Starting phenix.real_space_refine on Sat Sep 12 01:02:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6feq_4246/09_2026/6feq_4246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6feq_4246/09_2026/6feq_4246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6feq_4246/09_2026/6feq_4246.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6feq_4246/09_2026/6feq_4246.cif" model { file = "/net/cci-nas-00/data/ceres_data/6feq_4246/09_2026/6feq_4246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6feq_4246/09_2026/6feq_4246.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6feq_4246/09_2026/6feq_4246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6feq_4246/09_2026/6feq_4246.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.016 sd= 0.107 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 68 5.16 5 C 8006 2.51 5 N 2040 2.21 5 O 2283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12397 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'D6T': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.47, per 1000 atoms: 0.20 Number of scatterers: 12397 At special positions: 0 Unit cell: (102.24, 96.915, 145.905, 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 68 16.00 O 2283 8.00 N 2040 7.00 C 8006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.05 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 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 NAG-ASN " NAG A1001 " - " ASN A 596 " " NAG B1001 " - " ASN B 596 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 579.2 milliseconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 16 sheets defined 44.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 84 through 87 removed outlier: 4.515A pdb=" N SER A 87 " --> pdb=" O GLY A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.666A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.673A pdb=" N GLU A 159 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.745A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.517A pdb=" N ASN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.284A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 removed outlier: 3.744A pdb=" N ILE A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 338 removed outlier: 3.629A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 354 removed outlier: 3.592A pdb=" N GLU A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.617A pdb=" N GLN A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 413 removed outlier: 3.608A pdb=" N ILE A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 440 removed outlier: 3.582A pdb=" N PHE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 444 Processing helix chain 'A' and resid 445 through 451 removed outlier: 3.713A pdb=" N VAL A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 451' Processing helix chain 'A' and resid 451 through 462 removed outlier: 3.664A pdb=" N HIS A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 479 through 498 Proline residue: A 485 - end of helix removed outlier: 3.656A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 529 removed outlier: 3.601A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 549 removed outlier: 3.507A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 553 removed outlier: 4.070A pdb=" N GLY A 553 " --> pdb=" O ILE A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 550 through 553' Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.646A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.960A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.581A pdb=" N LYS A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 650 removed outlier: 3.639A pdb=" N LEU A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.931A pdb=" N ASP B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 4.065A pdb=" N LYS B 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.602A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 187 through 198 removed outlier: 3.721A pdb=" N LYS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.595A pdb=" N ASN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.847A pdb=" N PHE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.573A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.615A pdb=" N GLU B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 354 removed outlier: 3.758A pdb=" N LYS B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.525A pdb=" N TRP B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 413 removed outlier: 3.638A pdb=" N ILE B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 441 removed outlier: 3.513A pdb=" N PHE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 444 No H-bonds generated for 'chain 'B' and resid 442 through 444' Processing helix chain 'B' and resid 445 through 451 removed outlier: 3.746A pdb=" N VAL B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 445 through 451' Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 465 through 477 removed outlier: 3.513A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 498 Proline residue: B 485 - end of helix removed outlier: 3.574A pdb=" N VAL B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 529 removed outlier: 3.771A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 551 removed outlier: 3.836A pdb=" N