Starting phenix.real_space_refine on Sat Aug 23 14:33:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6feq_4246/08_2025/6feq_4246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6feq_4246/08_2025/6feq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6feq_4246/08_2025/6feq_4246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6feq_4246/08_2025/6feq_4246.map" model { file = "/net/cci-nas-00/data/ceres_data/6feq_4246/08_2025/6feq_4246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6feq_4246/08_2025/6feq_4246.cif" } 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-2.0-5787/lib/python3.9/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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.31, per 1000 atoms: 0.27 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: 0.98 Conformation dependent library (CDL) restraints added in 515.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.31 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: 1.37 Time building geometry restraints manager: 1.40 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 - 17.75: 7176 17.75 - 35.51: 213 35.51 - 53.26: 57 53.26 - 71.01: 11 71.01 - 88.77: 15 Dihedral angle restraints: 7472 sinusoidal: 2936 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 7469 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: 1.480 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.900 Find NCS groups from input model: 0.140 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 11.017 88.766 4555 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 aren 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 covalent geometry : bond 0.01077 (12677) covalent geometry : angle 1.04691 (17178) SS BOND : bond 0.01263 ( 7) SS BOND : angle 2.07149 ( 14) hydrogen bonds : bond 0.28892 ( 539) hydrogen bonds : angle 9.28319 ( 1587) link_NAG-ASN : bond 0.01048 ( 2) link_NAG-ASN : angle 5.22645 ( 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 : 0.325 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: 0.1068 time to fit residues: 36.9512 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 : 0.335 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.088481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.066276 restraints weight = 34287.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.068609 restraints weight = 16793.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.070106 restraints weight = 10555.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.071055 restraints weight = 7744.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.071675 restraints weight = 6291.512| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12686 Z= 0.139 Angle : 0.688 9.530 17198 Z= 0.346 Chirality : 0.043 0.196 1954 Planarity : 0.005 0.052 2141 Dihedral : 8.434 86.308 1769 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.41 % Allowed : 8.15 % Favored : 90.44 % 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 aren not related in a simple way. whole: -1.93 (0.20), residues: 1558 helix: -0.55 (0.18), residues: 644 sheet: -1.24 (0.30), residues: 270 loop : -1.96 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 246 TYR 0.017 0.001 TYR B 336 PHE 0.016 0.002 PHE F 79 TRP 0.010 0.001 TRP F 109 HIS 0.005 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00299 (12677) covalent geometry : angle 0.68619 (17178) SS BOND : bond 0.00436 ( 7) SS BOND : angle 0.90367 ( 14) hydrogen bonds : bond 0.04906 ( 539) hydrogen bonds : angle 5.14880 ( 1587) link_NAG-ASN : bond 0.00118 ( 2) link_NAG-ASN : angle 2.58112 ( 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 197 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.9050 (mttt) cc_final: 0.8490 (tptm) REVERT: A 182 PHE cc_start: 0.8167 (m-80) cc_final: 0.7504 (t80) REVERT: A 266 PHE cc_start: 0.7191 (t80) cc_final: 0.6872 (t80) REVERT: A 334 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8775 (mm-30) REVERT: A 344 GLU cc_start: 0.8996 (tp30) cc_final: 0.8407 (tp30) REVERT: A 345 THR cc_start: 0.8982 (m) cc_final: 0.8777 (p) REVERT: A 391 ASN cc_start: 0.9132 (t0) cc_final: 0.8728 (t0) REVERT: B 164 VAL cc_start: 0.9443 (t) cc_final: 0.9207 (p) REVERT: B 172 LYS cc_start: 0.8930 (mttt) cc_final: 0.8381 (tmtt) REVERT: B 226 LEU cc_start: 0.9042 (mt) cc_final: 0.8717 (tp) REVERT: B 351 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6971 (pm20) REVERT: B 393 GLN cc_start: 0.5867 (mm-40) cc_final: 0.5529 (tp40) REVERT: B 402 THR cc_start: 0.9173 (m) cc_final: 0.8899 (p) REVERT: B 515 MET cc_start: 0.9247 (mmm) cc_final: 0.8955 (mmt) REVERT: C 24 LYS cc_start: 0.8092 (tptp) cc_final: 0.7840 (tppt) REVERT: C 55 GLU cc_start: 0.8394 (tp30) cc_final: 0.8081 (tp30) REVERT: C 79 GLN cc_start: 0.8307 (mm110) cc_final: 0.8091 (mm110) REVERT: E 79 GLN cc_start: 0.8965 (mm110) cc_final: 0.8576 (mm110) REVERT: E 82 ASP cc_start: 0.8227 (m-30) cc_final: 0.7833 (m-30) REVERT: F 55 ASP cc_start: 0.8582 (p0) cc_final: 0.8124 (p0) outliers start: 19 outliers final: 7 residues processed: 193 average time/residue: 0.0905 time to fit residues: 26.0255 Evaluate side-chains 128 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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: 0.4980 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.087476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.065299 restraints weight = 34599.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.067597 restraints weight = 16941.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.069098 restraints weight = 10627.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.070072 restraints weight = 7750.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070683 restraints weight = 6279.717| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12686 Z= 0.137 Angle : 0.644 10.490 17198 Z= 0.322 Chirality : 0.042 0.181 1954 Planarity : 0.004 0.053 2141 Dihedral : 7.868 85.337 1767 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.15 % Allowed : 10.07 % Favored : 87.78 % 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 aren not related in a simple way. whole: -0.98 (0.21), residues: 1558 helix: 0.50 (0.20), residues: 648 sheet: -0.83 (0.31), residues: 262 loop : -1.73 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 163 TYR 0.017 0.001 TYR A 336 PHE 0.015 0.001 PHE F 79 TRP 0.009 0.001 TRP E 92 HIS 0.004 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00312 (12677) covalent geometry : angle 0.64233 (17178) SS BOND : bond 0.00533 ( 7) SS BOND : angle 1.10020 ( 14) hydrogen bonds : bond 0.03946 ( 539) hydrogen bonds : angle 4.63440 ( 1587) link_NAG-ASN : bond 0.00158 ( 2) link_NAG-ASN : angle 2.24492 ( 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 167 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8308 (mmm) cc_final: 0.8013 (mmm) REVERT: A 172 LYS cc_start: 0.9033 (mttt) cc_final: 0.8503 (tptm) REVERT: A 182 PHE cc_start: 0.8253 (m-80) cc_final: 0.7404 (t80) REVERT: A 265 MET cc_start: 0.7764 (mtp) cc_final: 0.7527 (mtt) REVERT: A 266 PHE cc_start: 0.7256 (t80) cc_final: 0.6968 (t80) REVERT: A 274 LEU cc_start: 0.8490 (tp) cc_final: 0.8250 (pp) REVERT: A 334 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8799 (mm-30) REVERT: A 344 GLU cc_start: 0.8957 (tp30) cc_final: 0.8364 (tp30) REVERT: A 345 THR cc_start: 0.9002 (m) cc_final: 0.8776 (p) REVERT: A 391 ASN cc_start: 0.9114 (t0) cc_final: 0.8659 (t0) REVERT: B 172 LYS cc_start: 0.8980 (mttt) cc_final: 0.8411 (tmtt) REVERT: B 226 LEU cc_start: 0.9102 (mt) cc_final: 0.8743 (tp) REVERT: B 393 GLN cc_start: 0.6122 (mm-40) cc_final: 0.5775 (tp40) REVERT: B 402 THR cc_start: 0.9167 (m) cc_final: 0.8885 (p) REVERT: B 515 MET cc_start: 0.9278 (mmm) cc_final: 0.8995 (mmt) REVERT: C 24 LYS cc_start: 0.8067 (tptp) cc_final: 0.7848 (ttmm) REVERT: C 