Starting phenix.real_space_refine on Fri Nov 15 18:55:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/11_2024/8hgo_34744.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/11_2024/8hgo_34744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/11_2024/8hgo_34744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/11_2024/8hgo_34744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/11_2024/8hgo_34744.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgo_34744/11_2024/8hgo_34744.cif" } resolution = 3.31 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 109 5.16 5 C 5714 2.51 5 N 1636 2.21 5 O 1768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9227 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: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 385 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} 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: 6.45, per 1000 atoms: 0.70 Number of scatterers: 9227 At special positions: 0 Unit cell: (78.11, 131.61, 126.26, 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 109 16.00 O 1768 8.00 N 1636 7.00 C 5714 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=2.02 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=2.03 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 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 31 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 42 " 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: 2.76 Conformation dependent library (CDL) restraints added in 1.2 seconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 21 sheets defined 11.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.825A pdb=" N GLN B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.965A pdb=" N GLN B 75 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 4.076A pdb=" N ILE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.566A pdb=" N ASP B 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N CYS B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 212' Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.534A pdb=" N PHE B 364 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.865A pdb=" N VAL B 399 " --> pdb=" O GLN B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 removed outlier: 3.601A pdb=" N GLN B 426 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.063A pdb=" N GLY B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.787A pdb=" N GLY B 518 " --> pdb=" O CYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 removed outlier: 3.586A pdb=" N GLN B 583 " --> pdb=" O GLU B 580 " (cutoff:3.500A) removed outlier: 3.706A 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: 3.798A pdb=" N THR A 81 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.746A pdb=" N GLY A 197 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 3.726A 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 342 through 346 removed outlier: 3.793A pdb=" N PHE A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 346' Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.934A pdb=" N LYS A 360 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.573A pdb=" N LEU A 392 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP A 393 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.888A pdb=" N PHE A 420 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 421 " --> pdb=" O HIS A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 421' Processing helix chain 'A' and resid 431 through 434 Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.516A pdb=" N LYS A 479 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 523 removed outlier: 4.427A pdb=" N CYS A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 26 removed outlier: 3.743A pdb=" N CYS B 26 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.411A pdb=" N LEU B 60 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ALA B 87 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU B 62 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 114 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLN B 156 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL B 116 " --> pdb=" O GLN B 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AA4, first strand: chain 'B' and resid 272 through 275 Processing sheet with id=AA5, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AA6, first strand: chain 'B' and resid 319 through 320 removed outlier: 3.695A pdb=" N GLU B 332 " --> pdb=" O GLN B 320 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AA8, first strand: chain 'B' and resid 374 through 376 removed outlier: 6.440A pdb=" N LEU B 374 " --> pdb=" O TYR B 411 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS B 469 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 553 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AB2, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.976A pdb=" N GLN A 40 " --> pdb=" O CYS C 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.670A pdb=" N LEU A 65 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ALA A 92 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 67 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 89 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU A 122 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 91 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 119 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER A 151 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 121 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 148 " --> pdb=" O SER A 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 236 through 240 removed outlier: 3.574A pdb=" N ALA A 237 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL A 250 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N GLY A 239 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS A 248 " --> pdb=" O GLY A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 