Starting phenix.real_space_refine on Wed Apr 30 16:53:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgp_34745/04_2025/8hgp_34745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgp_34745/04_2025/8hgp_34745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hgp_34745/04_2025/8hgp_34745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgp_34745/04_2025/8hgp_34745.map" model { file = "/net/cci-nas-00/data/ceres_data/8hgp_34745/04_2025/8hgp_34745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgp_34745/04_2025/8hgp_34745.cif" } resolution = 4.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 315 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 5672 2.51 5 N 1629 2.21 5 O 1758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9169 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4345 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 35, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 4391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4391 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 26, 'TRANS': 541} Chain: "C" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 327 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ASN A 182 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 182 " occ=0.00 residue: pdb=" N HIS A 183 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS A 183 " occ=0.00 residue: pdb=" N LEU A 184 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 184 " occ=0.00 residue: pdb=" N GLY A 203 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 203 " occ=0.00 residue: pdb=" N CYS A 329 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 329 " occ=0.00 residue: pdb=" N GLU A 330 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 330 " occ=0.00 residue: pdb=" N GLY A 331 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 331 " occ=0.00 residue: pdb=" N PRO A 332 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 332 " occ=0.00 residue: pdb=" N CYS A 333 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 333 " occ=0.00 Time building chain proxies: 6.97, per 1000 atoms: 0.76 Number of scatterers: 9169 At special positions: 0 Unit cell: (78.11, 131.61, 127.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 1758 8.00 N 1629 7.00 C 5672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 504 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 260 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 337 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 499 " distance=2.04 Simple disulfide: pdb=" SG CYS A 506 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 523 " distance=2.04 Simple disulfide: pdb=" SG CYS A 526 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 539 " - pdb=" SG CYS A 555 " distance=2.04 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 19 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 41 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-3 " NAG D 2 " - " BMA D 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A 801 " - " ASN A 56 " " NAG A 802 " - " ASN A 175 " " NAG D 1 " - " ASN A 352 " " NAG E 1 " - " ASN B 259 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.2 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: 1.05 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: 2.29 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3115 1.35 - 1.46: 1988 1.46 - 1.58: 4129 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 9358 Sorted by residual: bond pdb=" C5 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.418 1.475 -0.057 2.00e-02 2.50e+03 8.22e+00 bond pdb=" C PRO B 593 " pdb=" N PRO B 594 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.32e+00 bond pdb=" C LYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.28e+00 bond pdb=" C1 NAG A 801 " pdb=" O5 NAG A 801 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.32e+00 bond pdb=" C1 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.399 1.442 -0.043 2.00e-02 2.50e+03 4.62e+00 ... (remaining 9353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 12358 1.88 - 3.76: 273 3.76 - 5.64: 36 5.64 - 7.52: 9 7.52 - 9.40: 4 Bond angle restraints: 12680 Sorted by residual: angle pdb=" C ALA B 324 " pdb=" N GLU B 325 " pdb=" CA GLU B 325 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C GLU A 204 " pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" CA PRO B 593 " pdb=" C PRO B 593 " pdb=" N PRO B 594 " ideal model delta sigma weight residual 117.93 122.18 -4.25 1.20e+00 6.94e-01 1.25e+01 angle pdb=" N LEU A 509 " pdb=" CA LEU A 509 " pdb=" C LEU A 509 " ideal model delta sigma weight residual 111.74 116.29 -4.55 1.35e+00 5.49e-01 1.14e+01 angle pdb=" N PRO B 593 " pdb=" CA PRO B 593 " pdb=" C PRO B 593 " ideal model delta sigma weight residual 110.70 114.75 -4.05 1.22e+00 6.72e-01 1.10e+01 ... (remaining 12675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.72: 5691 22.72 - 45.43: 153 