_start: 0.7537 (mm-30) cc_final: 0.6352 (tm-30) REVERT: B 577 PHE cc_start: 0.8386 (m-80) cc_final: 0.8012 (m-80) REVERT: B 580 GLU cc_start: 0.8418 (tp30) cc_final: 0.7927 (tp30) REVERT: A 29 LYS cc_start: 0.7875 (pttm) cc_final: 0.7619 (pttm) REVERT: A 40 GLN cc_start: 0.6168 (pt0) cc_final: 0.4760 (pt0) REVERT: A 44 PHE cc_start: 0.8289 (m-10) cc_final: 0.7848 (m-10) REVERT: A 45 GLU cc_start: 0.8385 (mp0) cc_final: 0.8109 (mp0) REVERT: A 46 ASP cc_start: 0.7414 (t70) cc_final: 0.6919 (t70) REVERT: A 47 HIS cc_start: 0.7799 (t70) cc_final: 0.6701 (t70) REVERT: A 51 LEU cc_start: 0.8963 (tp) cc_final: 0.8631 (tp) REVERT: A 55 PHE cc_start: 0.7979 (m-10) cc_final: 0.7660 (m-10) REVERT: A 61 VAL cc_start: 0.8433 (m) cc_final: 0.8063 (p) REVERT: A 74 TYR cc_start: 0.8098 (m-80) cc_final: 0.7069 (m-80) REVERT: A 98 ARG cc_start: 0.7371 (ttt90) cc_final: 0.6892 (tpp80) REVERT: A 102 GLU cc_start: 0.7574 (mt-10) cc_final: 0.6929 (mt-10) REVERT: A 110 ASN cc_start: 0.7830 (m110) cc_final: 0.7586 (p0) REVERT: A 112 TYR cc_start: 0.7396 (m-80) cc_final: 0.6896 (m-80) REVERT: A 119 LEU cc_start: 0.7333 (tp) cc_final: 0.6801 (tp) REVERT: A 122 LEU cc_start: 0.7743 (mp) cc_final: 0.7321 (mm) REVERT: A 132 LEU cc_start: 0.7367 (mm) cc_final: 0.6855 (mm) REVERT: A 143 ILE cc_start: 0.8974 (mt) cc_final: 0.8723 (pt) REVERT: A 163 GLN cc_start: 0.8356 (tt0) cc_final: 0.7664 (pp30) REVERT: A 176 MET cc_start: 0.8484 (ptp) cc_final: 0.7841 (ptp) REVERT: A 209 LYS cc_start: 0.8251 (mttt) cc_final: 0.7628 (mtmm) REVERT: A 230 ASP cc_start: 0.8140 (m-30) cc_final: 0.7101 (p0) REVERT: A 252 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7207 (ttp-110) REVERT: A 254 PHE cc_start: 0.7372 (m-10) cc_final: 0.7043 (m-80) REVERT: A 257 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8077 (mm-30) REVERT: A 261 LYS cc_start: 0.7210 (ptmt) cc_final: 0.6747 (ptmt) REVERT: A 268 MET cc_start: 0.6263 (mtm) cc_final: 0.5193 (mtm) REVERT: A 277 MET cc_start: 0.6872 (mtt) cc_final: 0.5779 (mtt) REVERT: A 293 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7087 (mtpp) REVERT: A 325 LYS cc_start: 0.8224 (mttt) cc_final: 0.7723 (mttt) REVERT: A 338 ASN cc_start: 0.7682 (p0) cc_final: 0.6276 (p0) REVERT: A 344 GLU cc_start: 0.7380 (tt0) cc_final: 0.7126 (tt0) REVERT: A 345 PHE cc_start: 0.8442 (m-80) cc_final: 0.7428 (m-80) REVERT: A 360 LYS cc_start: 0.8630 (tttt) cc_final: 0.8300 (tttt) REVERT: A 387 LEU cc_start: 0.8463 (mt) cc_final: 0.8234 (mt) REVERT: A 396 LYS cc_start: 0.8418 (tppp) cc_final: 0.7783 (tppp) REVERT: A 404 PHE cc_start: 0.7327 (p90) cc_final: 0.6457 (p90) REVERT: A 421 GLU cc_start: 0.8682 (tt0) cc_final: 0.7903 (tt0) REVERT: A 430 THR cc_start: 0.7394 (m) cc_final: 0.6575 (m) REVERT: A 432 GLN cc_start: 0.8518 (tp40) cc_final: 0.8096 (tp-100) REVERT: A 433 HIS cc_start: 0.8526 (m90) cc_final: 0.8115 (m90) REVERT: A 457 SER cc_start: 0.7941 (m) cc_final: 0.7195 (t) REVERT: A 476 ASN cc_start: 0.7619 (t0) cc_final: 0.6647 (t0) REVERT: A 479 LYS cc_start: 0.7922 (mtpt) cc_final: 0.7143 (mtpt) REVERT: A 496 GLU cc_start: 0.7746 (mp0) cc_final: 0.7397 (mp0) REVERT: A 521 ARG cc_start: 0.7888 (ptt180) cc_final: 0.7150 (ttp-110) REVERT: A 559 HIS cc_start: 0.7685 (t70) cc_final: 0.7199 (t-170) REVERT: A 567 MET cc_start: 0.7486 (tmm) cc_final: 0.7279 (tmm) REVERT: C 18 GLN cc_start: 0.7882 (tt0) cc_final: 0.7426 (tt0) REVERT: C 25 MET cc_start: 0.7908 (mmp) cc_final: 0.7413 (mmp) REVERT: C 29 TYR cc_start: 0.5824 (t80) cc_final: 0.4246 (t80) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.2577 time to fit residues: 117.6374 Evaluate side-chains 337 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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: 0.0970 chunk 76 optimal weight: 0.4980 chunk 115 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 92 optimal weight: 0.0050 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.2370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** 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** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9358 Z= 0.162 Angle : 0.608 9.406 12680 Z= 0.304 Chirality : 0.045 0.258 1417 Planarity : 0.004 0.054 1669 Dihedral : 5.713 56.815 1407 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % 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: -2.33 (0.24), residues: 1164 helix: -2.09 (0.70), residues: 54 sheet: -1.49 (0.59), residues: 79 loop : -1.70 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 200 HIS 0.005 0.001 HIS B 267 PHE 0.016 0.001 PHE B 73 TYR 0.018 0.001 TYR A 113 ARG 0.009 0.001 ARG B 143 ********************** 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 347 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.7443 (mtp) cc_final: 0.6437 (ptp) REVERT: B 40 GLU cc_start: 0.8545 (mp0) cc_final: 0.8313 (pm20) REVERT: B 44 ASP cc_start: 0.7273 (t0) cc_final: 0.6509 (t0) REVERT: B 45 MET cc_start: 0.8270 (tmm) cc_final: 0.8053 (tmm) REVERT: B 46 LEU cc_start: 0.8614 (mt) cc_final: 0.8248 (mt) REVERT: B 47 ARG cc_start: 0.7532 (ttp80) cc_final: 0.7097 (ttp80) REVERT: B 61 GLU cc_start: 0.6633 (tm-30) cc_final: 0.3273 (tm-30) REVERT: B 65 LEU cc_start: 0.8036 (mt) cc_final: 0.7770 (mt) REVERT: B 75 GLN cc_start: 0.7799 (pt0) cc_final: 0.7026 (pp30) REVERT: B 78 GLN cc_start: 0.7680 (pm20) cc_final: 0.7379 (pm20) REVERT: B 79 GLU cc_start: 0.6958 (tt0) cc_final: 0.6437 (tt0) REVERT: B 81 GLN cc_start: 0.6494 (mt0) cc_final: 0.6144 (mt0) REVERT: B 100 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7557 (mmm-85) REVERT: B 106 GLN cc_start: 0.7718 (mt0) cc_final: 0.7410 (mp10) REVERT: B 112 TYR cc_start: 0.7290 (m-80) cc_final: 0.6744 (m-80) REVERT: B 139 GLU cc_start: 0.7153 (mp0) cc_final: 0.6913 (mp0) REVERT: B 160 GLN cc_start: 0.6906 (tp40) cc_final: 0.6679 (tp-100) REVERT: B 164 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7831 (mp10) REVERT: B 168 LEU cc_start: 0.8383 (tp) cc_final: 0.8164 (tp) REVERT: B 185 ASP cc_start: 0.7036 (t0) cc_final: 0.6825 (t0) REVERT: B 193 HIS cc_start: 0.7737 (m90) cc_final: 0.7235 (m90) REVERT: B 226 ARG cc_start: 0.7788 (mmp80) cc_final: 0.7079 (mmm160) REVERT: B 237 HIS cc_start: 0.7346 (t-90) cc_final: 0.7140 (t-90) REVERT: B 248 LYS cc_start: 0.8513 (mmtt) cc_final: 0.7852 (mmtt) REVERT: B 251 ASP cc_start: 0.7788 (p0) cc_final: 0.7394 (p0) REVERT: B 265 GLU cc_start: 0.6714 (pm20) cc_final: 0.6360 (pm20) REVERT: B 274 TYR cc_start: 0.6631 (t80) cc_final: 0.6148 (t80) REVERT: B 282 MET cc_start: 