ILE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.516A pdb=" N THR B 560 " --> pdb=" O ASN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 571 removed outlier: 3.520A pdb=" N GLN B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.783A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 removed outlier: 3.561A pdb=" N LYS B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 650 removed outlier: 3.789A pdb=" N LEU B 626 " --> pdb=" O SER B 622 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.697A pdb=" N ASP C 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.698A pdb=" N ASP E 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 71 removed outlier: 3.524A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 6.394A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 241 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 240 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 75 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR A 257 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA A 77 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU A 259 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 79 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 68 through 71 Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.442A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER B 241 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU B 75 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR B 257 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA B 77 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU B 259 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU B 79 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.384A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N SER C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.520A pdb=" N CYS D 22 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.875A pdb=" N LEU D 46 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE D 41 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 108 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.875A pdb=" N LEU D 46 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE D 41 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.384A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 6 through 7 removed outlier: 3.519A pdb=" N CYS F 22 " --> pdb=" O PHE F 79 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.876A pdb=" N LEU F 46 " --> pdb=" O PHE F 41 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE F 41 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR F 108 " --> pdb=" O THR F 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.876A pdb=" N LEU F 46 " --> pdb=" O PHE F 41 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE F 41 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) 565 hydrogen bonds defined for protein. 1587 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: 1.98 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1939 1.31 - 1.44: 3587 1.44 - 1.56: 7041 1.56 - 1.69: 4 1.69 - 1.82: 106 Bond restraints: 12677 Sorted by residual: bond pdb=" C27 D6T A1002 " pdb=" C31 D6T A1002 " ideal model delta sigma weight residual 1.400 1.618 -0.218 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C28 D6T A1002 " pdb=" C34 D6T A1002 " ideal model delta sigma weight residual 1.400 1.615 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C32 D6T A1002 " pdb=" C33 D6T A1002 " ideal model delta sigma weight residual 1.411 1.241 0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" C19 D6T A1002 " pdb=" C20 D6T A1002 " ideal model delta sigma weight residual 1.386 1.550 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" C18 D6T A1002 " pdb=" C23 D6T A1002 " ideal model delta sigma weight residual 1.388 1.542 -0.154 2.00e-02 2.50e+03 5.95e+01 ... (remaining 12672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 17017 3.89 - 7.78: 140 7.78 - 11.66: 17 11.66 - 15.55: 1 15.55 - 19.44: 3 Bond angle restraints: 17178 Sorted by residual: angle pdb=" C29 D6T A1002 " pdb=" C30 D6T A1002 " pdb=" N6 D6T A1002 " ideal model delta sigma weight residual 110.04 129.48 -19.44 3.00e+00 1.11e-01 4.20e+01 angle pdb=" C SER B 572 " pdb=" N ILE B 573 " pdb=" CA ILE B 573 " ideal model delta sigma weight residual 120.33 125.16 -4.83 8.00e-01 1.56e+00 3.65e+01 angle pdb=" C27 D6T A1002 " pdb=" C26 D6T A1002 " pdb=" N6 D6T A1002 " ideal model delta sigma weight residual 112.58 129.64 -17.06 3.00e+00 1.11e-01 3.23e+01 angle pdb=" CA LEU A 64 " pdb=" CB LEU A 64 " pdb=" CG LEU A 64 " ideal model delta sigma weight residual 116.30 131.90 -15.60 3.50e+00 8.16e-02 1.99e+01 angle pdb=" C ILE B 63 " pdb=" N LEU B 64 " pdb=" CA LEU B 64 " ideal model delta sigma weight residual 121.54 129.82 -8.28 1.91e+00 2.74e-01 1.88e+01 ... (remaining 17173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 7131 17.62 - 35.23: 219 35.23 - 52.85: 54 52.85 - 70.47: 8 70.47 - 88.08: 10 Dihedral angle restraints: 7422 sinusoidal: 2886 harmonic: 4536 Sorted by residual: dihedral pdb=" CA PHE A 414 " pdb=" C PHE A 414 " pdb=" N GLY A 415 " pdb=" CA GLY A 415 " ideal model delta harmonic sigma weight residual -180.00 -137.37 -42.63 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA PHE B 414 " pdb=" C PHE B 414 " pdb=" N GLY B 415 " pdb=" CA GLY B 415 " ideal model