45.43 - 68.15: 33 68.15 - 90.86: 19 90.86 - 113.58: 7 Dihedral angle restraints: 5903 sinusoidal: 2540 harmonic: 3363 Sorted by residual: dihedral pdb=" CB CYS B 299 " pdb=" SG CYS B 299 " pdb=" SG CYS B 311 " pdb=" CB CYS B 311 " ideal model delta sinusoidal sigma weight residual -86.00 -175.48 89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS B 544 " pdb=" SG CYS B 544 " pdb=" SG CYS B 560 " pdb=" CB CYS B 560 " ideal model delta sinusoidal sigma weight residual 93.00 -179.23 -87.77 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS A 215 " pdb=" SG CYS A 215 " pdb=" SG CYS A 223 " pdb=" CB CYS A 223 " ideal model delta sinusoidal sigma weight residual -86.00 -172.55 86.55 1 1.00e+01 1.00e-02 9.02e+01 ... (remaining 5900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1233 0.078 - 0.155: 178 0.155 - 0.233: 3 0.233 - 0.311: 2 0.311 - 0.388: 1 Chirality restraints: 1417 Sorted by residual: chirality pdb=" C2 NAG A 802 " pdb=" C1 NAG A 802 " pdb=" C3 NAG A 802 " pdb=" N2 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 352 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1414 not shown) Planarity restraints: 1673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 511 " 0.040 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO A 512 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 519 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO A 520 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 520 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 550 " -0.034 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO B 551 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 551 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 551 " -0.028 5.00e-02 4.00e+02 ... (remaining 1670 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2178 2.80 - 3.32: 7398 3.32 - 3.85: 14321 3.85 - 4.37: 16134 4.37 - 4.90: 27582 Nonbonded interactions: 67613 Sorted by model distance: nonbonded pdb=" OH TYR B 163 " pdb=" O HIS B 193 " model vdw 2.270 3.040 nonbonded pdb=" O VAL B 356 " pdb=" OG SER B 380 " model vdw 2.328 3.040 nonbonded pdb=" NH1 ARG B 103 " pdb=" O LEU B 256 " model vdw 2.392 3.120 nonbonded pdb=" OG SER B 373 " pdb=" O TYR B 409 " model vdw 2.396 3.040 nonbonded pdb=" NH2 ARG B 34 " pdb=" OD1 ASN B 438 " model vdw 2.398 3.120 ... (remaining 67608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.470 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.190 ------------------------------------------------------------------------------- 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 9413 Z= 0.180 Angle : 0.703 12.013 12798 Z= 0.382 Chirality : 0.052 0.388 1417 Planarity : 0.007 0.061 1669 Dihedral : 10.200 113.578 3600 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.20 % Allowed : 0.78 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.19), residues: 1164 helix: -3.84 (0.43), residues: 41 sheet: -2.91 (0.57), residues: 67 loop : -2.85 (0.15), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 452 HIS 0.011 0.001 HIS B 48 PHE 0.017 0.001 PHE A 404 TYR 0.012 0.001 TYR B 554 ARG 0.004 0.000 ARG B 536 Details of bonding type rmsd link_NAG-ASN : bond 0.00743 ( 4) link_NAG-ASN : angle 3.64396 ( 12) link_BETA1-4 : bond 0.00695 ( 2) link_BETA1-4 : angle 2.05562 ( 6) link_ALPHA1-3 : bond 0.01525 ( 1) link_ALPHA1-3 : angle 3.10665 ( 3) hydrogen bonds : bond 0.30789 ( 81) hydrogen bonds : angle 9.11590 ( 174) SS BOND : bond 0.00237 ( 47) SS BOND : angle 0.98931 ( 94) link_BETA1-3 : bond 0.01442 ( 1) link_BETA1-3 : angle 7.24006 ( 3) covalent geometry : bond 0.00345 ( 9358) covalent geometry : angle 0.67972 (12680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 394 time to evaluate : 0.962 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: 0.2580 time to fit residues: 135.1623 Evaluate side-chains 347 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.0770 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 105 optimal weight: 0.0870 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 260 HIS B 302 ASN ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 47 HIS A 57 ASN A 64 ASN A 158 ASN A 408 GLN A 432 GLN A 433 HIS A 486 GLN A 493 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.143591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117964 restraints weight = 16651.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.123364 restraints weight = 9365.