0.8213 (mtp) cc_final: 0.7887 (mtp) REVERT: B 286 GLU cc_start: 0.8110 (pp20) cc_final: 0.7280 (tm-30) REVERT: B 303 TYR cc_start: 0.7895 (m-80) cc_final: 0.7430 (m-80) REVERT: B 311 CYS cc_start: 0.4032 (p) cc_final: 0.3249 (m) REVERT: B 320 GLN cc_start: 0.6606 (mt0) cc_final: 0.6131 (pm20) REVERT: B 323 THR cc_start: 0.7676 (t) cc_final: 0.7344 (p) REVERT: B 351 ARG cc_start: 0.7974 (mmp80) cc_final: 0.7732 (tpp-160) REVERT: B 364 PHE cc_start: 0.8761 (m-80) cc_final: 0.8125 (m-80) REVERT: B 398 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7880 (mp10) REVERT: B 411 TYR cc_start: 0.7236 (t80) cc_final: 0.6442 (t80) REVERT: B 422 LEU cc_start: 0.8485 (mt) cc_final: 0.7694 (mt) REVERT: B 426 GLN cc_start: 0.7726 (pt0) cc_final: 0.6974 (pp30) REVERT: B 436 LEU cc_start: 0.7849 (mt) cc_final: 0.7581 (mt) REVERT: B 444 THR cc_start: 0.7366 (m) cc_final: 0.6139 (m) REVERT: B 451 SER cc_start: 0.8419 (m) cc_final: 0.7748 (m) REVERT: B 452 TRP cc_start: 0.8004 (p90) cc_final: 0.7405 (p90) REVERT: B 467 LEU cc_start: 0.7120 (tp) cc_final: 0.6337 (pp) REVERT: B 481 PRO cc_start: 0.8205 (Cg_endo) cc_final: 0.7883 (Cg_exo) REVERT: B 483 ASP cc_start: 0.8483 (m-30) cc_final: 0.8228 (m-30) REVERT: B 484 GLN cc_start: 0.8748 (mt0) cc_final: 0.8456 (mp10) REVERT: B 487 ARG cc_start: 0.7977 (mmm-85) cc_final: 0.7463 (mtt90) REVERT: B 488 ASN cc_start: 0.8276 (t0) cc_final: 0.7807 (t0) REVERT: B 517 ARG cc_start: 0.8392 (mtt180) cc_final: 0.8087 (mtt180) REVERT: B 556 ASN cc_start: 0.7858 (t0) cc_final: 0.7352 (t0) REVERT: B 566 GLU cc_start: 0.7679 (mm-30) cc_final: 0.6362 (tm-30) REVERT: B 577 PHE cc_start: 0.8387 (m-80) cc_final: 0.8025 (m-80) REVERT: B 580 GLU cc_start: 0.8410 (tp30) cc_final: 0.7924 (tp30) REVERT: A 40 GLN cc_start: 0.6209 (pt0) cc_final: 0.4743 (pt0) REVERT: A 44 PHE cc_start: 0.8349 (m-10) cc_final: 0.7947 (m-10) REVERT: A 45 GLU cc_start: 0.8404 (mp0) cc_final: 0.8130 (mp0) REVERT: A 46 ASP cc_start: 0.7327 (t70) cc_final: 0.6860 (t70) REVERT: A 47 HIS cc_start: 0.7852 (t70) cc_final: 0.6771 (t70) REVERT: A 51 LEU cc_start: 0.8992 (tp) cc_final: 0.8638 (tp) REVERT: A 55 PHE cc_start: 0.7984 (m-10) cc_final: 0.7697 (m-10) REVERT: A 61 VAL cc_start: 0.8401 (m) cc_final: 0.8073 (p) REVERT: A 74 TYR cc_start: 0.8143 (m-80) cc_final: 0.7080 (m-80) REVERT: A 83 GLN cc_start: 0.7342 (pm20) cc_final: 0.6745 (mp10) REVERT: A 98 ARG cc_start: 0.7426 (ttt90) cc_final: 0.6931 (tpp80) REVERT: A 102 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6916 (mt-10) REVERT: A 110 ASN cc_start: 0.7836 (m110) cc_final: 0.7601 (p0) REVERT: A 112 TYR cc_start: 0.7451 (m-80) cc_final: 0.6902 (m-80) REVERT: A 119 LEU cc_start: 0.7136 (tp) cc_final: 0.6813 (tp) REVERT: A 122 LEU cc_start: 0.7899 (mp) cc_final: 0.7518 (mm) REVERT: A 132 LEU cc_start: 0.7328 (mm) cc_final: 0.6799 (mm) REVERT: A 135 LEU cc_start: 0.8219 (tp) cc_final: 0.8017 (tt) REVERT: A 163 GLN cc_start: 0.8497 (tt0) cc_final: 0.7654 (pp30) REVERT: A 176 MET cc_start: 0.8462 (ptp) cc_final: 0.7888 (ptp) REVERT: A 209 LYS cc_start: 0.8350 (mttt) cc_final: 0.7758 (mtmm) REVERT: A 230 ASP cc_start: 0.8171 (m-30) cc_final: 0.7099 (p0) REVERT: A 252 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7128 (ttp-110) REVERT: A 254 PHE cc_start: 0.7424 (m-10) cc_final: 0.7100 (m-80) REVERT: A 257 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8093 (mm-30) REVERT: A 261 LYS cc_start: 0.7240 (ptmt) cc_final: 0.6712 (ptmt) REVERT: A 268 MET cc_start: 0.6295 (mtm) cc_final: 0.5232 (mtm) REVERT: A 277 MET cc_start: 0.6908 (mtt) cc_final: 0.5802 (mtt) REVERT: A 325 LYS cc_start: 0.8258 (mttt) cc_final: 0.7781 (mttt) REVERT: A 338 ASN cc_start: 0.7724 (p0) cc_final: 0.6313 (p0) REVERT: A 340 ILE cc_start: 0.7411 (mp) cc_final: 0.7087 (mp) REVERT: A 344 GLU cc_start: 0.7394 (tt0) cc_final: 0.7152 (tt0) REVERT: A 345 PHE cc_start: 0.8432 (m-80) cc_final: 0.7445 (m-80) REVERT: A 360 LYS cc_start: 0.8653 (tttt) cc_final: 0.8319 (tttt) REVERT: A 396 LYS cc_start: 0.8414 (tppp) cc_final: 0.7774 (tppp) REVERT: A 404 PHE cc_start: 0.7181 (p90) cc_final: 0.6412 (p90) REVERT: A 421 GLU cc_start: 0.8689 (tt0) cc_final: 0.7924 (tt0) REVERT: A 430 THR cc_start: 0.7398 (m) cc_final: 0.6596 (m) REVERT: A 431 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7816 (mtmm) REVERT: A 432 GLN cc_start: 0.8556 (tp40) cc_final: 0.8167 (tp-100) REVERT: A 433 HIS cc_start: 0.8783 (m90) cc_final: 0.8118 (m90) REVERT: A 454 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8139 (mmtt) REVERT: A 457 SER cc_start: 0.7943 (m) cc_final: 0.7183 (t) REVERT: A 476 ASN cc_start: 0.7649 (t0) cc_final: 0.6673 (t0) REVERT: A 479 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7029 (mtpt) REVERT: A 496 GLU cc_start: 0.7758 (mp0) cc_final: 0.7473 (mp0) REVERT: A 521 ARG cc_start: 0.7826 (ptt180) cc_final: 0.7139 (ttp-110) REVERT: A 551 GLU cc_start: 0.8643 (pt0) cc_final: 0.8171 (mp0) REVERT: A 559 HIS cc_start: 0.7721 (t70) cc_final: 0.7228 (t-170) REVERT: C 18 GLN cc_start: 0.7944 (tt0) cc_final: 0.7480 (tt0) REVERT: C 25 MET cc_start: 0.7928 (mmp) cc_final: 0.7468 (mmp) REVERT: C 29 TYR cc_start: 0.5877 (t80) cc_final: 0.4260 (t80) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2644 time to fit residues: 119.4450 Evaluate side-chains 330 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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: 0.0170 chunk 13 optimal weight: 0.0470 chunk 25 optimal weight: 0.3980 chunk 92 optimal weight: 0.1980 chunk 38 optimal weight: 0.2980 chunk 94 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.131406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105426 restraints weight = 16429.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110891 restraints weight = 9421.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.114865 restraints weight = 6022.195| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9358 Z= 0.155 Angle : 0.599 9.428 12680 Z= 0.298 Chirality : 0.045 0.260 1417 Planarity : 0.004 0.058 1669 Dihedral : 5.621 56.571 1407 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.22 (0.24), residues: 1164 helix: -1.62 (0.78), residues: 48 sheet: -1.50 (0.59), residues: 81 loop : -1.63 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 200 HIS 0.005 0.001 HIS B 267 PHE 0.014 0.001 PHE B 73 TYR 0.018 0.001 TYR A 113 ARG 0.008 0.001 ARG B 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3117.78 seconds wall clock time: 56 minutes 39.96 seconds (3399.96 seconds total)