254 through 256 removed outlier: 3.564A pdb=" N PHE A 254 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 261 " --> pdb=" O PHE A 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AB7, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AB8, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AB9, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.569A pdb=" N LEU A 369 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 405 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE A 462 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA A 439 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 461 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 548 through 549 removed outlier: 3.600A pdb=" N PHE A 549 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 556 " --> pdb=" O PHE A 549 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 585 through 587 Processing sheet with id=AC3, first strand: chain 'C' and resid 37 through 38 97 hydrogen bonds defined for protein. 186 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: 2.47 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3127 1.34 - 1.46: 2001 1.46 - 1.58: 4168 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 9420 Sorted by residual: bond pdb=" C5 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.418 1.473 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" C PRO B 593 " pdb=" N PRO B 594 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.51e+00 bond pdb=" C LYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.17e+00 bond pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.417 1.462 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" C1 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.399 1.443 -0.044 2.00e-02 2.50e+03 4.86e+00 ... (remaining 9415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 12498 2.16 - 4.32: 242 4.32 - 6.48: 20 6.48 - 8.64: 7 8.64 - 10.79: 2 Bond angle restraints: 12769 Sorted by residual: angle pdb=" N LEU A 509 " pdb=" CA LEU A 509 " pdb=" C LEU A 509 " ideal model delta sigma weight residual 110.80 121.59 -10.79 2.13e+00 2.20e-01 2.57e+01 angle pdb=" N ARG A 334 " pdb=" CA ARG A 334 " pdb=" C ARG A 334 " ideal model delta sigma weight residual 110.97 115.32 -4.35 1.09e+00 8.42e-01 1.59e+01 angle pdb=" C ALA B 324 " pdb=" N GLU B 325 " pdb=" CA GLU B 325 " ideal model delta sigma weight residual 122.08 127.78 -5.70 1.47e+00 4.63e-01 1.50e+01 angle pdb=" C GLU A 204 " pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 angle pdb=" N PRO B 593 " pdb=" CA PRO B 593 " pdb=" C PRO B 593 " ideal model delta sigma weight residual 110.70 114.91 -4.21 1.22e+00 6.72e-01 1.19e+01 ... (remaining 12764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 5723 22.60 - 45.20: 152 45.20 - 67.79: 35 67.79 - 90.39: 18 90.39 - 112.99: 8 Dihedral angle restraints: 5936 sinusoidal: 2554 harmonic: 3382 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 93.00 -176.55 -90.45 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS A 219 " pdb=" SG CYS A 219 " pdb=" SG CYS A 231 " pdb=" CB CYS A 231 " ideal model delta sinusoidal sigma weight residual 93.00 -179.51 -87.49 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 190 " pdb=" SG CYS A 190 " pdb=" SG CYS A 199 " pdb=" CB CYS A 199 " ideal model delta sinusoidal sigma weight residual -86.00 -168.44 82.44 1 1.00e+01 1.00e-02 8.34e+01 ... (remaining 5933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1224 0.076 - 0.152: 190 0.152 - 0.228: 6 0.228 - 0.304: 2 0.304 - 0.380: 3 Chirality restraints: 1425 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 -2.11 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA LEU A 509 " pdb=" N LEU A 509 " pdb=" C LEU A 509 " pdb=" CB LEU A 509 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 175 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1422 not shown) Planarity restraints: 1683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 519 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A 520 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " 0.027 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 SER A 511 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 512 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 372 " -0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO A 373 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.028 5.00e-02 4.00e+02 ... (remaining 1680 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2411 2.81 - 3.33: 7501 3.33 - 3.85: 14605 3.85 - 4.38: 16494 4.38 - 4.90: 28622 Nonbonded interactions: 69633 Sorted by model distance: nonbonded pdb=" OH TYR B 163 " pdb=" O HIS B 193 " model vdw 2.284 3.040 nonbonded pdb=" ND1 HIS A 507 " pdb=" O ALA A 508 " model vdw 2.315 3.120 nonbonded pdb=" OG SER B 38 " pdb=" OG1 THR B 41 " model vdw 2.324 3.040 nonbonded pdb=" OE2 GLU A 66 " pdb=" OH TYR A 88 " model vdw 2.349 3.040 nonbonded pdb=" O VAL B 356 " pdb=" OG SER B 380 " model vdw 2.365 3.040 ... (remaining 69628 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 individual isotropic 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: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.260 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 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 : 0.004 0.060 9420 Z= 0.239 Angle : 0.711 10.795 12769 Z= 0.397 Chirality : 0.054 0.380 1425 Planarity : 0.007 0.053 1679 Dihedral : 10.134 112.989 3621 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.03 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.20), residues: 1170 helix: -3.97 (0.38), residues: 41 sheet: -2.80 (0.49), residues: 91 loop : -2.68 (0.16), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 452 HIS 0.015 0.001 HIS B 48 PHE 0.019 0.002 PHE A 404 TYR 0.014 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) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7294 (t70) cc_final: 