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127227 restraints weight = 5969.443| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9413 Z= 0.143 Angle : 0.641 9.743 12798 Z= 0.321 Chirality : 0.047 0.256 1417 Planarity : 0.006 0.061 1669 Dihedral : 9.410 94.387 1426 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % 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: -3.44 (0.21), residues: 1164 helix: -2.71 (0.63), residues: 57 sheet: -2.78 (0.54), residues: 71 loop : -2.49 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.004 0.001 HIS A 507 PHE 0.019 0.001 PHE A 180 TYR 0.013 0.001 TYR B 301 ARG 0.008 0.001 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 4) link_NAG-ASN : angle 2.78515 ( 12) link_BETA1-4 : bond 0.00482 ( 2) link_BETA1-4 : angle 0.96653 ( 6) link_ALPHA1-3 : bond 0.01868 ( 1) link_ALPHA1-3 : angle 2.58902 ( 3) hydrogen bonds : bond 0.05102 ( 81) hydrogen bonds : angle 7.02414 ( 174) SS BOND : bond 0.00474 ( 47) SS BOND : angle 1.65657 ( 94) link_BETA1-3 : bond 0.00843 ( 1) link_BETA1-3 : angle 4.20191 ( 3) covalent geometry : bond 0.00302 ( 9358) covalent geometry : angle 0.61690 (12680) *********************** 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 378 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 1.095 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: 0.5976 (pp30) cc_final: 0.4704 (mm-40) REVERT: B 31 MET cc_start: 0.7812 (mtp) cc_final: 0.7262 (ptp) REVERT: B 32 LYS cc_start: 0.8038 (mptt) cc_final: 0.7641 (mmtt) REVERT: B 46 LEU cc_start: 0.8723 (mt) cc_final: 0.8439 (mt) REVERT: B 54 GLN cc_start: 0.6906 (mt0) cc_final: 0.6606 (tp-100) REVERT: B 56 VAL cc_start: 0.8107 (t) cc_final: 0.7703 (t) REVERT: B 59 ASN cc_start: 0.6746 (m-40) cc_final: 0.6296 (m-40) REVERT: B 73 PHE cc_start: 0.8082 (p90) cc_final: 0.7826 (p90) REVERT: B 74 LEU cc_start: 0.8377 (mt) cc_final: 0.8118 (mt) REVERT: B 75 GLN cc_start: 0.7785 (pt0) cc_final: 0.7474 (pt0) REVERT: B 79 GLU cc_start: 0.7244 (tt0) cc_final: 0.6637 (tt0) REVERT: B 81 GLN cc_start: 0.6719 (mt0) cc_final: 0.6251 (mt0) REVERT: B 92 ARG cc_start: 0.7482 (mtt90) cc_final: 0.7156 (mmm-85) REVERT: B 93 GLN cc_start: 0.8478 (pp30) cc_final: 0.7703 (tm-30) REVERT: B 94 VAL cc_start: 0.8917 (t) cc_final: 0.8583 (t) REVERT: B 105 THR cc_start: 0.7734 (p) cc_final: 0.6776 (t) REVERT: B 106 GLN cc_start: 0.7665 (mt0) cc_final: 0.7107 (mp-120) REVERT: B 116 VAL cc_start: 0.6976 (t) cc_final: 0.6519 (p) REVERT: B 143 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7263 (mmt90) REVERT: B 160 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7224 (tp40) REVERT: B 171 ASP cc_start: 0.7955 (t70) cc_final: 0.6677 (t70) REVERT: B 173 PHE cc_start: 0.6696 (m-10) cc_final: 0.6331 (m-10) REVERT: B 185 ASP cc_start: 0.7084 (t0) cc_final: 0.6752 (t0) REVERT: B 193 HIS cc_start: 0.7906 (m90) cc_final: 0.7278 (m90) REVERT: B 211 ASP cc_start: 0.8053 (m-30) cc_final: 0.7659 (m-30) REVERT: B 213 GLN cc_start: 0.7572 (tm-30) cc_final: 0.7270 (tm-30) REVERT: B 248 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8029 (mmtt) REVERT: B 251 ASP cc_start: 0.7635 (p0) cc_final: 0.7387 (p0) REVERT: B 253 LEU cc_start: 0.7462 (mt) cc_final: 0.6963 (mt) REVERT: B 265 GLU cc_start: 0.6966 (pm20) cc_final: 0.6610 (pm20) REVERT: B 271 LEU cc_start: 0.8549 (mp) cc_final: 0.8274 (mt) REVERT: B 275 ASN cc_start: 0.8273 (t0) cc_final: 0.7556 (t0) REVERT: B 282 MET cc_start: 0.8113 (mtp) cc_final: 0.7726 (mtp) REVERT: B 303 TYR cc_start: 0.7891 (m-80) cc_final: 0.7340 (m-80) REVERT: B 320 GLN cc_start: 0.6553 (mt0) cc_final: 0.6264 (mt0) REVERT: B 332 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6496 (mp0) REVERT: B 376 PHE cc_start: 0.8116 (m-10) cc_final: 0.7528 (m-10) REVERT: B 377 LEU cc_start: 0.8415 (tp) cc_final: 0.8147 (tt) REVERT: B 407 THR cc_start: 0.7754 (p) cc_final: 0.7450 (m) REVERT: B 411 TYR cc_start: 0.7160 (t80) cc_final: 0.6687 (t80) REVERT: B 420 PRO cc_start: 0.8417 (Cg_endo) cc_final: 0.8035 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7731 (p0) cc_final: 0.7406 (p0) REVERT: B 422 LEU cc_start: 0.8601 (tp) cc_final: 0.7703 (pp) REVERT: B 426 GLN cc_start: 0.7746 (pt0) cc_final: 0.6933 (pp30) REVERT: B 430 VAL cc_start: 0.7440 (p) cc_final: 0.7072 (t) REVERT: B 434 ARG cc_start: 0.7442 (mtt90) cc_final: 0.7217 (mpt-90) REVERT: B 436 LEU cc_start: 0.7962 (mt) cc_final: 0.7415 (mt) REVERT: B 443 LEU cc_start: 0.7931 (tp) cc_final: 0.7451 (mm) REVERT: B 444 THR cc_start: 0.7455 (m) cc_final: 0.6857 (m) REVERT: B 452 TRP cc_start: 0.7705 (p90) cc_final: 0.7181 (p90) REVERT: B 463 SER cc_start: 0.7475 (t) cc_final: 0.7026 (m) REVERT: B 481 PRO cc_start: 0.8299 (Cg_endo) cc_final: 0.7692 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8505 (m100) cc_final: 0.8305 (m100) REVERT: B 488 ASN cc_start: 0.8022 (t0) cc_final: 0.7810 (t0) REVERT: B 494 LEU cc_start: 0.8495 (mt) cc_final: 0.8252 (mm) REVERT: B 517 ARG cc_start: 0.8274 (mtt180) cc_final: 0.7988 (mtm110) REVERT: B 556 ASN cc_start: 0.8074 (t0) cc_final: 0.7449 (t0) REVERT: B 566 GLU cc_start: 0.7537 (mm-30) cc_final: 0.6595 (tm-30) REVERT: B 577 PHE cc_start: 0.8089 (m-80) cc_final: 0.7864 (m-80) REVERT: B 580 GLU cc_start: 0.8458 (tp30) cc_final: 0.8088 (tp30) REVERT: A 29 LYS cc_start: 0.7934 (pttm) cc_final: 0.7583 (pttm) REVERT: A 36 ASN cc_start: 0.8273 (p0) cc_final: 0.7806 (p0) REVERT: A 46 