delta harmonic sigma weight residual -180.00 -137.92 -42.08 0 5.00e+00 4.00e-02 7.08e+01 dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual -86.00 -19.98 -66.02 1 1.00e+01 1.00e-02 5.70e+01 ... (remaining 7419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1297 0.052 - 0.104: 532 0.104 - 0.156: 102 0.156 - 0.209: 18 0.209 - 0.261: 5 Chirality restraints: 1954 Sorted by residual: chirality pdb=" CG LEU A 565 " pdb=" CB LEU A 565 " pdb=" CD1 LEU A 565 " pdb=" CD2 LEU A 565 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA THR C 94 " pdb=" N THR C 94 " pdb=" C THR C 94 " pdb=" CB THR C 94 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA THR E 94 " pdb=" N THR E 94 " pdb=" C THR E 94 " pdb=" CB THR E 94 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1951 not shown) Planarity restraints: 2143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 63 " -0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ILE B 63 " 0.075 2.00e-02 2.50e+03 pdb=" O ILE B 63 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU B 64 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 63 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C ILE A 63 " 0.073 2.00e-02 2.50e+03 pdb=" O ILE A 63 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU A 64 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 87 " -0.040 5.00e-02 4.00e+02 6.12e-02 5.98e+00 pdb=" N PRO F 88 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " -0.034 5.00e-02 4.00e+02 ... (remaining 2140 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3489 2.80 - 3.32: 11074 3.32 - 3.85: 19829 3.85 - 4.37: 23270 4.37 - 4.90: 39977 Nonbonded interactions: 97639 Sorted by model distance: nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.271 3.040 nonbonded pdb=" OG SER E 63 " pdb=" OG SER E 74 " model vdw 2.276 3.040 nonbonded pdb=" OG SER C 63 " pdb=" OG SER C 74 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.277 3.040 nonbonded pdb=" O SER B 486 " pdb=" OG1 THR B 490 " model vdw 2.281 3.040 ... (remaining 97634 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 35 through 1001) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.250 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 : 0.011 0.218 12686 Z= 0.502 Angle : 1.053 19.441 17198 Z= 0.550 Chirality : 0.057 0.261 1954 Planarity : 0.006 0.061 2141 Dihedral : 10.447 88.082 4505 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.15 % Allowed : 3.48 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.17 (0.16), residues: 1558 helix: -3.35 (0.11), residues: 602 sheet: -1.64 (0.30), residues: 252 loop : -2.54 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 96 TYR 0.024 0.003 TYR F 51 PHE 0.030 0.003 PHE E 98 TRP 0.030 0.003 TRP F 109 HIS 0.015 0.003 HIS B 583 Details of bonding type rmsd/Z covalent geometry : bond 0.01077 / 0.50 (12677) covalent geometry : angle 1.04691 / 0.55 (17178) SS BOND : bond 0.01263 / 0.82 ( 7) SS BOND : angle 2.07149 / 1.30 ( 14) hydrogen bonds : bond 0.28892 / 19.12 ( 539) hydrogen bonds : angle 9.28319 / 6.51 ( 1587) link_NAG-ASN : bond 0.01048 / 0.53 ( 2) link_NAG-ASN : angle 5.22645 / 3.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.9090 (mttt) cc_final: 0.8515 (tptm) REVERT: A 243 HIS cc_start: 0.9213 (t70) cc_final: 0.8905 (t-170) REVERT: A 344 GLU cc_start: 0.8980 (tp30) cc_final: 0.8342 (tp30) REVERT: A 391 ASN cc_start: 0.9041 (t160) cc_final: 0.8704 (t0) REVERT: A 523 MET cc_start: 0.9291 (ttt) cc_final: 0.8959 (ttp) REVERT: B 172 LYS cc_start: 0.8989 (mttt) cc_final: 0.8406 (tmtt) REVERT: B 226 LEU cc_start: 0.8912 (mt) cc_final: 0.8557 (tp) REVERT: B 336 TYR cc_start: 0.9002 (t80) cc_final: 0.8777 (t80) REVERT: B 343 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8699 (mttp) REVERT: B 391 ASN cc_start: 0.9206 (t160) cc_final: 0.8628 (m-40) REVERT: B 393 GLN cc_start: 0.6098 (mm-40) cc_final: 0.5758 (tp40) REVERT: B 515 MET cc_start: 0.9399 (mmm) cc_final: 0.9098 (mmp) REVERT: B 523 MET cc_start: 0.9272 (ttt) cc_final: 0.9070 (ttm) REVERT: C 79 GLN cc_start: 0.8351 (mm110) cc_final: 0.8026 (mm110) REVERT: C 82 ASP cc_start: 0.8154 (m-30) cc_final: 0.7646 (m-30) REVERT: C 90 GLN cc_start: 0.8504 (pp30) cc_final: 0.7819 (pp30) REVERT: E 15 LEU cc_start: 0.9088 (mp) cc_final: 0.8803 (tt) REVERT: E 79 GLN cc_start: 0.9167 (mm110) cc_final: 0.8680 (mm-40) REVERT: E 82 ASP cc_start: 0.8270 (m-30) cc_final: 0.7763 (m-30) REVERT: E 94 THR cc_start: 0.8703 (p) cc_final: 0.8498 (t) REVERT: F 53 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8444 (t0) REVERT: F 100 TYR cc_start: 0.8226 (t80) cc_final: 0.7985 (t80) outliers start: 2 outliers final: 0 residues processed: 249 average time/residue: 0.1148 time to fit residues: 40.2457 Evaluate side-chains 125 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 ASN A 109 ASN A 116 ASN A 222 ASN A 375 HIS A 391 ASN A 425 ASN A 437 GLN A 583 HIS B 41 ASN B 68 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 375 HIS B 391 ASN B 425 ASN B 437 GLN B 457 HIS B 583 HIS C 6 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN F 40 GLN F 53 ASN F 77 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.088584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.066370 restraints weight = 34287.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.068712 restraints weight = 16816.