0.6925 (t70) REVERT: B 89 ASN cc_start: 0.7573 (m-40) cc_final: 0.7250 (m110) REVERT: B 103 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7373 (mtp85) REVERT: B 112 TYR cc_start: 0.6756 (m-80) cc_final: 0.6533 (m-80) REVERT: B 164 GLN cc_start: 0.6589 (pm20) cc_final: 0.6193 (pm20) REVERT: B 183 LEU cc_start: 0.8231 (mp) cc_final: 0.7844 (tp) REVERT: B 228 LYS cc_start: 0.7510 (mtpt) cc_final: 0.7278 (mtpt) REVERT: B 405 GLU cc_start: 0.6892 (tt0) cc_final: 0.6636 (tt0) REVERT: B 434 ARG cc_start: 0.8286 (mtt90) cc_final: 0.7945 (mtt180) REVERT: B 460 GLU cc_start: 0.6684 (tt0) cc_final: 0.6187 (tt0) REVERT: B 467 LEU cc_start: 0.8448 (tp) cc_final: 0.7783 (tp) REVERT: B 541 VAL cc_start: 0.7565 (m) cc_final: 0.7159 (p) REVERT: B 561 LEU cc_start: 0.7389 (mt) cc_final: 0.7124 (mt) REVERT: A 45 GLU cc_start: 0.7186 (mp0) cc_final: 0.6738 (mp0) REVERT: A 46 ASP cc_start: 0.7642 (t70) cc_final: 0.7218 (t0) REVERT: A 152 ASN cc_start: 0.7274 (m110) cc_final: 0.6942 (m110) REVERT: A 160 GLU cc_start: 0.7180 (pm20) cc_final: 0.6471 (pm20) REVERT: A 234 ASN cc_start: 0.7890 (t0) cc_final: 0.7649 (t0) REVERT: A 268 MET cc_start: 0.5860 (mtm) cc_final: 0.5359 (mtm) REVERT: A 277 MET cc_start: 0.5040 (mtt) cc_final: 0.4820 (mtt) REVERT: A 292 VAL cc_start: 0.7916 (m) cc_final: 0.7545 (p) REVERT: A 293 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7713 (mtpp) REVERT: A 294 LYS cc_start: 0.7981 (tttt) cc_final: 0.7751 (tttt) REVERT: A 325 LYS cc_start: 0.7243 (mttt) cc_final: 0.6891 (mtmm) REVERT: A 360 LYS cc_start: 0.7592 (tttt) cc_final: 0.7361 (tttt) REVERT: A 425 ILE cc_start: 0.8526 (tt) cc_final: 0.7990 (tt) REVERT: A 430 THR cc_start: 0.7999 (m) cc_final: 0.7331 (p) REVERT: A 431 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7855 (mtmm) REVERT: A 593 LYS cc_start: 0.6587 (tptp) cc_final: 0.6324 (tptp) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2908 time to fit residues: 108.9798 Evaluate side-chains 231 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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: 0.3980 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.0040 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 105 optimal weight: 0.0980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 HIS B 81 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN B 329 GLN B 438 ASN A 47 HIS A 64 ASN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 110 ASN A 206 ASN A 233 HIS A 235 GLN A 486 GLN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS A 565 GLN A 584 HIS C 16 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9420 Z= 0.263 Angle : 0.699 9.966 12769 Z= 0.353 Chirality : 0.050 0.298 1425 Planarity : 0.006 0.048 1679 Dihedral : 8.954 92.431 1433 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.56 % Allowed : 7.22 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.22), residues: 1170 helix: -3.53 (0.45), residues: 69 sheet: -2.51 (0.50), residues: 94 loop : -2.29 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 452 HIS 0.010 0.001 HIS B 237 PHE 0.024 0.002 PHE A 549 TYR 0.021 0.002 TYR B 409 ARG 0.013 0.001 ARG B 499 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 275 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7578 (t70) cc_final: 0.6870 (t70) REVERT: B 89 ASN cc_start: 0.7673 (m-40) cc_final: 0.7353 (m-40) REVERT: B 93 GLN cc_start: 0.6969 (pp30) cc_final: 0.6720 (pp30) REVERT: B 147 GLU cc_start: 0.6763 (tp30) cc_final: 0.6399 (tp30) REVERT: B 156 GLN cc_start: 0.7778 (mt0) cc_final: 0.7514 (mt0) REVERT: B 164 GLN cc_start: 0.6859 (pm20) cc_final: 0.6584 (pm20) REVERT: B 183 LEU cc_start: 0.8292 (mp) cc_final: 0.7906 (tp) REVERT: B 228 LYS cc_start: 0.7669 (mtpt) cc_final: 0.7367 (mtpt) REVERT: B 274 TYR cc_start: 0.8151 (t80) cc_final: 0.7807 (t80) REVERT: B 403 LEU cc_start: 0.6956 (tp) cc_final: 0.6693 (tp) REVERT: B 438 ASN cc_start: 0.7583 (m-40) cc_final: 0.7312 (m110) REVERT: B 460 GLU cc_start: 0.6910 (tt0) cc_final: 0.6612 (tt0) REVERT: B 561 LEU cc_start: 0.7355 (mt) cc_final: 0.7083 (mt) REVERT: A 45 GLU cc_start: 0.7271 (mp0) cc_final: 0.6878 (mp0) REVERT: A 46 ASP cc_start: 0.7811 (t70) cc_final: 0.7418 (t0) REVERT: A 80 LYS cc_start: 0.8423 (mttp) cc_final: 0.8171 (mttp) REVERT: A 98 ARG cc_start: 0.7915 (mtp-110) cc_final: 0.7707 (mtp180) REVERT: A 152 ASN cc_start: 0.7330 (m110) cc_final: 0.6965 (m110) REVERT: A 160 GLU cc_start: 0.7412 (pm20) cc_final: 0.6601 (pm20) REVERT: A 198 SER cc_start: 0.8072 (m) cc_final: 0.7444 (p) REVERT: A 235 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7672 (mm110) REVERT: A 254 PHE cc_start: 0.7682 (m-10) cc_final: 0.7457 (m-10) REVERT: A 255 ARG cc_start: 0.6462 (ttt-90) cc_final: 0.6079 (tmt-80) REVERT: A 268 MET cc_start: 0.5835 (mtm) cc_final: 0.5342 (mtm) REVERT: A 277 MET cc_start: 0.5226 (mtt) cc_final: 0.4940 (mtt) REVERT: A 284 LYS cc_start: 0.8212 (mtmm) cc_final: 0.7931 (mtmm) REVERT: A 292 VAL cc_start: 0.8147 (m) cc_final: 0.7733 (p) REVERT: A 293 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7741 (ptpp) REVERT: A 294 LYS cc_start: 0.8063 (tttt) cc_final: 0.7785 (tttt) REVERT: A 316 TYR cc_start: 0.6348 (t80) cc_final: 0.6097 (t80) REVERT: A 325 LYS cc_start: 0.7353 (mttt) cc_final: 0.7018 (mtmt) REVERT: A 347 ASP cc_start: 0.6577 (t0) cc_final: 0.6051 (t0) REVERT: A 396 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7869 (mttp) REVERT: A 430 THR cc_start: 0.8100 (m) cc_final: 0.7447 (p) REVERT: A 578 ASN cc_start: 0.6720 (m-40) cc_final: 0.6414 (m-40) REVERT: A 593 LYS cc_start: 0.6596 (tptp) cc_final: 0.6386 (tptp) REVERT: C 38 ILE cc_start: 0.8378 (tt) cc_final: 0.8051 (pt) outliers start: 16 outliers final: 9 residues processed: 277 average time/residue: 0.2492 time to fit residues: 90.3306 Evaluate side-chains 271 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 262 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 