ASP cc_start: 0.7365 (t70) cc_final: 0.6580 (t70) REVERT: A 47 HIS cc_start: 0.7900 (t70) cc_final: 0.6693 (t70) REVERT: A 51 LEU cc_start: 0.8710 (tp) cc_final: 0.8485 (tp) REVERT: A 55 PHE cc_start: 0.7836 (m-10) cc_final: 0.7441 (m-10) REVERT: A 61 VAL cc_start: 0.8097 (t) cc_final: 0.7894 (m) REVERT: A 62 LEU cc_start: 0.8458 (mt) cc_final: 0.8138 (mm) REVERT: A 74 TYR cc_start: 0.7761 (m-80) cc_final: 0.6916 (m-80) REVERT: A 80 LYS cc_start: 0.8275 (mttm) cc_final: 0.7867 (mttm) REVERT: A 83 GLN cc_start: 0.7955 (mm110) cc_final: 0.7428 (mm110) REVERT: A 93 LEU cc_start: 0.8218 (mp) cc_final: 0.7997 (mt) REVERT: A 110 ASN cc_start: 0.7926 (m-40) cc_final: 0.7433 (p0) REVERT: A 114 GLU cc_start: 0.7442 (tt0) cc_final: 0.6966 (tt0) REVERT: A 132 LEU cc_start: 0.7869 (tp) cc_final: 0.7635 (mm) REVERT: A 143 ILE cc_start: 0.8965 (mt) cc_final: 0.8694 (mm) REVERT: A 163 GLN cc_start: 0.8634 (pt0) cc_final: 0.7987 (tt0) REVERT: A 176 MET cc_start: 0.7922 (ptp) cc_final: 0.7546 (ptt) REVERT: A 209 LYS cc_start: 0.8102 (mttt) cc_final: 0.7515 (mtmm) REVERT: A 226 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7238 (mtpt) REVERT: A 227 SER cc_start: 0.8120 (t) cc_final: 0.7890 (p) REVERT: A 233 HIS cc_start: 0.7580 (t-90) cc_final: 0.7090 (t-90) REVERT: A 253 LYS cc_start: 0.8142 (tptm) cc_final: 0.7430 (tptm) REVERT: A 256 ASP cc_start: 0.6932 (t70) cc_final: 0.6549 (t0) REVERT: A 261 LYS cc_start: 0.7339 (mttm) cc_final: 0.6854 (mttm) REVERT: A 262 ASP cc_start: 0.7559 (t0) cc_final: 0.7173 (t0) REVERT: A 268 MET cc_start: 0.6215 (mtm) cc_final: 0.5078 (mtm) REVERT: A 277 MET cc_start: 0.6383 (mtt) cc_final: 0.5338 (mtt) REVERT: A 293 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7007 (mmmt) REVERT: A 316 TYR cc_start: 0.7470 (t80) cc_final: 0.7055 (t80) REVERT: A 318 MET cc_start: 0.7743 (tpp) cc_final: 0.6924 (tpp) REVERT: A 338 ASN cc_start: 0.6909 (p0) cc_final: 0.6158 (p0) REVERT: A 345 PHE cc_start: 0.8148 (m-80) cc_final: 0.7764 (m-80) REVERT: A 358 HIS cc_start: 0.8231 (m90) cc_final: 0.7714 (m90) REVERT: A 360 LYS cc_start: 0.8697 (tttt) cc_final: 0.8334 (tttt) REVERT: A 368 ASP cc_start: 0.5216 (m-30) cc_final: 0.4050 (m-30) REVERT: A 369 LEU cc_start: 0.7242 (mt) cc_final: 0.6997 (mm) REVERT: A 396 LYS cc_start: 0.8231 (tppp) cc_final: 0.7807 (tppp) REVERT: A 404 PHE cc_start: 0.7469 (p90) cc_final: 0.6116 (p90) REVERT: A 421 GLU cc_start: 0.8680 (tt0) cc_final: 0.8007 (tt0) REVERT: A 430 THR cc_start: 0.7760 (m) cc_final: 0.6426 (t) REVERT: A 432 GLN cc_start: 0.8633 (tp40) cc_final: 0.8096 (tp-100) REVERT: A 433 HIS cc_start: 0.8297 (m90) cc_final: 0.8080 (m90) REVERT: A 476 ASN cc_start: 0.7699 (t0) cc_final: 0.7341 (t0) REVERT: A 489 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7695 (mtpp) REVERT: A 496 GLU cc_start: 0.7576 (mp0) cc_final: 0.7307 (mp0) REVERT: A 521 ARG cc_start: 0.7844 (ptt180) cc_final: 0.7575 (tmm-80) REVERT: A 551 GLU cc_start: 0.8566 (pt0) cc_final: 0.8091 (pm20) REVERT: C 18 GLN cc_start: 0.7731 (tt0) cc_final: 0.7277 (pm20) REVERT: C 22 LEU cc_start: 0.7575 (mt) cc_final: 0.7242 (mt) REVERT: C 25 MET cc_start: 0.7924 (mmp) cc_final: 0.7249 (mmp) outliers start: 1 outliers final: 1 residues processed: 378 average time/residue: 0.2466 time to fit residues: 122.6729 Evaluate side-chains 346 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 345 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 54 optimal weight: 0.0170 chunk 21 optimal weight: 0.6980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 267 HIS ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 145 HIS A 435 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.134734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108925 restraints weight = 16689.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.114367 restraints weight = 9358.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.118254 restraints weight = 5936.801| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9413 Z= 0.146 Angle : 0.627 9.559 12798 Z= 0.315 Chirality : 0.047 0.276 1417 Planarity : 0.005 0.045 1669 Dihedral : 8.286 86.864 1426 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.22), residues: 1164 helix: -2.14 (0.69), residues: 57 sheet: -2.00 (0.56), residues: 86 loop : -2.23 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 415 HIS 0.006 0.001 HIS A 145 PHE 0.019 0.001 PHE B 486 TYR 0.013 0.001 TYR B 301 ARG 0.006 0.001 ARG A 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 4) link_NAG-ASN : angle 2.74348 ( 12) link_BETA1-4 : bond 0.00269 ( 2) link_BETA1-4 : angle 0.95267 ( 6) link_ALPHA1-3 : bond 0.02078 ( 1) link_ALPHA1-3 : angle 2.19309 ( 3) hydrogen bonds : bond 0.04351 ( 81) hydrogen bonds : angle 6.38617 ( 174) SS BOND : bond 0.00412 ( 47) SS BOND : angle 1.22829 ( 94) link_BETA1-3 : bond 0.00563 ( 1) link_BETA1-3 : angle 4.06794 ( 3) covalent geometry : bond 0.00302 ( 