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070211 restraints weight = 10553.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.071168 restraints weight = 7737.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.071791 restraints weight = 6281.262| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12686 Z= 0.135 Angle : 0.691 9.415 17198 Z= 0.347 Chirality : 0.043 0.199 1954 Planarity : 0.005 0.052 2141 Dihedral : 6.488 67.277 1719 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.41 % Allowed : 7.93 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.20), residues: 1558 helix: -0.46 (0.18), residues: 644 sheet: -1.22 (0.30), residues: 270 loop : -1.95 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 246 TYR 0.018 0.001 TYR B 336 PHE 0.016 0.002 PHE F 79 TRP 0.009 0.001 TRP F 109 HIS 0.005 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (12677) covalent geometry : angle 0.68905 / 0.35 (17178) SS BOND : bond 0.00466 / 0.30 ( 7) SS BOND : angle 0.90164 / 0.55 ( 14) hydrogen bonds : bond 0.04549 / 3.04 ( 539) hydrogen bonds : angle 5.10805 / 3.53 ( 1587) link_NAG-ASN : bond 0.00084 / 0.04 ( 2) link_NAG-ASN : angle 2.40191 / 1.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.9056 (mttt) cc_final: 0.8490 (tptm) REVERT: A 182 PHE cc_start: 0.8177 (m-80) cc_final: 0.7508 (t80) REVERT: A 266 PHE cc_start: 0.7222 (t80) cc_final: 0.6825 (t80) REVERT: A 334 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8783 (mm-30) REVERT: A 344 GLU cc_start: 0.8995 (tp30) cc_final: 0.8404 (tp30) REVERT: A 345 THR cc_start: 0.8992 (m) cc_final: 0.8785 (p) REVERT: A 391 ASN cc_start: 0.9134 (t0) cc_final: 0.8729 (t0) REVERT: B 164 VAL cc_start: 0.9441 (t) cc_final: 0.9206 (p) REVERT: B 172 LYS cc_start: 0.8934 (mttt) cc_final: 0.8380 (tmtt) REVERT: B 226 LEU cc_start: 0.9047 (mt) cc_final: 0.8725 (tp) REVERT: B 351 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6752 (pp30) REVERT: B 393 GLN cc_start: 0.5869 (mm-40) cc_final: 0.5529 (tp40) REVERT: B 402 THR cc_start: 0.9176 (m) cc_final: 0.8906 (p) REVERT: B 515 MET cc_start: 0.9238 (mmm) cc_final: 0.8975 (mmt) REVERT: C 24 LYS cc_start: 0.8079 (tptp) cc_final: 0.7843 (tppt) REVERT: C 55 GLU cc_start: 0.8398 (tp30) cc_final: 0.8086 (tp30) REVERT: C 79 GLN cc_start: 0.8305 (mm110) cc_final: 0.8088 (mm110) REVERT: E 79 GLN cc_start: 0.8963 (mm110) cc_final: 0.8567 (mm110) REVERT: E 82 ASP cc_start: 0.8239 (m-30) cc_final: 0.7836 (m-30) REVERT: F 55 ASP cc_start: 0.8587 (p0) cc_final: 0.8131 (p0) outliers start: 19 outliers final: 7 residues processed: 194 average time/residue: 0.0979 time to fit residues: 28.3855 Evaluate side-chains 127 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 68 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN A 222 ASN A 457 HIS B 76 ASN D 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.085597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.063353 restraints weight = 34889.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.065559 restraints weight = 17195.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.067037 restraints weight = 10874.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067980 restraints weight = 7963.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068583 restraints weight = 6480.307| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12686 Z= 0.218 Angle : 0.691 11.103 17198 Z= 0.346 Chirality : 0.043 0.169 1954 Planarity : 0.004 0.065 2141 Dihedral : 5.989 60.546 1717 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.15 % Allowed : 10.44 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.21), residues: 1558 helix: 0.54 (0.20), residues: 650 sheet: -0.88 (0.31), residues: 262 loop : -1.73 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 163 TYR 0.019 0.002 TYR B 336 PHE 0.020 0.002 PHE F 79 TRP 0.010 0.001 TRP F 37 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 (12677) covalent geometry : angle 0.68921 / 0.35 (17178) SS BOND : bond 0.00636 / 0.46 ( 7) SS BOND : angle 1.26620 / 0.80 ( 14) hydrogen bonds : bond 0.04094 / 2.71 ( 539) hydrogen bonds : angle 4.74602 / 3.27 ( 1587) link_NAG-ASN : bond 0.00456 / 0.23 ( 2) link_NAG-ASN : angle 2.20460 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8314 (mmm) cc_final: 0.8017 (mmm) REVERT: A 172 LYS cc_start: 0.9030 (mttt) cc_final: 0.8517 (tptm) REVERT: A 182 PHE cc_start: 0.8246 (m-80) cc_final: 0.7457 (t80) REVERT: A 265 MET cc_start: 0.7814 (mtp) cc_final: 0.7574 (mtt) REVERT: A 266 PHE cc_start: 0.7281 (t80) cc_final: 0.6988 (t80) REVERT: A 274 LEU cc_start: 0.8484 (tp) cc_final: 0.8235 (pp) REVERT: A 334 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8811 (mm-30) REVERT: A 344 GLU cc_start: 0.9000 (tp30) cc_final: 0.8382 (tp30) REVERT: A 345 THR cc_start: 0.8987 (m) cc_final: 0.8750 (p) REVERT: A 391 ASN cc_start: 0.9156 (t0) cc_final: 0.8714 (t0) REVERT: B 152 MET cc_start: 0.8288 (ttm) cc_final: 0.7997 (mpp) REVERT: B 172 LYS cc_start: 0.9022 (mttt) cc_final: 0.8397 (tmtt) REVERT: B 226 LEU cc_start: 0.9089 (mt) cc_final: 0.8742 (tp) REVERT: B 393 GLN cc_start: 0.6187 (mm-40) cc_final: 0.5809 (tp40) REVERT: B 402 THR cc_start: 0.9130 (m) cc_final: 0.8866 (p) REVERT: B 515 MET cc_start: 0.9289 (mmm) cc_final: 0.9047 (mmt) REVERT: C 55 GLU cc_start: 0.8439 (tp30) cc_final: 0.8079 (tp30) REVERT: E 79 GLN cc_start: 0.8962 (mm110) cc_final: 0.8548 (mm-40) REVERT: E 82 ASP cc_start: 0.8233 (m-30) cc_final: 0.7824 (m-30) REVERT: F 55 ASP cc_start: 0.8610 (p0) cc_final: 0.8270 (p0) outliers start: 29 outliers final: 15 residues processed: 146 average time/residue: 0.0887 time to fit residues: 20.3293 Evaluate side-chains 127 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 99 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 617 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.087935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.065974 restraints weight = 34251.