442 SER 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: 0.5980 chunk 87 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 0.0070 chunk 114 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 HIS B 329 GLN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 HIS A 57 ASN A 153 ASN A 493 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9420 Z= 0.282 Angle : 0.665 9.803 12769 Z= 0.340 Chirality : 0.050 0.296 1425 Planarity : 0.005 0.047 1679 Dihedral : 8.493 90.700 1433 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.44 % Allowed : 9.46 % Favored : 88.10 % 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: -3.00 (0.22), residues: 1170 helix: -3.27 (0.50), residues: 65 sheet: -2.39 (0.50), residues: 92 loop : -2.07 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 49 HIS 0.007 0.001 HIS B 237 PHE 0.019 0.002 PHE A 549 TYR 0.021 0.002 TYR B 409 ARG 0.011 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 273 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 THR cc_start: 0.7891 (m) cc_final: 0.7678 (m) REVERT: B 93 GLN cc_start: 0.6911 (pp30) cc_final: 0.6618 (pp30) REVERT: B 100 ARG cc_start: 0.7818 (tpp80) cc_final: 0.7509 (tpp80) REVERT: B 112 TYR cc_start: 0.7043 (m-80) cc_final: 0.6736 (m-80) REVERT: B 147 GLU cc_start: 0.6817 (tp30) cc_final: 0.6432 (tp30) REVERT: B 156 GLN cc_start: 0.7742 (mt0) cc_final: 0.7496 (mt0) REVERT: B 164 GLN cc_start: 0.7159 (pm20) cc_final: 0.6434 (pm20) REVERT: B 228 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7407 (mtmm) REVERT: B 284 ASN cc_start: 0.7670 (t0) cc_final: 0.7320 (t0) REVERT: B 405 GLU cc_start: 0.6905 (tt0) cc_final: 0.6671 (tt0) REVERT: B 421 ASP cc_start: 0.6305 (p0) cc_final: 0.6104 (p0) REVERT: B 438 ASN cc_start: 0.7564 (m-40) cc_final: 0.7289 (m110) REVERT: B 441 TYR cc_start: 0.8374 (m-80) cc_final: 0.8017 (m-80) REVERT: B 459 ARG cc_start: 0.7428 (ptt90) cc_final: 0.7121 (ptt90) REVERT: B 460 GLU cc_start: 0.6919 (tt0) cc_final: 0.6690 (tt0) REVERT: B 499 ARG cc_start: 0.6883 (ttt90) cc_final: 0.6675 (ttt-90) REVERT: B 538 GLN cc_start: 0.6502 (pp30) cc_final: 0.6237 (pm20) REVERT: B 553 GLU cc_start: 0.6122 (mt-10) cc_final: 0.5843 (mt-10) REVERT: A 45 GLU cc_start: 0.7248 (mp0) cc_final: 0.6956 (mp0) REVERT: A 46 ASP cc_start: 0.7764 (t70) cc_final: 0.7375 (t70) REVERT: A 97 GLU cc_start: 0.6457 (mp0) cc_final: 0.6059 (mp0) REVERT: A 133 LYS cc_start: 0.7074 (mttt) cc_final: 0.6849 (mmmm) REVERT: A 142 GLU cc_start: 0.7038 (tt0) cc_final: 0.6774 (tt0) REVERT: A 148 VAL cc_start: 0.8256 (t) cc_final: 0.7881 (m) REVERT: A 198 SER cc_start: 0.8180 (m) cc_final: 0.7510 (p) REVERT: A 252 ARG cc_start: 0.7451 (mtp85) cc_final: 0.7232 (mtp85) REVERT: A 255 ARG cc_start: 0.6360 (ttt-90) cc_final: 0.6095 (tmt-80) REVERT: A 256 ASP cc_start: 0.7220 (t70) cc_final: 0.6922 (t70) REVERT: A 268 MET cc_start: 0.5978 (mtm) cc_final: 0.5500 (mtm) REVERT: A 277 MET cc_start: 0.5433 (mtt) cc_final: 0.5117 (mtt) REVERT: A 292 VAL cc_start: 0.8204 (m) cc_final: 0.7877 (p) REVERT: A 294 LYS cc_start: 0.8079 (tttt) cc_final: 0.7820 (tttt) REVERT: A 307 CYS cc_start: 0.6207 (m) cc_final: 0.5958 (m) REVERT: A 316 TYR cc_start: 0.6561 (t80) cc_final: 0.6246 (t80) REVERT: A 325 LYS cc_start: 0.7495 (mttt) cc_final: 0.7040 (mtmt) REVERT: A 391 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7157 (mm-30) REVERT: A 430 THR cc_start: 0.7975 (m) cc_final: 0.7351 (p) REVERT: A 479 LYS cc_start: 0.7729 (pttt) cc_final: 0.7504 (pttm) REVERT: A 487 LYS cc_start: 0.6964 (mtmm) cc_final: 0.6678 (mtmm) REVERT: A 584 HIS cc_start: 0.6156 (m90) cc_final: 0.5811 (m170) REVERT: A 593 LYS cc_start: 0.6627 (tptp) cc_final: 0.6038 (tptp) outliers start: 25 outliers final: 17 residues processed: 280 average time/residue: 0.2685 time to fit residues: 99.1385 Evaluate side-chains 275 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 258 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.0470 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 105 optimal weight: 0.1980 chunk 112 optimal weight: 0.0870 chunk 55 optimal weight: 0.4980 chunk 100 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 GLN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9420 Z= 0.187 Angle : 0.614 11.654 12769 Z= 0.311 Chirality : 0.048 0.455 1425 Planarity : 0.004 0.042 1679 Dihedral : 7.988 82.915 1433 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.95 % Allowed : 12.00 % Favored : 86.05 % 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: -2.77 (0.22), residues: 1170 helix: -2.71 (0.61), residues: 59 sheet: -2.49 (0.49), residues: 94 loop : -1.91 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 49 HIS 0.005 0.001 HIS A 507 PHE 0.009 0.001 PHE A 481 TYR 0.020 0.001 TYR B 409 ARG 0.008 0.001 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 THR cc_start: 0.7837 (m) cc_final: 0.7608 (m) REVERT: B 30 ASP cc_start: 0.7644 (t70) cc_final: 0.6967 (t0) REVERT: B 93 GLN cc_start: 0.6925 (pp30) cc_final: 0.6593 (pp30) REVERT: B 112 TYR cc_start: 0.6960 (m-80) cc_final: 0.6709 (m-80) REVERT: B 147 GLU cc_start: 0.6797 (tp30) cc_final: 0.6388 (tp30) REVERT: B 228 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7382 (mtmm) REVERT: B 274 TYR cc_start: 0.8058 (t80) cc_final: 0.7780 (t80) REVERT: B 284 ASN cc_start: 0.7581 (t0) cc_final: 0.7259 (t0) REVERT: B 405 GLU cc_start: 0.6889 (tt0) cc_final: 0.6652 (tt0) REVERT: B 421 ASP cc_start: 0.6572 (p0) cc_final: 0.6306 (p0) REVERT: B 438 ASN cc_start: 0.7534 (m-40) cc_final: 0.7277 (m110) REVERT: B 538 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.6197 (pm20) REVERT: B 553 GLU cc_start: 0.6140 (mt-10) cc_final: 0.5856 (mt-10) REVERT: B 568 GLN cc_start: 0.6873 (tm-30) cc_final: 0.6408 (tm-30) REVERT: A 45 GLU cc_start: 0.7241 (mp0) cc_final: 0.6988 (mp0) REVERT: A 46 ASP cc_start: 0.7754 (t70) cc_final: 0.7289 (t70) REVERT: A 80 LYS cc_start: 0.8434 (mttm) cc_final: 0.8198 (mttp) REVERT: A 142 GLU cc_start: 0.7081 (tt0) cc_final: 0.6809 (tt0) REVERT: A 148 VAL cc_start: 0.8236 (t) cc_final: 0.7816 (m) REVERT: A 198 SER cc_start: 0.8230 (m) cc_final: 0.7554 (p) REVERT: A 255 ARG cc_start: 0.6533 (ttt-90) cc_final: 0.6275 (tmt-80) REVERT: A 268 MET cc_start: 0.5994 (mtm) cc_final: 0.5484 (mtm) REVERT: A 277 MET cc_start: 0.5455 (mtt) cc_final: 0.5149 (mtt) REVERT: A 292 VAL cc_start: 0.8161 (m) cc_final: 0.7851 (p) REVERT: A 294 LYS cc_start: 0.8074 (tttt) cc_final: 0.7842 (tttt) REVERT: A 308 VAL cc_start: 0.8116 (p) cc_final: 0.7883 (p) REVERT: A 316 TYR cc_start: 0.6550 (t80) cc_final: 0.6084 (t80) REVERT: A 325 LYS cc_start: 0.7414 (mttt) cc_final: 0.6944 (mtmt) REVERT: A 347 ASP cc_start: 0.6736 (t0) cc_final: 0.6184 (t0) REVERT: A 391 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7153 (mm-30) REVERT: A 430 THR cc_start: 0.7918 (m) cc_final: 0.7360 (p) REVERT: A 455 GLU cc_start: 0.7209 (tt0) cc_final: 0.6845 (tt0) REVERT: A 479 LYS cc_start: 0.7772 (pttt) cc_final: 0.7517 (pttm) REVERT: A 487 LYS cc_start: 0.6925 (mtmm) cc_final: 0.6636 (mtmm) REVERT: A 489 LYS cc_start: 0.7866 (ttmm) cc_final: 0.7338 (ttmm) REVERT: A 593 LYS cc_start: 0.6645 (tptp) cc_final: 0.6427 (tptp) REVERT: C 38 ILE cc_start: 0.8379 (tt) cc_final: 0.8047 (pt) outliers start: 20 outliers final: 12 residues processed: 261 average time/residue: 0.2550 time to fit residues: 87.9568 Evaluate side-chains 266 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 253 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 559 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 0.0270 chunk 1 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN B 329 GLN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN B 527 GLN A 444 ASN C 16 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9420 Z= 0.326 Angle : 0.680 9.915 12769 Z= 0.347 Chirality : 0.051 0.435 1425 Planarity : 0.005 0.046 1679 Dihedral : 8.201 86.243 1433 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.02 % Allowed : 12.00 % Favored : 84.98 % 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: -2.73 (0.22), residues: 1170 helix: -2.69 (0.59), residues: 59 sheet: -2.33 (0.53), residues: 82 loop : -1.91 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 49 HIS 0.039 0.002 HIS A 559 PHE 0.041 0.002 PHE A 549 TYR 0.026 0.002 TYR B 409 ARG 0.007 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 271 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 THR cc_start: 0.7800 (m) cc_final: 0.7593 (m) REVERT: B 30 ASP cc_start: 0.7707 (t70) cc_final: 0.7046 (t0) REVERT: B 139 GLU cc_start: 0.6622 (mp0) cc_final: 0.6275 (mp0) REVERT: B 147 GLU cc_start: 0.6809 (tp30) cc_final: 0.6330 (tp30) REVERT: B 228 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7518 (mtmm) REVERT: B 261 SER cc_start: 0.7850 (m) cc_final: 0.7518 (p) REVERT: B 274 TYR cc_start: 0.8064 (t80) cc_final: 0.7818 (t80) REVERT: B 284 ASN cc_start: 0.7812 (t0) cc_final: 0.7493 (t0) REVERT: B 405 GLU cc_start: 0.6941 (tt0) cc_final: 0.6631 (tt0) REVERT: B 411 TYR cc_start: 0.8102 (t80) cc_final: 0.7868 (t80) REVERT: B 421 ASP cc_start: 0.6541 (p0) cc_final: 0.6238 (p0) REVERT: B 438 ASN cc_start: 0.7574 (m-40) cc_final: 0.7332 (m110) REVERT: B 441 TYR cc_start: 0.8377 (m-80) cc_final: 0.8047 (m-80) REVERT: B 460 GLU cc_start: 0.7139 (tt0) cc_final: 0.6848 (tt0) REVERT: B 499 ARG cc_start: 0.6861 (ttt-90) cc_final: 0.6655 (ttt-90) REVERT: B 538 GLN cc_start: 0.6569 (OUTLIER) cc_final: 0.6226 (pm20) REVERT: B 553 GLU cc_start: 0.6268 (mt-10) cc_final: 0.5936 (mt-10) REVERT: A 46 ASP cc_start: 0.7695 (t70) cc_final: 0.7257 (t70) REVERT: A 80 LYS cc_start: 0.8480 (mttm) cc_final: 0.8229 (mttp) REVERT: A 97 GLU cc_start: 0.6445 (mp0) cc_final: 0.6097 (mp0) REVERT: A 142 GLU cc_start: 0.7064 (tt0) cc_final: 0.6826 (tt0) REVERT: A 148 VAL cc_start: 0.8311 (t) cc_final: 0.7930 (m) REVERT: A 198 SER cc_start: 0.8211 (m) cc_final: 0.7469 (p) REVERT: A 256 ASP cc_start: 0.7342 (t70) cc_final: 0.6980 (t70) REVERT: A 263 THR cc_start: 0.7909 (m) cc_final: 0.7632 (p) REVERT: A 292 VAL cc_start: 0.8204 (m) cc_final: 0.7888 (p) REVERT: A 294 LYS cc_start: 0.8136 (tttt) cc_final: 0.7909 (tttt) REVERT: A 308 VAL cc_start: 0.8196 (p) cc_final: 0.7981 (p) REVERT: A 316 TYR cc_start: 0.6691 (t80) cc_final: 0.6371 (t80) REVERT: A 325 LYS cc_start: 0.7520 (mttt) cc_final: 0.7071 (mtmt) REVERT: A 430 THR cc_start: 0.8004 (m) cc_final: 0.7441 (p) REVERT: A 455 GLU cc_start: 0.7203 (tt0) cc_final: 0.6716 (tt0) REVERT: A 487 LYS cc_start: 0.7257 (mtmm) cc_final: 0.6966 (mtmm) REVERT: A 489 LYS cc_start: 0.7899 (ttmm) cc_final: 0.7533 (ttmm) REVERT: A 584 HIS cc_start: 0.6022 (m90) cc_final: 0.5751 (m170) REVERT: A 593 LYS cc_start: 0.6707 (tptp) cc_final: 0.6204 (tptp) outliers start: 31 outliers final: 20 residues processed: 282 average time/residue: 0.2574 time to fit residues: 95.5139 Evaluate side-chains 275 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 254 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 54 GLN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 559 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 0.0980 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 HIS B 54 GLN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 444 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9420 Z= 0.295 Angle : 0.671 9.537 12769 Z= 0.343 Chirality : 0.050 0.397 1425 Planarity : 0.004 0.042 1679 Dihedral : 8.185 87.314 1433 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.83 % Allowed : 14.24 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.23), residues: 1170 helix: -2.46 (0.63), residues: 59 sheet: -2.51 (0.50), residues: 84 loop : -1.83 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 49 HIS 0.006 0.001 HIS A 559 PHE 0.017 0.002 PHE A 481 TYR 0.026 0.002 TYR B 409 ARG 0.009 