9358) covalent geometry : angle 0.61100 (12680) *********************** 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 382 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6356 (pp30) cc_final: 0.5172 (mm-40) REVERT: B 31 MET cc_start: 0.7817 (mtp) cc_final: 0.7349 (ptp) REVERT: B 34 ARG cc_start: 0.7817 (ptp90) cc_final: 0.7595 (mtm110) REVERT: B 44 ASP cc_start: 0.7459 (t0) cc_final: 0.6629 (t0) REVERT: B 46 LEU cc_start: 0.8796 (mt) cc_final: 0.8415 (mt) REVERT: B 47 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7418 (ttp80) REVERT: B 54 GLN cc_start: 0.7015 (mt0) cc_final: 0.6649 (tp40) REVERT: B 56 VAL cc_start: 0.7980 (t) cc_final: 0.7725 (m) REVERT: B 65 LEU cc_start: 0.8307 (mt) cc_final: 0.8048 (mt) REVERT: B 73 PHE cc_start: 0.8208 (p90) cc_final: 0.7804 (p90) REVERT: B 75 GLN cc_start: 0.7812 (pt0) cc_final: 0.7426 (pt0) REVERT: B 79 GLU cc_start: 0.7171 (tt0) cc_final: 0.6386 (tt0) REVERT: B 81 GLN cc_start: 0.6855 (mt0) cc_final: 0.6319 (mt0) REVERT: B 93 GLN cc_start: 0.8538 (pp30) cc_final: 0.8203 (tm-30) REVERT: B 100 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7460 (mmm-85) REVERT: B 103 ARG cc_start: 0.7364 (ttm110) cc_final: 0.6703 (ttm110) REVERT: B 105 THR cc_start: 0.7983 (p) cc_final: 0.7483 (t) REVERT: B 106 GLN cc_start: 0.7748 (mt0) cc_final: 0.7327 (mp10) REVERT: B 112 TYR cc_start: 0.7115 (m-80) cc_final: 0.6829 (m-80) REVERT: B 143 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7336 (mtt180) REVERT: B 171 ASP cc_start: 0.7899 (t70) cc_final: 0.7687 (t70) REVERT: B 173 PHE cc_start: 0.7014 (m-10) cc_final: 0.6588 (m-10) REVERT: B 185 ASP cc_start: 0.7091 (t0) cc_final: 0.6858 (t0) REVERT: B 193 HIS cc_start: 0.7882 (m90) cc_final: 0.7303 (m90) REVERT: B 210 GLU cc_start: 0.7617 (pm20) cc_final: 0.7303 (pm20) REVERT: B 211 ASP cc_start: 0.7958 (m-30) cc_final: 0.7291 (m-30) REVERT: B 226 ARG cc_start: 0.7991 (tpp-160) cc_final: 0.7590 (mmm160) REVERT: B 248 LYS cc_start: 0.8643 (mmtt) cc_final: 0.8044 (mmtt) REVERT: B 251 ASP cc_start: 0.7633 (p0) cc_final: 0.7412 (p0) REVERT: B 265 GLU cc_start: 0.7033 (pm20) cc_final: 0.6476 (pm20) REVERT: B 266 LEU cc_start: 0.8307 (tp) cc_final: 0.8040 (tp) REVERT: B 267 HIS cc_start: 0.7552 (m170) cc_final: 0.6925 (m170) REVERT: B 271 LEU cc_start: 0.8612 (mp) cc_final: 0.8373 (mt) REVERT: B 274 TYR cc_start: 0.6955 (t80) cc_final: 0.6514 (t80) REVERT: B 275 ASN cc_start: 0.7932 (t0) cc_final: 0.7641 (t0) REVERT: B 282 MET cc_start: 0.8330 (mtp) cc_final: 0.7833 (mtp) REVERT: B 288 ARG cc_start: 0.7933 (mmt-90) cc_final: 0.7566 (mtt90) REVERT: B 291 PHE cc_start: 0.7685 (t80) cc_final: 0.7481 (t80) REVERT: B 303 TYR cc_start: 0.7921 (m-80) cc_final: 0.7372 (m-80) REVERT: B 332 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7087 (mt-10) REVERT: B 364 PHE cc_start: 0.8516 (m-80) cc_final: 0.7757 (m-80) REVERT: B 371 PHE cc_start: 0.7725 (m-10) cc_final: 0.7472 (m-10) REVERT: B 377 LEU cc_start: 0.8437 (tp) cc_final: 0.8076 (tt) REVERT: B 398 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7874 (mm-40) REVERT: B 407 THR cc_start: 0.7782 (p) cc_final: 0.7346 (m) REVERT: B 411 TYR cc_start: 0.7239 (t80) cc_final: 0.6418 (t80) REVERT: B 420 PRO cc_start: 0.8466 (Cg_endo) cc_final: 0.8152 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7675 (p0) cc_final: 0.7396 (p0) REVERT: B 422 LEU cc_start: 0.8569 (tp) cc_final: 0.8181 (mt) REVERT: B 426 GLN cc_start: 0.7872 (pt0) cc_final: 0.7177 (pp30) REVERT: B 430 VAL cc_start: 0.7680 (p) cc_final: 0.7202 (t) REVERT: B 436 LEU cc_start: 0.8038 (mt) cc_final: 0.7402 (mt) REVERT: B 443 LEU cc_start: 0.7984 (tp) cc_final: 0.7386 (mm) REVERT: B 444 THR cc_start: 0.7495 (m) cc_final: 0.6965 (m) REVERT: B 451 SER cc_start: 0.8051 (p) cc_final: 0.7610 (m) REVERT: B 452 TRP cc_start: 0.7748 (p90) cc_final: 0.7485 (p90) REVERT: B 467 LEU cc_start: 0.7204 (tp) cc_final: 0.6928 (tp) REVERT: B 481 PRO cc_start: 0.8229 (Cg_endo) cc_final: 0.7683 (Cg_exo) REVERT: B 482 TRP cc_start: 0.8663 (m100) cc_final: 0.8369 (m100) REVERT: B 494 LEU cc_start: 0.8723 (mt) cc_final: 0.8331 (mt) REVERT: B 556 ASN cc_start: 0.8105 (t0) cc_final: 0.7471 (t0) REVERT: B 566 GLU cc_start: 0.7616 (mm-30) cc_final: 0.6581 (tm-30) REVERT: B 577 PHE cc_start: 0.8128 (m-80) cc_final: 0.7877 (m-80) REVERT: B 580 GLU cc_start: 0.8447 (tp30) cc_final: 0.8074 (tp30) REVERT: B 592 ASP cc_start: 0.7592 (m-30) cc_final: 0.7389 (m-30) REVERT: A 35 SER cc_start: 0.8153 (t) cc_final: 0.7892 (p) REVERT: A 36 ASN cc_start: 0.8340 (p0) cc_final: 0.7862 (p0) REVERT: A 46 ASP cc_start: 0.7281 (t70) cc_final: 0.6682 (t70) REVERT: A 47 HIS cc_start: 0.7901 (t70) cc_final: 0.6811 (t70) REVERT: A 51 LEU cc_start: 0.8816 (tp) cc_final: 0.8578 (tp) REVERT: A 55 PHE cc_start: 0.7911 (m-10) cc_final: 0.7505 (m-10) REVERT: A 65 LEU cc_start: 0.7895 (tp) cc_final: 0.7616 (tt) REVERT: A 74 TYR cc_start: 0.7921 (m-80) cc_final: 