55 GLU cc_start: 0.8418 (tp30) cc_final: 0.8075 (tp30) REVERT: E 79 GLN cc_start: 0.8953 (mm110) cc_final: 0.8547 (mm-40) REVERT: E 82 ASP cc_start: 0.8235 (m-30) cc_final: 0.7795 (m-30) REVERT: F 55 ASP cc_start: 0.8610 (p0) cc_final: 0.8190 (p0) outliers start: 29 outliers final: 13 residues processed: 161 average time/residue: 0.0811 time to fit residues: 19.8409 Evaluate side-chains 133 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 295 LEU 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 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: 10.0000 chunk 140 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 617 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 425 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 = 0.3481 r_free = 0.3481 target = 0.085881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.063752 restraints weight = 34615.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.066014 restraints weight = 16991.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.067454 restraints weight = 10680.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068372 restraints weight = 7818.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.069004 restraints weight = 6384.287| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12686 Z= 0.191 Angle : 0.657 11.412 17198 Z= 0.328 Chirality : 0.042 0.188 1954 Planarity : 0.004 0.050 2141 Dihedral : 7.852 88.388 1767 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.70 % Allowed : 11.56 % Favored : 86.74 % 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 aren not related in a simple way. whole: -0.46 (0.22), residues: 1558 helix: 1.06 (0.21), residues: 650 sheet: -0.75 (0.31), residues: 270 loop : -1.53 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 246 TYR 0.015 0.002 TYR A 336 PHE 0.018 0.002 PHE F 79 TRP 0.009 0.001 TRP A 564 HIS 0.004 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00440 (12677) covalent geometry : angle 0.65482 (17178) SS BOND : bond 0.00536 ( 7) SS BOND : angle 1.14265 ( 14) hydrogen bonds : bond 0.03683 ( 539) hydrogen bonds : angle 4.47625 ( 1587) link_NAG-ASN : bond 0.00387 ( 2) link_NAG-ASN : angle 2.21393 ( 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 146 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8359 (mmm) cc_final: 0.8067 (mmm) REVERT: A 172 LYS cc_start: 0.9033 (mttt) cc_final: 0.8529 (tptm) REVERT: A 182 PHE cc_start: 0.8229 (m-80) cc_final: 0.7414 (t80) REVERT: A 201 ILE cc_start: 0.9450 (mm) cc_final: 0.9219 (mt) REVERT: A 259 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8557 (tp) REVERT: A 344 GLU cc_start: 0.9015 (tp30) cc_final: 0.8376 (tp30) REVERT: A 345 THR cc_start: 0.8986 (m) cc_final: 0.8747 (p) REVERT: A 391 ASN cc_start: 0.9120 (t0) cc_final: 0.8618 (t0) REVERT: B 172 LYS cc_start: 0.9024 (mttt) cc_final: 0.8443 (tmtt) REVERT: B 226 LEU cc_start: 0.9120 (mt) cc_final: 0.8770 (tp) REVERT: B 265 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8226 (mmm) REVERT: B 515 MET cc_start: 0.9288 (mmm) cc_final: 0.9011 (mmt) REVERT: C 55 GLU cc_start: 0.8423 (tp30) cc_final: 0.8044 (tp30) REVERT: E 55 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8103 (tp30) REVERT: E 79 GLN cc_start: 0.8921 (mm110) cc_final: 0.8506 (mm-40) REVERT: E 82 ASP cc_start: 0.8226 (m-30) cc_final: 0.7781 (m-30) REVERT: F 55 ASP cc_start: 0.8618 (p0) cc_final: 0.8317 (p0) outliers start: 23 outliers final: 12 residues processed: 140 average time/residue: 0.0753 time to fit residues: 16.5000 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 : 0.295 ------------------------------------------------------------------------------- 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 259 LEU Chi-restraints excluded: chain A residue 348 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 55 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 139 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS A 244 GLN A 424 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.086777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.064206 restraints weight = 34533.