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7682 (t70) cc_final: 0.7014 (t0) REVERT: B 139 GLU cc_start: 0.6556 (mp0) cc_final: 0.6205 (mp0) REVERT: B 228 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7622 (mtpt) REVERT: B 261 SER cc_start: 0.7866 (m) cc_final: 0.7534 (p) REVERT: B 284 ASN cc_start: 0.7874 (t0) cc_final: 0.7391 (t0) REVERT: B 405 GLU cc_start: 0.6860 (tt0) cc_final: 0.6569 (tt0) REVERT: B 421 ASP cc_start: 0.6709 (p0) cc_final: 0.6396 (p0) REVERT: B 438 ASN cc_start: 0.7575 (m-40) cc_final: 0.7328 (m110) REVERT: B 441 TYR cc_start: 0.8360 (m-80) cc_final: 0.8019 (m-80) REVERT: B 460 GLU cc_start: 0.7185 (tt0) cc_final: 0.6825 (tp30) REVERT: B 538 GLN cc_start: 0.6536 (OUTLIER) cc_final: 0.6269 (pm20) REVERT: B 553 GLU cc_start: 0.6265 (mt-10) cc_final: 0.5911 (mt-10) REVERT: B 568 GLN cc_start: 0.6881 (tm-30) cc_final: 0.6478 (tm-30) REVERT: A 46 ASP cc_start: 0.7670 (t70) cc_final: 0.7208 (t70) REVERT: A 80 LYS cc_start: 0.8459 (mttm) cc_final: 0.8201 (mttp) REVERT: A 142 GLU cc_start: 0.7092 (tt0) cc_final: 0.6826 (tt0) REVERT: A 148 VAL cc_start: 0.8320 (t) cc_final: 0.7970 (m) REVERT: A 198 SER cc_start: 0.8274 (m) cc_final: 0.7533 (p) REVERT: A 256 ASP cc_start: 0.7298 (t70) cc_final: 0.6926 (t70) REVERT: A 263 THR cc_start: 0.7960 (m) cc_final: 0.7687 (p) REVERT: A 292 VAL cc_start: 0.8210 (m) cc_final: 0.7901 (p) REVERT: A 294 LYS cc_start: 0.8134 (tttt) cc_final: 0.7908 (tttt) REVERT: A 303 ASP cc_start: 0.7462 (p0) cc_final: 0.7246 (p0) REVERT: A 308 VAL cc_start: 0.8145 (p) cc_final: 0.7758 (m) REVERT: A 325 LYS cc_start: 0.7104 (mttt) cc_final: 0.6664 (mtmt) REVERT: A 430 THR cc_start: 0.8012 (m) cc_final: 0.7443 (p) REVERT: A 455 GLU cc_start: 0.7175 (tt0) cc_final: 0.6703 (tt0) REVERT: A 487 LYS cc_start: 0.7360 (mtmm) cc_final: 0.7042 (mtmm) REVERT: A 489 LYS cc_start: 0.7871 (ttmm) cc_final: 0.7376 (ttmm) REVERT: A 593 LYS cc_start: 0.6713 (tptp) cc_final: 0.6223 (tptp) outliers start: 29 outliers final: 20 residues processed: 277 average time/residue: 0.2584 time to fit residues: 94.5139 Evaluate side-chains 272 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 GLN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 515 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 0.0470 chunk 94 optimal weight: 0.4980 chunk 62 optimal weight: 0.1980 chunk 111 optimal weight: 0.0970 chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 overall best weight: 0.2076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN B 329 GLN B 446 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** 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: 0.6996 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9420 Z= 0.201 Angle : 0.646 9.498 12769 Z= 0.328 Chirality : 0.048 0.388 1425 Planarity : 0.004 0.042 1679 Dihedral : 7.833 81.843 1433 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.05 % Allowed : 16.49 % Favored : 81.46 % 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: -2.61 (0.23), residues: 1170 helix: -2.41 (0.64), residues: 59 sheet: -2.76 (0.45), residues: 102 loop : -1.74 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 49 HIS 0.004 0.001 HIS A 559 PHE 0.009 0.001 PHE A 481 TYR 0.024 0.002 TYR B 409 ARG 0.008 0.001 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7662 (t70) cc_final: 0.6978 (t0) REVERT: B 138 ARG cc_start: 0.6945 (mmm160) cc_final: 0.6566 (mmm160) REVERT: B 139 GLU cc_start: 0.6490 (mp0) cc_final: 0.6122 (mp0) REVERT: B 147 GLU cc_start: 0.6807 (tp30) cc_final: 0.6477 (tp30) REVERT: B 228 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7563 (mtpt) REVERT: B 284 ASN cc_start: 0.7941 (t0) cc_final: 0.7608 (t0) REVERT: B 405 GLU cc_start: 0.6940 (tt0) cc_final: 0.6650 (tt0) REVERT: B 421 ASP cc_start: 0.6690 (p0) cc_final: 0.6363 (p0) REVERT: B 438 ASN cc_start: 0.7554 (m-40) cc_final: 0.7305 (m110) REVERT: B 460 GLU cc_start: 0.7173 (tt0) cc_final: 0.6811 (tp30) REVERT: B 491 GLN cc_start: 0.8008 (mt0) cc_final: 0.7796 (mt0) REVERT: B 538 GLN cc_start: 0.6512 (OUTLIER) cc_final: 0.6273 (pm20) REVERT: B 553 GLU cc_start: 0.6238 (mt-10) cc_final: 0.5891 (mt-10) REVERT: A 46 ASP cc_start: 0.7618 (t70) cc_final: 0.7216 (t70) REVERT: A 97 GLU cc_start: 0.6451 (mp0) cc_final: 0.6056 (mp0) REVERT: A 142 GLU cc_start: 0.7088 (tt0) cc_final: 0.6825 (tt0) REVERT: A 148 VAL cc_start: 0.8297 (t) cc_final: 0.7952 (m) REVERT: A 158 ASN cc_start: 0.6862 (m110) cc_final: 0.6534 (m110) REVERT: A 160 GLU cc_start: 0.7827 (pm20) cc_final: 0.7037 (pm20) REVERT: A 166 ASP cc_start: 0.7542 (t70) cc_final: 0.7232 (t0) REVERT: A 198 SER cc_start: 0.8285 (m) cc_final: 0.7564 (p) REVERT: A 256 ASP cc_start: 0.7294 (t70) cc_final: 0.6895 (t70) REVERT: A 263 THR cc_start: 0.7947 (m) cc_final: 0.7698 (p) REVERT: A 292 VAL cc_start: 0.8175 (m) cc_final: 0.7846 (p) REVERT: A 294 LYS cc_start: 0.8116 (tttt) cc_final: 0.7854 (ptmm) REVERT: A 303 ASP cc_start: 0.7375 (p0) cc_final: 0.7147 (p0) REVERT: A 308 VAL cc_start: 0.8081 (p) cc_final: 0.7742 (m) REVERT: A 325 LYS cc_start: 0.7128 (mttt) cc_final: 0.6699 (mtmt) REVERT: A 360 LYS cc_start: 0.7939 (tttt) cc_final: 0.7543 (ttmm) REVERT: A 399 LYS cc_start: 0.7895 (ttmm) cc_final: 0.7480 (mtpp) REVERT: A 430 THR cc_start: 0.7948 (m) cc_final: 0.7392 (p) REVERT: A 455 GLU cc_start: 0.7209 (tt0) cc_final: 0.6747 (tt0) REVERT: A 487 LYS cc_start: 0.7340 (mtmm) cc_final: 0.7034 (mtmm) REVERT: A 593 LYS cc_start: 0.6856 (tptp) cc_final: 0.6482 (tptp) outliers start: 21 outliers final: 12 residues processed: 253 average time/residue: 0.2486 time to fit residues: 83.9011 Evaluate side-chains 254 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 241 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 519 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.0370 chunk 10 optimal weight: 0.2980 chunk 87 optimal weight: 0.0770 chunk 101 optimal weight: 0.0770 chunk 107 optimal weight: 0.8980 