0.6993 (m-80) REVERT: A 80 LYS cc_start: 0.8363 (mttm) cc_final: 0.8123 (mttm) REVERT: A 83 GLN cc_start: 0.7845 (mm110) cc_final: 0.7124 (mm110) REVERT: A 98 ARG cc_start: 0.7582 (ttt90) cc_final: 0.7165 (tpp80) REVERT: A 102 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6900 (mt-10) REVERT: A 103 ASN cc_start: 0.7393 (m-40) cc_final: 0.6492 (m-40) REVERT: A 110 ASN cc_start: 0.7963 (m-40) cc_final: 0.7693 (p0) REVERT: A 112 TYR cc_start: 0.6841 (m-80) cc_final: 0.6583 (m-80) REVERT: A 132 LEU cc_start: 0.7677 (tp) cc_final: 0.7183 (mm) REVERT: A 143 ILE cc_start: 0.8984 (mt) cc_final: 0.8609 (mm) REVERT: A 163 GLN cc_start: 0.8552 (pt0) cc_final: 0.8246 (tt0) REVERT: A 167 ILE cc_start: 0.8521 (mp) cc_final: 0.8294 (mp) REVERT: A 172 PHE cc_start: 0.8162 (m-80) cc_final: 0.7889 (m-10) REVERT: A 176 MET cc_start: 0.8168 (ptp) cc_final: 0.7791 (ptt) REVERT: A 209 LYS cc_start: 0.8215 (mttt) cc_final: 0.7591 (mtmm) REVERT: A 226 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7394 (mtpt) REVERT: A 227 SER cc_start: 0.8132 (t) cc_final: 0.7926 (p) REVERT: A 229 SER cc_start: 0.8093 (p) cc_final: 0.7784 (t) REVERT: A 233 HIS cc_start: 0.7750 (t-90) cc_final: 0.7171 (t-90) REVERT: A 255 ARG cc_start: 0.6806 (ttt-90) cc_final: 0.6452 (ttp80) REVERT: A 257 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7852 (mm-30) REVERT: A 268 MET cc_start: 0.6162 (mtm) cc_final: 0.5040 (mtm) REVERT: A 277 MET cc_start: 0.6313 (mtt) cc_final: 0.5257 (mtt) REVERT: A 290 THR cc_start: 0.6962 (t) cc_final: 0.6501 (t) REVERT: A 293 LYS cc_start: 0.7725 (mtpp) cc_final: 0.7242 (tppt) REVERT: A 298 ASN cc_start: 0.8254 (p0) cc_final: 0.7386 (p0) REVERT: A 338 ASN cc_start: 0.7137 (p0) cc_final: 0.6309 (p0) REVERT: A 340 ILE cc_start: 0.7518 (mp) cc_final: 0.7282 (mp) REVERT: A 345 PHE cc_start: 0.8278 (m-80) cc_final: 0.7702 (m-80) REVERT: A 358 HIS cc_start: 0.8335 (m90) cc_final: 0.7757 (m90) REVERT: A 360 LYS cc_start: 0.8707 (tttt) cc_final: 0.8358 (tttt) REVERT: A 396 LYS cc_start: 0.8302 (tppp) cc_final: 0.7863 (tppp) REVERT: A 404 PHE cc_start: 0.7571 (p90) cc_final: 0.6457 (p90) REVERT: A 421 GLU cc_start: 0.8712 (tt0) cc_final: 0.7571 (tt0) REVERT: A 429 ARG cc_start: 0.7878 (mtt180) cc_final: 0.7298 (mtt-85) REVERT: A 430 THR cc_start: 0.7663 (m) cc_final: 0.6537 (p) REVERT: A 431 LYS cc_start: 0.8301 (mtmm) cc_final: 0.7971 (mtmt) REVERT: A 432 GLN cc_start: 0.8682 (tp40) cc_final: 0.8090 (tp-100) REVERT: A 433 HIS cc_start: 0.8279 (m90) cc_final: 0.7971 (m90) REVERT: A 451 ARG cc_start: 0.6952 (mtt90) cc_final: 0.6676 (ptp-170) REVERT: A 476 ASN cc_start: 0.7753 (t0) cc_final: 0.7340 (t0) REVERT: A 489 LYS cc_start: 0.7795 (ttmm) cc_final: 0.7591 (mmmm) REVERT: A 496 GLU cc_start: 0.7584 (mp0) cc_final: 0.7335 (mp0) REVERT: A 551 GLU cc_start: 0.8674 (pt0) cc_final: 0.8256 (pm20) REVERT: C 22 LEU cc_start: 0.7616 (mt) cc_final: 0.7312 (mt) REVERT: C 25 MET cc_start: 0.7965 (mmp) cc_final: 0.7382 (mmp) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.2580 time to fit residues: 128.2481 Evaluate side-chains 363 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 96 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 98 optimal weight: 0.0470 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 73 optimal weight: 0.0670 chunk 16 optimal weight: 0.0980 chunk 111 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 110 ASN A 280 ASN A 435 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.134540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108520 restraints weight = 16572.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.114168 restraints weight = 9372.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.118153 restraints weight = 5947.698| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9413 Z= 0.123 Angle : 0.607 9.459 12798 Z= 0.307 Chirality : 0.047 0.264 1417 Planarity : 0.004 0.052 1669 Dihedral : 7.624 82.394 1426 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.10 % Allowed : 2.06 % 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: -2.74 (0.23), residues: 1164 helix: -1.47 (0.79), residues: 48 sheet: -1.47 (0.63), residues: 72 loop : -2.09 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 164 HIS 0.004 0.001 HIS A 507 PHE 0.022 0.001 PHE C 44 TYR 0.041 0.002 TYR A 117 ARG 0.011 0.001 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 4) link_NAG-ASN : angle 2.54611 ( 12) link_BETA1-4 : bond 0.00107 ( 2) link_BETA1-4 : angle 0.92523 ( 6) link_ALPHA1-3 : bond 0.02236 ( 1) link_ALPHA1-3 : angle 2.44607 ( 3) hydrogen bonds : bond 0.04166 ( 81) hydrogen bonds : angle 5.92511 ( 174) SS BOND : bond 0.00247 ( 47) SS BOND : angle 1.28185 ( 94) link_BETA1-3 : bond 0.00553 ( 1) link_BETA1-3 : angle 4.01539 ( 3) covalent geometry : bond 0.00268 ( 9358) covalent geometry : angle 0.59033 (12680) *********************** 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 