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.066532 restraints weight = 16876.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.068034 restraints weight = 10597.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069003 restraints weight = 7757.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.069620 restraints weight = 6311.170| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12686 Z= 0.145 Angle : 0.619 11.286 17198 Z= 0.309 Chirality : 0.042 0.204 1954 Planarity : 0.004 0.050 2141 Dihedral : 7.732 89.955 1767 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.15 % Allowed : 11.78 % 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 aren not related in a simple way. whole: -0.23 (0.22), residues: 1558 helix: 1.28 (0.21), residues: 654 sheet: -0.55 (0.31), residues: 270 loop : -1.49 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 263 TYR 0.015 0.001 TYR A 336 PHE 0.016 0.001 PHE A 545 TRP 0.007 0.001 TRP A 624 HIS 0.010 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00330 (12677) covalent geometry : angle 0.61734 (17178) SS BOND : bond 0.00461 ( 7) SS BOND : angle 0.96936 ( 14) hydrogen bonds : bond 0.03399 ( 539) hydrogen bonds : angle 4.30335 ( 1587) link_NAG-ASN : bond 0.00206 ( 2) link_NAG-ASN : angle 2.16428 ( 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 152 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8292 (mmm) cc_final: 0.7993 (mmm) REVERT: A 172 LYS cc_start: 0.9050 (mttt) cc_final: 0.8533 (tptm) REVERT: A 182 PHE cc_start: 0.8294 (m-80) cc_final: 0.7491 (t80) REVERT: A 201 ILE cc_start: 0.9463 (mm) cc_final: 0.9225 (mt) REVERT: A 266 PHE cc_start: 0.6862 (t80) cc_final: 0.6482 (t80) REVERT: A 344 GLU cc_start: 0.8951 (tp30) cc_final: 0.8307 (tp30) REVERT: A 345 THR cc_start: 0.8999 (m) cc_final: 0.8762 (p) REVERT: A 391 ASN cc_start: 0.9104 (t0) cc_final: 0.8589 (t0) REVERT: B 71 MET cc_start: 0.8306 (mtm) cc_final: 0.7963 (mtm) REVERT: B 172 LYS cc_start: 0.9045 (mttt) cc_final: 0.8442 (tmtt) REVERT: B 226 LEU cc_start: 0.9096 (mt) cc_final: 0.8788 (tp) REVERT: B 336 TYR cc_start: 0.8916 (t80) cc_final: 0.8304 (t80) REVERT: B 402 THR cc_start: 0.9155 (m) cc_final: 0.8893 (p) REVERT: B 437 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7883 (mm-40) REVERT: B 515 MET cc_start: 0.9279 (mmm) cc_final: 0.8977 (mmt) REVERT: C 55 GLU cc_start: 0.8408 (tp30) cc_final: 0.8025 (tp30) REVERT: E 11 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7239 (m-80) REVERT: E 55 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8082 (tp30) REVERT: E 79 GLN cc_start: 0.8885 (mm110) cc_final: 0.8471 (mm-40) REVERT: E 82 ASP cc_start: 0.8184 (m-30) cc_final: 0.7699 (m-30) REVERT: F 55 ASP cc_start: 0.8610 (p0) cc_final: 0.8303 (p0) outliers start: 29 outliers final: 15 residues processed: 145 average time/residue: 0.0671 time to fit residues: 15.6468 Evaluate side-chains 129 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 295 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 C residue 97 THR Chi-restraints excluded: chain E residue 11 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.086066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.064277 restraints weight = 34476.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.066522 restraints weight = 16650.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.067965 restraints weight = 10393.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.068904 restraints weight = 7584.