chunk 97 optimal weight: 0.0980 chunk 104 optimal weight: 0.6980 overall best weight: 0.1174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 GLN B 446 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9420 Z= 0.174 Angle : 0.628 9.567 12769 Z= 0.318 Chirality : 0.047 0.386 1425 Planarity : 0.004 0.040 1679 Dihedral : 7.388 72.746 1433 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.34 % Allowed : 16.10 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.23), residues: 1170 helix: -2.08 (0.64), residues: 59 sheet: -2.44 (0.49), residues: 92 loop : -1.72 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 49 HIS 0.003 0.001 HIS A 507 PHE 0.014 0.001 PHE A 48 TYR 0.022 0.002 TYR B 409 ARG 0.009 0.001 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7691 (t70) cc_final: 0.6986 (t0) REVERT: B 64 TYR cc_start: 0.8600 (m-80) cc_final: 0.8046 (m-80) REVERT: B 71 LEU cc_start: 0.7743 (mm) cc_final: 0.7534 (mt) REVERT: B 138 ARG cc_start: 0.6939 (mmm160) cc_final: 0.6581 (mmm160) REVERT: B 139 GLU cc_start: 0.6488 (mp0) cc_final: 0.6105 (mp0) REVERT: B 147 GLU cc_start: 0.6767 (tp30) cc_final: 0.6449 (tp30) REVERT: B 228 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7598 (mtpt) REVERT: B 248 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8176 (mmpt) REVERT: B 284 ASN cc_start: 0.7949 (t0) cc_final: 0.7681 (t0) REVERT: B 297 THR cc_start: 0.8363 (m) cc_final: 0.8087 (p) REVERT: B 405 GLU cc_start: 0.6925 (tt0) cc_final: 0.6651 (tt0) REVERT: B 421 ASP cc_start: 0.6670 (p0) cc_final: 0.6351 (p0) REVERT: B 438 ASN cc_start: 0.7528 (m-40) cc_final: 0.7233 (m110) REVERT: B 460 GLU cc_start: 0.7191 (tt0) cc_final: 0.6844 (tp30) REVERT: B 538 GLN cc_start: 0.6486 (OUTLIER) cc_final: 0.6253 (pm20) REVERT: B 553 GLU cc_start: 0.6215 (mt-10) cc_final: 0.5872 (mt-10) REVERT: B 568 GLN cc_start: 0.7034 (tm-30) cc_final: 0.6618 (tm-30) REVERT: A 46 ASP cc_start: 0.7650 (t70) cc_final: 0.7225 (t70) REVERT: A 97 GLU cc_start: 0.6393 (mp0) cc_final: 0.6017 (mp0) REVERT: A 142 GLU cc_start: 0.7019 (tt0) cc_final: 0.6746 (tt0) REVERT: A 148 VAL cc_start: 0.8250 (t) cc_final: 0.7901 (m) REVERT: A 158 ASN cc_start: 0.6862 (m110) cc_final: 0.6585 (m110) REVERT: A 160 GLU cc_start: 0.7782 (pm20) cc_final: 0.6978 (pm20) REVERT: A 166 ASP cc_start: 0.7492 (t70) cc_final: 0.7163 (t0) REVERT: A 198 SER cc_start: 0.8222 (m) cc_final: 0.7449 (p) REVERT: A 222 ARG cc_start: 0.7676 (ttm-80) cc_final: 0.7211 (ttm-80) REVERT: A 256 ASP cc_start: 0.7308 (t70) cc_final: 0.6962 (t70) REVERT: A 263 THR cc_start: 0.7986 (m) cc_final: 0.7736 (p) REVERT: A 292 VAL cc_start: 0.8145 (m) cc_final: 0.7805 (p) REVERT: A 294 LYS cc_start: 0.8090 (tttt) cc_final: 0.7832 (ptmm) REVERT: A 303 ASP cc_start: 0.7362 (p0) cc_final: 0.6948 (p0) REVERT: A 308 VAL cc_start: 0.8050 (p) cc_final: 0.7728 (m) REVERT: A 325 LYS cc_start: 0.7050 (mttt) cc_final: 0.6622 (mtmt) REVERT: A 347 ASP cc_start: 0.6834 (t0) cc_final: 0.6262 (t0) REVERT: A 391 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7342 (mm-30) REVERT: A 399 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7508 (mtpp) REVERT: A 430 THR cc_start: 0.8006 (m) cc_final: 0.7460 (p) REVERT: A 455 GLU cc_start: 0.7218 (tt0) cc_final: 0.6760 (tt0) REVERT: A 593 LYS cc_start: 0.6834 (tptp) cc_final: 0.6440 (tptp) outliers start: 24 outliers final: 17 residues processed: 262 average time/residue: 0.2475 time to fit residues: 86.5578 Evaluate side-chains 261 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 524 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 45 optimal weight: 0.0970 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 0.0570 chunk 110 optimal weight: 0.0370 chunk 67 optimal weight: 0.6980 overall best weight: 0.1974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 GLN B 446 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9420 Z= 0.191 Angle : 0.627 9.871 12769 Z= 0.317 Chirality : 0.048 0.389 1425 Planarity : 0.004 0.041 1679 Dihedral : 7.118 66.855 1433 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.15 % Allowed : 16.49 % Favored : 81.37 % 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 (0.23), residues: 1170 helix: -2.09 (0.65), residues: 59 sheet: -2.43 (0.49), residues: 94 loop : -1.67 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 49 HIS 0.005 0.001 HIS A 304 PHE 0.012 0.001 PHE A 48 TYR 0.023 0.002 TYR B 409 ARG 0.008 0.001 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 246 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: B 30 ASP cc_start: 0.7706 (t70) cc_final: 0.7052 (t0) REVERT: B 138 ARG cc_start: 0.6937 (mmm160) cc_final: 0.6610 (mmm160) REVERT: B 139 GLU cc_start: 0.6531 (mp0) cc_final: 0.6144 (mp0) REVERT: B 147 GLU cc_start: 0.6766 (tp30) cc_final: 0.6441 (tp30) REVERT: B 248 LYS cc_start: 0.8407 (mmtt) cc_final: 0.8182 (mmpt) REVERT: B 284 ASN cc_start: 0.7997 (t0) cc_final: 0.7714 (t0) REVERT: B 297 THR cc_start: 0.8346 (m) cc_final: 0.8093 (p) REVERT: B 405 GLU cc_start: 0.6941 (tt0) cc_final: 0.6662 (tt0) REVERT: B 421 ASP cc_start: 0.6674 (p0) cc_final: 0.6355 (p0) REVERT: B 460 GLU cc_start: 0.7175 (tt0) cc_final: 0.6823 (tp30) REVERT: B 538 GLN cc_start: 0.6493 (OUTLIER) cc_final: 0.6265 (pm20) REVERT: B 553 GLU cc_start: 0.6188 (mt-10) cc_final: 0.5859 (mt-10) REVERT: B 561 LEU cc_start: 0.7383 (mt) cc_final: 0.7161 (mt) REVERT: B 568 GLN cc_start: 0.6950 (tm-30) cc_final: 0.6546 (tm-30) REVERT: A 46 ASP cc_start: 0.7632 (t70) cc_final: 0.7191 (t70) REVERT: A 97 GLU cc_start: 0.6387 (mp0) cc_final: 0.6047 (mp0) REVERT: A 142 GLU cc_start: 0.7025 (tt0) cc_final: 0.6748 (tt0) REVERT: A 148 VAL cc_start: 0.8240 (t) cc_final: 0.7903 (m) REVERT: A 160 GLU cc_start: 0.7773 (pm20) cc_final: 0.6894 (pm20) REVERT: A 166 ASP cc_start: 0.7449 (t70) cc_final: 0.7134 (t0) REVERT: A 198 SER cc_start: 0.8272 (m) cc_final: 0.7479 (p) REVERT: A 222 