382 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6572 (pp30) cc_final: 0.5396 (mm-40) REVERT: B 31 MET cc_start: 0.7685 (mtp) cc_final: 0.6915 (ptp) REVERT: B 32 LYS cc_start: 0.8175 (mptt) cc_final: 0.7819 (mmtt) REVERT: B 44 ASP cc_start: 0.7472 (t0) cc_final: 0.6502 (t0) REVERT: B 46 LEU cc_start: 0.8776 (mt) cc_final: 0.8363 (mt) REVERT: B 47 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7326 (ttp80) REVERT: B 54 GLN cc_start: 0.7062 (mt0) cc_final: 0.6658 (tp40) REVERT: B 55 VAL cc_start: 0.7420 (t) cc_final: 0.6746 (t) REVERT: B 59 ASN cc_start: 0.7167 (m-40) cc_final: 0.6825 (m-40) REVERT: B 61 GLU cc_start: 0.7012 (tm-30) cc_final: 0.4997 (tm-30) REVERT: B 65 LEU cc_start: 0.8351 (mt) cc_final: 0.8110 (mt) REVERT: B 73 PHE cc_start: 0.8128 (p90) cc_final: 0.7817 (p90) REVERT: B 75 GLN cc_start: 0.7856 (pt0) cc_final: 0.7465 (pt0) REVERT: B 79 GLU cc_start: 0.7282 (tt0) cc_final: 0.6479 (tt0) REVERT: B 81 GLN cc_start: 0.6821 (mt0) cc_final: 0.6278 (mt0) REVERT: B 93 GLN cc_start: 0.8529 (pp30) cc_final: 0.8301 (tm-30) REVERT: B 100 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7730 (mmm-85) REVERT: B 103 ARG cc_start: 0.7307 (mmt90) cc_final: 0.6889 (ttm110) REVERT: B 105 THR cc_start: 0.7961 (p) cc_final: 0.7094 (t) REVERT: B 106 GLN cc_start: 0.7714 (mt0) cc_final: 0.7342 (mp-120) REVERT: B 112 TYR cc_start: 0.7204 (m-80) cc_final: 0.6682 (m-80) REVERT: B 143 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7297 (mtt180) REVERT: B 173 PHE cc_start: 0.6885 (m-10) cc_final: 0.6359 (m-10) REVERT: B 193 HIS cc_start: 0.7882 (m90) cc_final: 0.7267 (m90) REVERT: B 211 ASP cc_start: 0.7872 (m-30) cc_final: 0.7154 (m-30) REVERT: B 213 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7730 (tm-30) REVERT: B 248 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8035 (mmtt) REVERT: B 251 ASP cc_start: 0.7628 (p0) cc_final: 0.7388 (p0) REVERT: B 265 GLU cc_start: 0.7046 (pm20) cc_final: 0.6539 (pm20) REVERT: B 267 HIS cc_start: 0.7514 (m170) cc_final: 0.7260 (m170) REVERT: B 271 LEU cc_start: 0.8575 (mp) cc_final: 0.8301 (mt) REVERT: B 274 TYR cc_start: 0.6870 (t80) cc_final: 0.6466 (t80) REVERT: B 275 ASN cc_start: 0.8058 (t0) cc_final: 0.7630 (t0) REVERT: B 282 MET cc_start: 0.8362 (mtp) cc_final: 0.7835 (mtp) REVERT: B 303 TYR cc_start: 0.7979 (m-80) cc_final: 0.7360 (m-80) REVERT: B 323 THR cc_start: 0.7384 (t) cc_final: 0.6902 (p) REVERT: B 332 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7088 (mt-10) REVERT: B 364 PHE cc_start: 0.8500 (m-80) cc_final: 0.7760 (m-80) REVERT: B 398 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7859 (mm-40) REVERT: B 407 THR cc_start: 0.7815 (p) cc_final: 0.7266 (m) REVERT: B 411 TYR cc_start: 0.7296 (t80) cc_final: 0.6544 (t80) REVERT: B 420 PRO cc_start: 0.8482 (Cg_endo) cc_final: 0.8121 (Cg_exo) REVERT: B 421 ASP cc_start: 0.7737 (p0) cc_final: 0.7378 (p0) REVERT: B 422 LEU cc_start: 0.8572 (tp) cc_final: 0.8325 (tp) REVERT: B 426 GLN cc_start: 0.7891 (pt0) cc_final: 0.7242 (pp30) REVERT: B 430 VAL cc_start: 0.7727 (p) cc_final: 0.7483 (t) REVERT: B 436 LEU cc_start: 0.8092 (mt) cc_final: 0.7405 (mt) REVERT: B 444 THR cc_start: 0.7433 (m) cc_final: 0.7025 (m) REVERT: B 451 SER cc_start: 0.8073 (p) cc_final: 0.7580 (m) REVERT: B 452 TRP cc_start: 0.7737 (p90) cc_final: 0.7507 (p90) REVERT: B 481 PRO cc_start: 0.8084 (Cg_endo) cc_final: 0.7540 (Cg_exo) REVERT: B 487 ARG cc_start: 0.7875 (mmt90) cc_final: 0.7406 (tpp80) REVERT: B 488 ASN cc_start: 0.8066 (t0) cc_final: 0.7618 (t0) REVERT: B 494 LEU cc_start: 0.8689 (mt) cc_final: 0.8324 (mt) REVERT: B 556 ASN cc_start: 0.8159 (t0) cc_final: 0.7500 (t0) REVERT: B 566 GLU cc_start: 0.7633 (mm-30) cc_final: 0.6555 (tm-30) REVERT: B 577 PHE cc_start: 0.8261 (m-80) cc_final: 0.7963 (m-80) REVERT: B 580 GLU cc_start: 0.8472 (tp30) cc_final: 0.8093 (tp30) REVERT: B 592 ASP cc_start: 0.7572 (m-30) cc_final: 0.7371 (m-30) REVERT: A 29 LYS cc_start: 0.7838 (pttm) cc_final: 0.7393 (pttm) REVERT: A 36 ASN cc_start: 0.8351 (p0) cc_final: 0.7901 (p0) REVERT: A 46 ASP cc_start: 0.7228 (t70) cc_final: 0.6604 (t70) REVERT: A 47 HIS cc_start: 0.7811 (t70) cc_final: 0.6752 (t70) REVERT: A 51 LEU cc_start: 0.8808 (tp) cc_final: 0.8540 (tp) REVERT: A 55 PHE cc_start: 0.7775 (m-10) cc_final: 0.7565 (m-10) REVERT: A 61 VAL cc_start: 0.8120 (t) cc_final: 0.7771 (t) REVERT: A 74 TYR cc_start: 0.7940 (m-80) cc_final: 0.6996 (m-80) REVERT: A 80 LYS cc_start: 0.8404 (mttm) cc_final: 0.8169 (mttm) REVERT: A 83 GLN cc_start: 0.7798 (mm110) cc_final: 0.7054 (mm110) REVERT: A 98 ARG cc_start: 0.7545 (ttt90) cc_final: 0.7232 (tpp80) REVERT: A 102 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6923 (mt-10) REVERT: A 103 ASN cc_start: 0.7385 (m-40) cc_final: 0.6456 (m-40) REVERT: A 107 ILE cc_start: 0.8592 (mm) cc_final: 0.8334 (mm) REVERT: A 110 ASN cc_start: 0.7921 (m110) cc_final: 0.7680 (p0) REVERT: A 112 TYR cc_start: 0.6755 (m-80) cc_final: 0.6435 (m-10) REVERT: A 122 LEU cc_start: 0.8079 (mp) cc_final: 0.7878 (mp) REVERT: A 143 ILE cc_start: 0.8934 (mt) cc_final: 0.8534 (mm) REVERT: A 163 GLN cc_start: 0.8562 (pt0) cc_final: 0.8068 (tt0) REVERT: A 209 LYS cc_start: 0.8195 (mttt) cc_final: 0.7633 (mtmt) REVERT: A 227 SER cc_start: 0.8107 (t) cc_final: 0.7848 (p) REVERT: A 230 ASP cc_start: 0.8327 (m-30) cc_final: 0.8080 (m-30) REVERT: A 233 HIS cc_start: 0.7447 (t-90) cc_final: 0.7114 (t-90) REVERT: A 252 ARG cc_start: 0.7444 (mtp85) cc_final: 0.7080 (mtp85) REVERT: A 257 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7983 (mm-30) REVERT: A 261 LYS cc_start: 0.7158 (ptmt) cc_final: 0.6631 (ptmt) REVERT: A 262 ASP cc_start: 0.8122 (t0) cc_final: 0.7349 (t0) REVERT: A 268 MET cc_start: 0.6195 (mtm) cc_final: 0.4867 (mtm) REVERT: A 277 MET cc_start: 0.6215 (mtt) cc_final: 0.5159 (mtt) REVERT: A 293 LYS cc_start: 0.7737 (mtpp) cc_final: 0.6824 (mtpp) REVERT: A 338 ASN cc_start: 0.7268 (p0) cc_final: 0.6332 (p0) REVERT: A 344 GLU cc_start: 0.7203 (tt0) cc_final: 0.6891 (tt0) REVERT: A 345 PHE cc_start: 0.8238 (m-80) cc_final: 0.7473 (m-80) REVERT: A 358 HIS cc_start: 0.8360 (m90) cc_final: 0.8104 (m90) REVERT: A 360 LYS cc_start: 0.8715 (tttt) cc_final: 0.8387 (tttt) REVERT: A 368 ASP cc_start: 0.5136 (m-30) cc_final: 0.3703 (m-30) REVERT: A 396 LYS cc_start: 0.8336 (tppp) cc_final: 0.7837 (tppp) REVERT: A 404 PHE cc_start: 0.7487 (p90) cc_final: 0.6217 (p90) REVERT: A 421 GLU cc_start: 0.8677 (tt0) cc_final: 0.7688 (tt0) REVERT: A 429 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7481 (mtt-85) REVERT: A 430 THR cc_start: 0.7703 (m) cc_final: 0.6425 (p) REVERT: A 432 GLN cc_start: 0.8661 (tp40) cc_final: 0.8198 (tp-100) REVERT: A 451 ARG cc_start: 0.7009 (mtt90) cc_final: 0.6763 (ptp-170) REVERT: A 456 ILE cc_start: 0.8411 (mm) cc_final: 0.7507 (pt) REVERT: A 457 SER cc_start: 0.7882 (m) cc_final: 0.7447 (m) REVERT: A 460 ASP cc_start: 0.6703 (t70) cc_final: 0.6341 (t70) REVERT: A 476 ASN cc_start: 0.7731 (t0) cc_final: 0.7328 (t0) REVERT: A 496 GLU cc_start: 0.7535 (mp0) cc_final: 0.7195 (mp0) REVERT: A 551 GLU cc_start: 0.8664 (pt0) cc_final: 0.8207 (pm20) REVERT: C 18 GLN cc_start: 0.7986 (tt0) cc_final: 0.7236 (tt0) REVERT: C 22 LEU cc_start: 0.7681 (mt) cc_final: 0.7368 (mt) REVERT: C 25 MET cc_start: 0.7901 (mmp) cc_final: 0.7330 (mmp) outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.2570 time to fit residues: 127.1007 Evaluate side-chains 358 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.8958 > 50: distance: 15 - 20: 5.092 distance: 20 - 21: 20.675 distance: 20 - 26: 17.441 distance: 21 - 22: 3.304 distance: 21 - 24: 11.593 distance: 22 - 23: 8.410 distance: 22 - 27: 16.988 distance: 24 - 25: 11.135 distance: 25 - 26: 40.572 distance: 27 - 28: 11.009 distance: 28 - 29: 11.852 distance: 28 - 31: 5.192 distance: 29 - 30: 22.253 distance: 29 - 35: 23.372 distance: 31 - 32: 7.395 distance: 32 - 33: 6.179 distance: 32 - 34: 6.335 distance: 35 - 36: 16.567 distance: 36 - 37: 8.284 distance: 36 - 39: 19.539 distance: 37 - 38: 5.722 distance: 37 - 43: 15.859 distance: 39 - 40: 9.428 distance: 40 - 41: 13.587 distance: 41 - 42: 22.855 distance: 43 - 44: 15.614 distance: 44 - 45: 21.815 distance: 44 - 47: 13.006 distance: 45 - 46: 16.657 distance: 45 - 51: 41.259 distance: 47 - 48: 22.569 distance: 48 - 49: 9.154 distance: 48 - 50: 11.874 distance: 51 - 52: 12.190 distance: 52 - 53: 22.911 distance: 52 - 55: 10.268 distance: 53 - 54: 21.250 distance: 53 - 63: 11.110 distance: 55 - 56: 14.334 distance: 56 - 57: 16.547 distance: 56 - 58: 10.586 distance: 57 - 59: 10.874 distance: 58 - 60: 11.743 distance: 59 - 61: 7.487 distance: 60 - 61: 9.195 distance: 61 - 62: 6.985 distance: 63 - 64: 8.905 distance: 64 - 65: 19.799 distance: 64 - 67: 21.495 distance: 65 - 66: 9.761 distance: 65 - 71: 21.227 distance: 67 - 68: 24.210 distance: 68 - 69: 13.878 distance: 68 - 70: 13.178 distance: 71 - 72: 6.501 distance: 71 - 77: 21.789 distance: 72 - 73: 13.569 distance: 72 - 75: 20.189 distance: 73 - 74: 10.114 distance: 73 - 78: 36.627 distance: 75 - 76: 28.802 distance: 76 - 77: 22.804 distance: 78 - 79: 7.754 distance: 79 - 80: 9.658 distance: 79 - 82: 12.504 distance: 80 - 81: 7.686 distance: 80 - 85: 19.350 distance: 82 - 83: 9.133 distance: 82 - 84: 30.889 distance: 85 - 86: 20.691 distance: 86 - 87: 28.248 distance: 86 - 89: 24.502 distance: 87 - 88: 8.498 distance: 87 - 92: 24.779 distance: 89 - 90: 15.593 distance: 89 - 91: 24.534 distance: 92 - 93: 3.800 distance: 93 - 94: 6.927 distance: 93 - 96: 8.439 distance: 94 - 95: 19.109 distance: 94 - 104: 12.773 distance: 96 - 97: 12.222 distance: 97 - 98: 20.486 distance: 97 - 99: 13.929 distance: 98 - 100: 7.892 distance: 99 - 101: 7.328 distance: 100 - 102: 17.417 distance: 101 - 102: 18.646 distance: 102 - 103: 26.276