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.068301 restraints weight = 16622.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069801 restraints weight = 10368.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.070759 restraints weight = 7529.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071398 restraints weight = 6092.231| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12686 Z= 0.107 Angle : 0.608 10.616 17198 Z= 0.304 Chirality : 0.041 0.197 1954 Planarity : 0.004 0.049 2141 Dihedral : 5.621 61.552 1717 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.00 % Allowed : 10.96 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.22), residues: 1558 helix: 1.13 (0.21), residues: 646 sheet: -0.68 (0.31), residues: 270 loop : -1.50 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 246 TYR 0.017 0.001 TYR A 336 PHE 0.018 0.001 PHE A 545 TRP 0.012 0.001 TRP A 564 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (12677) covalent geometry : angle 0.60689 / 0.30 (17178) SS BOND : bond 0.00394 / 0.26 ( 7) SS BOND : angle 0.87761 / 0.52 ( 14) hydrogen bonds : bond 0.03405 / 2.26 ( 539) hydrogen bonds : angle 4.31133 / 2.98 ( 1587) link_NAG-ASN : bond 0.00085 / 0.04 ( 2) link_NAG-ASN : angle 2.06682 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8370 (mmm) cc_final: 0.8084 (mmm) REVERT: A 172 LYS cc_start: 0.9029 (mttt) cc_final: 0.8515 (tptm) REVERT: A 182 PHE cc_start: 0.8316 (m-80) cc_final: 0.7488 (t80) REVERT: A 201 ILE cc_start: 0.9388 (mm) cc_final: 0.9163 (mt) REVERT: A 259 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8576 (tp) REVERT: A 344 GLU cc_start: 0.9000 (tp30) cc_final: 0.8361 (tp30) REVERT: A 345 THR cc_start: 0.8998 (m) cc_final: 0.8762 (p) REVERT: A 391 ASN cc_start: 0.9109 (t0) cc_final: 0.8610 (t0) REVERT: A 479 LEU cc_start: 0.8447 (tp) cc_final: 0.8232 (tp) REVERT: B 172 LYS cc_start: 0.9013 (mttt) cc_final: 0.8385 (tmtt) REVERT: B 226 LEU cc_start: 0.9101 (mt) cc_final: 0.8760 (tp) REVERT: B 265 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8214 (mmm) REVERT: B 402 THR cc_start: 0.9137 (m) cc_final: 0.8871 (p) REVERT: B 515 MET cc_start: 0.9274 (mmm) cc_final: 0.8972 (mmt) REVERT: C 55 GLU cc_start: 0.8375 (tp30) cc_final: 0.8016 (tp30) REVERT: E 55 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8100 (tp30) REVERT: E 79 GLN cc_start: 0.8893 (mm110) cc_final: 0.8497 (mm-40) REVERT: E 82 ASP cc_start: 0.8190 (m-30) cc_final: 0.7695 (m-30) REVERT: F 55 ASP cc_start: 0.8622 (p0) cc_final: 0.8263 (p0) outliers start: 27 outliers final: 11 residues processed: 151 average time/residue: 0.0841 time to fit residues: 20.0963 Evaluate side-chains 126 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 55 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.086108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.064008 restraints weight = 34564.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.066294 restraints weight = 16860.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.067761 restraints weight = 10545.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068645 restraints weight = 7697.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069305 restraints weight = 6276.663| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12686 Z= 0.173 Angle : 0.646 11.766 17198 Z= 0.319 Chirality : 0.042 0.199 1954 Planarity : 0.004 0.051 2141 Dihedral : 5.579 59.055 1717 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.93 % Allowed : 11.56 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.22), residues: 1558 helix: 1.29 (0.21), residues: 654 sheet: -0.53 (0.31), residues: 270 loop : -1.44 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.016 0.001 TYR A 336 PHE 0.019 0.001 PHE A 545 TRP 0.007 0.001 TRP B 379 HIS 0.005 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (12677) covalent geometry : angle 0.64465 / 0.32 (17178) SS BOND : bond 0.00514 / 0.36 ( 7) SS BOND : angle 1.06057 / 0.65 ( 14) hydrogen bonds : bond 0.03461 / 2.29 ( 539) hydrogen bonds : angle 4.30379 / 2.98 ( 1587) link_NAG-ASN : bond 0.00269 / 0.14 ( 2) link_NAG-ASN : angle 2.02891 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8380 (mmm) cc_final: 0.8090 (mmm) REVERT: A 172 LYS cc_start: 0.9038 (mttt) cc_final: 0.8531 (tptm) REVERT: A 182 PHE cc_start: 0.8301 (m-80) cc_final: 0.7482 (t80) REVERT: A 201 ILE cc_start: 0.9461 (mm) cc_final: 0.9219 (mt) REVERT: A 266 PHE cc_start: 0.6886 (t80) cc_final: 0.6492 (t80) REVERT: A 274 LEU cc_start: 0.8572 (tp) cc_final: 0.8347 (pp) REVERT: A 344 GLU cc_start: 0.8931 (tp30) cc_final: 0.8198 (tp30) REVERT: A 345 THR cc_start: 0.9003 (m) cc_final: 0.8722 (p) REVERT: A 391 ASN cc_start: 0.9097 (t0) cc_final: 0.8593 (t0) REVERT: B 172 LYS cc_start: 0.9063 (mttt) cc_final: 0.8403 (tmtt) REVERT: B 226 LEU cc_start: 0.9116 (mt) cc_final: 0.8791 (tp) REVERT: B 265 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8173 (mmm) REVERT: B 402 THR cc_start: 0.9157 (m) cc_final: 0.8887 (p) REVERT: B 515 MET cc_start: 0.9286 (mmm) cc_final: 0.9033 (mmt) REVERT: C 55 GLU cc_start: 0.8405 (tp30) cc_final: 0.8028 (tp30) REVERT: E 55 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8097 (tp30) REVERT: E 79 GLN cc_start: 0.8907 (mm110) cc_final: 0.8469 (mm-40) REVERT: E 82 ASP cc_start: 0.8207 (m-30) cc_final: 0.7736 (m-30) REVERT: F 55 ASP cc_start: 0.8603 (p0) cc_final: 0.8299 (p0) outliers start: 26 outliers final: 13 residues processed: 136 average time/residue: 0.0818 time to fit residues: 17.8077 Evaluate side-chains 124 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 129 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 106 optimal weight: 0.4980 chunk 132 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.086993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.065114 restraints weight = 34085.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.067424 restraints weight = 16496.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.068903 restraints weight = 10220.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.069856 restraints weight = 7412.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.070321 restraints weight = 5986.226| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12686 Z= 0.128 Angle : 0.615 11.398 17198 Z= 0.302 Chirality : 0.041 0.203 1954 Planarity : 0.004 0.050 2141 Dihedral : 5.454 59.218 1717 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.30 % Allowed : 11.63 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.22), residues: 1558 helix: 1.50 (0.21), residues: 654 sheet: -0.43 (0.31), residues: 280 loop : -1.42 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.019 0.001 TYR A 336 PHE 0.019 0.001 PHE B 545 TRP 0.007 0.001 TRP F 35 HIS 0.004 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (12677) covalent geometry : angle 0.61379 / 0.30 (17178) SS BOND : bond 0.00420 / 0.29 ( 7) SS BOND : angle 0.88431 / 0.53 ( 14) hydrogen bonds : bond 0.03218 / 2.13 ( 539) hydrogen bonds : angle 4.12568 / 2.86 ( 1587) link_NAG-ASN : bond 0.00130 / 0.06 ( 2) link_NAG-ASN : angle 2.03394 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8461 (mmm) cc_final: 0.8175 (mmm) REVERT: A 172 LYS cc_start: 0.9040 (mttt) cc_final: 0.8547 (tptm) REVERT: A 182 PHE cc_start: 0.8339 (m-80) cc_final: 0.7468 (t80) REVERT: A 201 ILE cc_start: 0.9448 (mm) cc_final: 0.9216 (mt) REVERT: A 266 PHE cc_start: 0.6764 (t80) cc_final: 0.6422 (t80) REVERT: A 274 LEU cc_start: 0.8587 (tp) cc_final: 0.8332 (pp) REVERT: A 334 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8788 (mm-30) REVERT: A 344 GLU cc_start: 0.8882 (tp30) cc_final: 0.8208 (tp30) REVERT: A 345 THR cc_start: 0.9007 (m) cc_final: 0.8725 (p) REVERT: A 391 ASN cc_start: 0.9032 (t0) cc_final: 0.8498 (t0) REVERT: B 164 VAL cc_start: 0.9350 (t) cc_final: 0.9140 (p) REVERT: B 172 LYS cc_start: 0.9041 (mttt) cc_final: 0.8441 (tmtt) REVERT: B 226 LEU cc_start: 0.9119 (mt) cc_final: 0.8767 (tp) REVERT: B 265 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8145 (mmm) REVERT: B 402 THR cc_start: 0.9140 (m) cc_final: 0.8917 (p) REVERT: B 437 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8065 (mm-40) REVERT: B 515 MET cc_start: 0.9264 (mmm) cc_final: 0.8975 (mmt) REVERT: C 55 GLU cc_start: 0.8394 (tp30) cc_final: 0.8003 (tp30) REVERT: E 79 GLN cc_start: 0.8886 (mm110) cc_final: 0.8548 (mm-40) REVERT: F 55 ASP cc_start: 0.8581 (p0) cc_final: 0.8283 (p0) outliers start: 31 outliers final: 15 residues processed: 145 average time/residue: 0.0797 time to fit residues: 18.7044 Evaluate side-chains 132 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 151 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN A 244 GLN B 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.086285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064631 restraints weight = 34218.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.066897 restraints weight = 16556.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068340 restraints weight = 10307.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.069300 restraints weight = 7506.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.069890 restraints weight = 6087.360| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12686 Z= 0.202 Angle : 0.654 12.041 17198 Z= 0.324 Chirality : 0.043 0.228 1954 Planarity : 0.004 0.051 2141 Dihedral : 5.495 57.996 1717 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.63 % Allowed : 12.67 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.22), residues: 1558 helix: 1.55 (0.21), residues: 654 sheet: -0.38 (0.32), residues: 270 loop : -1.38 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.013 0.001 TYR A 336 PHE 0.017 0.001 PHE F 79 TRP 0.006 0.001 TRP C 92 HIS 0.004 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (12677) covalent geometry : angle 0.65265 / 0.32 (17178) SS BOND : bond 0.00544 / 0.39 ( 7) SS BOND : angle 1.03018 / 0.63 ( 14) hydrogen bonds : bond 0.03328 / 2.21 ( 539) hydrogen bonds : angle 4.21782 / 2.93 ( 1587) link_NAG-ASN : bond 0.00346 / 0.17 ( 2) link_NAG-ASN : angle 2.10098 / 1.