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.7250 (ttm-80) REVERT: A 261 LYS cc_start: 0.7779 (pttt) cc_final: 0.7571 (pttt) REVERT: A 263 THR cc_start: 0.8014 (m) cc_final: 0.7747 (p) REVERT: A 292 VAL cc_start: 0.8141 (m) cc_final: 0.7747 (p) REVERT: A 294 LYS cc_start: 0.8105 (tttt) cc_final: 0.7849 (ptmm) REVERT: A 308 VAL cc_start: 0.8070 (p) cc_final: 0.7707 (m) REVERT: A 325 LYS cc_start: 0.7044 (mttt) cc_final: 0.6689 (mtmt) REVERT: A 347 ASP cc_start: 0.6861 (t0) cc_final: 0.6284 (t0) REVERT: A 360 LYS cc_start: 0.7936 (tttt) cc_final: 0.7610 (ttmm) REVERT: A 391 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7380 (mm-30) REVERT: A 399 LYS cc_start: 0.7891 (ttmm) cc_final: 0.7469 (mtpp) REVERT: A 430 THR cc_start: 0.7998 (m) cc_final: 0.7459 (p) REVERT: A 455 GLU cc_start: 0.7217 (tt0) cc_final: 0.6762 (tt0) REVERT: A 593 LYS cc_start: 0.6864 (tptp) cc_final: 0.6467 (tptp) REVERT: C 38 ILE cc_start: 0.8280 (tt) cc_final: 0.7989 (pt) outliers start: 22 outliers final: 16 residues processed: 255 average time/residue: 0.2647 time to fit residues: 89.6776 Evaluate side-chains 256 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 519 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 0.0170 chunk 106 optimal weight: 0.9980 chunk 92 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN A 158 ASN A 444 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9420 Z= 0.245 Angle : 0.668 9.958 12769 Z= 0.336 Chirality : 0.049 0.402 1425 Planarity : 0.004 0.041 1679 Dihedral : 7.092 64.746 1433 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.46 % Allowed : 17.56 % Favored : 80.98 % 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: -2.46 (0.23), residues: 1170 helix: -2.11 (0.64), residues: 59 sheet: -2.36 (0.52), residues: 80 loop : -1.71 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 49 HIS 0.005 0.001 HIS A 507 PHE 0.014 0.002 PHE A 481 TYR 0.025 0.002 TYR B 409 ARG 0.009 0.001 ARG B 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: B 24 GLN cc_start: 0.6434 (pp30) cc_final: 0.6033 (pp30) REVERT: B 139 GLU cc_start: 0.6548 (mp0) cc_final: 0.6199 (mp0) REVERT: B 147 GLU cc_start: 0.6768 (tp30) cc_final: 0.6452 (tp30) REVERT: B 160 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7906 (mm-40) REVERT: B 228 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7783 (mtpt) REVERT: B 248 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8169 (mmpt) REVERT: B 284 ASN cc_start: 0.8107 (t0) cc_final: 0.7793 (t0) REVERT: B 297 THR cc_start: 0.8445 (m) cc_final: 0.8195 (p) REVERT: B 405 GLU cc_start: 0.6980 (tt0) cc_final: 0.6701 (tt0) REVERT: B 421 ASP cc_start: 0.6758 (p0) cc_final: 0.6439 (p0) REVERT: B 460 GLU cc_start: 0.7180 (tt0) cc_final: 0.6787 (tp30) REVERT: B 501 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6419 (mm-30) REVERT: B 538 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.6283 (pm20) REVERT: B 553 GLU cc_start: 0.6199 (mt-10) cc_final: 0.5853 (mt-10) REVERT: B 561 LEU cc_start: 0.7427 (mt) cc_final: 0.7207 (mt) REVERT: B 568 GLN cc_start: 0.6987 (tm-30) cc_final: 0.6572 (tm-30) REVERT: A 46 ASP cc_start: 0.7627 (t70) cc_final: 0.7194 (t70) REVERT: A 97 GLU cc_start: 0.6386 (mp0) cc_final: 0.6037 (mp0) REVERT: A 142 GLU cc_start: 0.7015 (tt0) cc_final: 0.6815 (tt0) REVERT: A 148 VAL cc_start: 0.8263 (t) cc_final: 0.7923 (m) REVERT: A 160 GLU cc_start: 0.7839 (pm20) cc_final: 0.6958 (pm20) REVERT: A 166 ASP cc_start: 0.7497 (t70) cc_final: 0.7199 (t0) REVERT: A 198 SER cc_start: 0.8204 (m) cc_final: 0.7484 (p) REVERT: A 256 ASP cc_start: 0.7452 (t70) cc_final: 0.7238 (t0) REVERT: A 263 THR cc_start: 0.7985 (m) cc_final: 0.7740 (p) REVERT: A 292 VAL cc_start: 0.8101 (m) cc_final: 0.7783 (p) REVERT: A 294 LYS cc_start: 0.8120 (tttt) cc_final: 0.7847 (ptmm) REVERT: A 308 VAL cc_start: 0.8115 (p) cc_final: 0.7720 (m) REVERT: A 325 LYS cc_start: 0.7059 (mttt) cc_final: 0.6761 (mtmt) REVERT: A 347 ASP cc_start: 0.6904 (t0) cc_final: 0.6333 (t0) REVERT: A 391 GLU cc_start: 0.7946 (mm-30) cc_final: 0.6802 (tp30) REVERT: A 399 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7585 (mtpp) REVERT: A 430 THR cc_start: 0.7988 (m) cc_final: 0.7474 (p) REVERT: A 455 GLU cc_start: 0.7214 (tt0) cc_final: 0.6749 (tt0) REVERT: A 593 LYS cc_start: 0.6877 (tptp) cc_final: 0.6483 (tptp) outliers start: 15 outliers final: 13 residues processed: 255 average time/residue: 0.2576 time to fit residues: 86.7273 Evaluate side-chains 261 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 247 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 519 GLU 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: 0.6980 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 0.4980 chunk 38 optimal weight: 0.3980 chunk 94 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 5 optimal weight: 0.0570 chunk 66 optimal weight: 1.9990 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN B 329 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN A 422 ASN ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.147848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125272 restraints weight = 13315.738| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.82 r_work: 0.3479 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9420 Z= 0.200 Angle : 0.650 10.184 12769 Z= 0.327 Chirality : 0.048 0.398 1425 Planarity : 0.005 0.042 1679 Dihedral : 6.849 59.430 1433 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.66 % Allowed : 18.24 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.23), residues: 1170 helix: -2.10 (0.64), residues: 59 sheet: -2.32 (0.52), residues: 80 loop : -1.65 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 49 HIS 0.004 0.001 HIS A 507 PHE 0.011 0.001 PHE A 48 TYR 0.026 0.002 TYR B 409 ARG 0.009 0.001 ARG B 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2821.64 seconds wall clock time: 56 minutes 0.71 seconds (3360.71 seconds total)