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8540 (mmm) cc_final: 0.8248 (mmm) REVERT: A 172 LYS cc_start: 0.8995 (mttt) cc_final: 0.8549 (tptm) REVERT: A 182 PHE cc_start: 0.8254 (m-80) cc_final: 0.7486 (t80) REVERT: A 266 PHE cc_start: 0.6881 (t80) cc_final: 0.6519 (t80) REVERT: A 274 LEU cc_start: 0.8644 (tp) cc_final: 0.8369 (pp) REVERT: A 334 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8751 (mm-30) REVERT: A 344 GLU cc_start: 0.8936 (tp30) cc_final: 0.8251 (tp30) REVERT: A 345 THR cc_start: 0.8944 (m) cc_final: 0.8685 (p) REVERT: A 391 ASN cc_start: 0.9004 (t0) cc_final: 0.8461 (t0) REVERT: B 172 LYS cc_start: 0.9052 (mttt) cc_final: 0.8445 (tmtt) REVERT: B 226 LEU cc_start: 0.9089 (mt) cc_final: 0.8775 (tp) REVERT: B 402 THR cc_start: 0.9123 (m) cc_final: 0.8882 (p) REVERT: B 515 MET cc_start: 0.9227 (mmm) cc_final: 0.8900 (mmt) REVERT: C 55 GLU cc_start: 0.8319 (tp30) cc_final: 0.7988 (tp30) REVERT: E 79 GLN cc_start: 0.8816 (mm110) cc_final: 0.8432 (mm-40) REVERT: F 55 ASP cc_start: 0.8417 (p0) cc_final: 0.8123 (p0) outliers start: 22 outliers final: 17 residues processed: 128 average time/residue: 0.0832 time to fit residues: 16.9541 Evaluate side-chains 126 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 103 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.087473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.065667 restraints weight = 34273.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.067983 restraints weight = 16370.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.069452 restraints weight = 10134.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070409 restraints weight = 7369.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071006 restraints weight = 5972.796| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12686 Z= 0.129 Angle : 0.622 11.626 17198 Z= 0.306 Chirality : 0.041 0.238 1954 Planarity : 0.004 0.050 2141 Dihedral : 5.430 59.939 1717 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.78 % Allowed : 12.52 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.22), residues: 1558 helix: 1.65 (0.21), residues: 654 sheet: -0.29 (0.32), residues: 270 loop : -1.31 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.012 0.001 TYR F 51 PHE 0.017 0.001 PHE B 545 TRP 0.007 0.001 TRP F 35 HIS 0.007 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (12677) covalent geometry : angle 0.62024 / 0.31 (17178) SS BOND : bond 0.00425 / 0.30 ( 7) SS BOND : angle 0.87585 / 0.52 ( 14) hydrogen bonds : bond 0.03134 / 2.07 ( 539) hydrogen bonds : angle 4.06182 / 2.83 ( 1587) link_NAG-ASN : bond 0.00123 / 0.06 ( 2) link_NAG-ASN : angle 2.05365 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.9004 (mttt) cc_final: 0.8553 (tptm) REVERT: A 182 PHE cc_start: 0.8289 (m-80) cc_final: 0.7526 (t80) REVERT: A 201 ILE cc_start: 0.9448 (mm) cc_final: 0.9231 (mt) REVERT: A 266 PHE cc_start: 0.6664 (t80) cc_final: 0.6350 (t80) REVERT: A 274 LEU cc_start: 0.8601 (tp) cc_final: 0.8322 (pp) REVERT: A 334 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8728 (mm-30) REVERT: A 344 GLU cc_start: 0.8927 (tp30) cc_final: 0.8238 (tp30) REVERT: A 345 THR cc_start: 0.9020 (m) cc_final: 0.8740 (p) REVERT: A 391 ASN cc_start: 0.8951 (t0) cc_final: 0.8412 (t0) REVERT: B 172 LYS cc_start: 0.9053 (mttt) cc_final: 0.8379 (tmtt) REVERT: B 226 LEU cc_start: 0.9082 (mt) cc_final: 0.8839 (tp) REVERT: B 348 GLU cc_start: 0.8502 (tp30) cc_final: 0.8281 (tp30) REVERT: B 402 THR cc_start: 0.9146 (m) cc_final: 0.8910 (p) REVERT: B 437 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8059 (mm-40) REVERT: C 55 GLU cc_start: 0.8284 (tp30) cc_final: 0.7969 (tp30) REVERT: F 55 ASP cc_start: 0.8396 (p0) cc_final: 0.8083 (p0) outliers start: 24 outliers final: 17 residues processed: 143 average time/residue: 0.0812 time to fit residues: 18.7032 Evaluate side-chains 134 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 90 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 133 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.086250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.064419 restraints weight = 34615.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.066693 restraints weight = 16689.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068153 restraints weight = 10410.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.069102 restraints weight = 7601.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.069727 restraints weight = 6170.665| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12686 Z= 0.201 Angle : 0.674 12.060 17198 Z= 0.333 Chirality : 0.043 0.255 1954 Planarity : 0.004 0.051 2141 Dihedral : 5.484 56.769 1717 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.70 % Allowed : 13.33 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.22), residues: 1558 helix: 1.64 (0.21), residues: 656 sheet: -0.29 (0.32), residues: 280 loop : -1.29 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.013 0.002 TYR E 86 PHE 0.017 0.001 PHE F 79 TRP 0.007 0.001 TRP F 37 HIS 0.008 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (12677) covalent geometry : angle 0.67273 / 0.33 (17178) SS BOND : bond 0.00562 / 0.40 ( 7) SS BOND : angle 1.09181 / 0.66 ( 14) hydrogen bonds : bond 0.03291 / 2.19 ( 539) hydrogen bonds : angle 4.18256 / 2.91 ( 1587) link_NAG-ASN : bond 0.00343 / 0.17 ( 2) link_NAG-ASN : angle 2.15080 / 1.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.489 Fit side-chains REVERT: A 172 LYS cc_start: 0.8995 (mttt) cc_final: 0.8545 (tptm) REVERT: A 182 PHE cc_start: 0.8294 (m-80) cc_final: 0.7589 (t80) REVERT: A 266 PHE cc_start: 0.6693 (t80) cc_final: 0.6377 (t80) REVERT: A 334 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8718 (mm-30) REVERT: A 391 ASN cc_start: 0.9003 (t0) cc_final: 0.8462 (t0) REVERT: B 172 LYS cc_start: 0.9059 (mttt) cc_final: 0.8418 (tmtt) REVERT: B 226 LEU cc_start: 0.9114 (mt) cc_final: 0.8840 (tp) REVERT: B 348 GLU cc_start: 0.8473 (tp30) cc_final: 0.8242 (tp30) REVERT: B 402 THR cc_start: 0.9178 (m) cc_final: 0.8936 (p) REVERT: C 55 GLU cc_start: 0.8358 (tp30) cc_final: 0.7963 (tp30) REVERT: E 79 GLN cc_start: 0.8831 (mm110) cc_final: 0.8626 (mm-40) REVERT: F 55 ASP cc_start: 0.8431 (p0) cc_final: 0.8165 (p0) outliers start: 23 outliers final: 19 residues processed: 132 average time/residue: 0.0919 time to fit residues: 19.1605 Evaluate side-chains 126 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 23 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN D 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.086951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.065341 restraints weight = 34436.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.067638 restraints weight = 16395.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.069103 restraints weight = 10149.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070063 restraints weight = 7361.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.070606 restraints weight = 5953.305| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12686 Z= 0.147 Angle : 0.652 11.923 17198 Z= 0.319 Chirality : 0.042 0.254 1954 Planarity : 0.004 0.051 2141 Dihedral : 5.447 57.259 1717 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.26 % Allowed : 13.70 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.22), residues: 1558 helix: 1.72 (0.21), residues: 654 sheet: -0.20 (0.32), residues: 280 loop : -1.23 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 230 TYR 0.012 0.001 TYR F 51 PHE 0.016 0.001 PHE B 545 TRP 0.009 0.001 TRP B 624 HIS 0.008 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (12677) covalent geometry : angle 0.65046 / 0.32 (17178) SS BOND : bond 0.00434 / 0.31 ( 7) SS BOND : angle 0.89838 / 0.54 ( 14) hydrogen bonds : bond 0.03107 / 2.06 ( 539) hydrogen bonds : angle 4.08582 / 2.85 ( 1587) link_NAG-ASN : bond 0.00192 / 0.10 ( 2) link_NAG-ASN : angle 2.16818 / 1.38 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.454 Fit side-chains REVERT: A 172 LYS cc_start: 0.8975 (mttt) cc_final: 0.8536 (tptm) REVERT: A 182 PHE cc_start: 0.8318 (m-80) cc_final: 0.7572 (t80) REVERT: A 266 PHE cc_start: 0.6598 (t80) cc_final: 0.6270 (t80) REVERT: A 334 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8716 (mm-30) REVERT: A 391 ASN cc_start: 0.8990 (t0) cc_final: 0.8478 (t0) REVERT: B 172 LYS cc_start: 0.9072 (mttt) cc_final: 0.8427 (tmtt) REVERT: B 226 LEU cc_start: 0.9115 (mt) cc_final: 0.8779 (tp) REVERT: B 402 THR cc_start: 0.9156 (m) cc_final: 0.8954 (p) REVERT: B 437 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7821 (mm-40) REVERT: C 55 GLU cc_start: 0.8315 (tp30) cc_final: 0.7932 (tp30) REVERT: E 79 GLN cc_start: 0.8818 (mm110) cc_final: 0.8465 (mm-40) REVERT: F 55 ASP cc_start: 0.8400 (p0) cc_final: 0.8107 (p0) outliers start: 17 outliers final: 17 residues processed: 128 average time/residue: 0.0832 time to fit residues: 17.0832 Evaluate side-chains 127 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.087141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.065402 restraints weight = 34348.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.067709 restraints weight = 16462.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069178 restraints weight = 10199.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.070137 restraints weight = 7414.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.070716 restraints weight = 6010.314| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12686 Z= 0.144 Angle : 0.645 11.875 17198 Z= 0.317 Chirality : 0.042 0.258 1954 Planarity : 0.004 0.051 2141 Dihedral : 5.383 55.343 1717 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.56 % Allowed : 13.48 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.22), residues: 1558 helix: 1.72 (0.21), residues: 654 sheet: -0.13 (0.32), residues: 280 loop : -1.20 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 263 TYR 0.012 0.001 TYR F 51 PHE 0.019 0.001 PHE B 545 TRP 0.008 0.001 TRP B 624 HIS 0.008 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (12677) covalent geometry : angle 0.64346 / 0.32 (17178) SS BOND : bond 0.00445 / 0.32 ( 7) SS BOND : angle 0.92848 / 0.55 ( 14) hydrogen bonds : bond 0.03087 / 2.05 ( 539) hydrogen bonds : angle 4.06867 / 2.84 ( 1587) link_NAG-ASN : bond 0.00150 / 0.08 ( 2) link_NAG-ASN : angle 2.14208 / 1.36 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1702.46 seconds wall clock time: 30 minutes 16.74 seconds (1816.74 seconds total)