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.069442 restraints weight = 6158.556| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12686 Z= 0.201 Angle : 0.655 12.069 17198 Z= 0.325 Chirality : 0.043 0.206 1954 Planarity : 0.004 0.051 2141 Dihedral : 7.764 87.570 1767 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.30 % Allowed : 12.07 % Favored : 85.63 % 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 aren not related in a simple way. whole: -0.08 (0.22), residues: 1558 helix: 1.42 (0.21), residues: 654 sheet: -0.47 (0.31), residues: 270 loop : -1.45 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.018 0.002 TYR A 336 PHE 0.018 0.001 PHE F 79 TRP 0.007 0.001 TRP C 92 HIS 0.003 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00463 (12677) covalent geometry : angle 0.65317 (17178) SS BOND : bond 0.00522 ( 7) SS BOND : angle 1.06429 ( 14) hydrogen bonds : bond 0.03426 ( 539) hydrogen bonds : angle 4.30872 ( 1587) link_NAG-ASN : bond 0.00394 ( 2) link_NAG-ASN : angle 2.18803 ( 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 146 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8478 (mmm) cc_final: 0.8178 (mmm) REVERT: A 172 LYS cc_start: 0.9016 (mttt) cc_final: 0.8550 (tptm) REVERT: A 182 PHE cc_start: 0.8250 (m-80) cc_final: 0.7473 (t80) REVERT: A 266 PHE cc_start: 0.6914 (t80) cc_final: 0.6547 (t80) REVERT: A 334 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8758 (mm-30) REVERT: A 344 GLU cc_start: 0.8903 (tp30) cc_final: 0.8221 (tp30) REVERT: A 345 THR cc_start: 0.8950 (m) cc_final: 0.8686 (p) REVERT: A 391 ASN cc_start: 0.9079 (t0) cc_final: 0.8587 (t0) REVERT: B 71 MET cc_start: 0.8325 (mtm) cc_final: 0.7937 (mtm) REVERT: B 172 LYS cc_start: 0.9055 (mttt) cc_final: 0.8447 (tmtt) REVERT: B 226 LEU cc_start: 0.9076 (mt) cc_final: 0.8782 (tp) REVERT: B 402 THR cc_start: 0.9146 (m) cc_final: 0.8893 (p) REVERT: B 437 GLN cc_start: 0.8416 (mm-40) cc_final: 0.7905 (mm-40) REVERT: B 515 MET cc_start: 0.9241 (mmm) cc_final: 0.8897 (mmt) REVERT: C 55 GLU cc_start: 0.8293 (tp30) cc_final: 0.7968 (tp30) REVERT: E 70 ASP cc_start: 0.8459 (m-30) cc_final: 0.8256 (m-30) REVERT: E 79 GLN cc_start: 0.8860 (mm110) cc_final: 0.8467 (mm-40) REVERT: E 82 ASP cc_start: 0.8194 (m-30) cc_final: 0.7736 (m-30) REVERT: F 55 ASP cc_start: 0.8443 (p0) cc_final: 0.8140 (p0) outliers start: 31 outliers final: 19 residues processed: 138 average time/residue: 0.0777 time to fit residues: 17.0972 Evaluate side-chains 132 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 HIS 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 153 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 540 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 151 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 153 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS A 244 GLN A 437 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.085272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.063799 restraints weight = 34347.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.066005 restraints weight = 16560.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.067423 restraints weight = 10302.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068356 restraints weight = 7501.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.068935 restraints weight = 6082.142| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12686 Z= 0.226 Angle : 0.672 12.367 17198 Z= 0.334 Chirality : 0.043 0.236 1954 Planarity : 0.004 0.051 2141 Dihedral : 7.754 85.600 1767 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.44 % Allowed : 12.44 % Favored : 85.11 % 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 aren not related in a simple way. whole: -0.00 (0.22), residues: 1558 helix: 1.50 (0.21), residues: 654 sheet: -0.44 (0.32), residues: 270 loop : -1.42 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.014 0.002 TYR C 91 PHE 0.019 0.002 PHE F 79 TRP 0.007 0.001 TRP C 92 HIS 0.005 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00518 (12677) covalent geometry : angle 0.67066 (17178) SS BOND : bond 0.00575 ( 7) SS BOND : angle 1.13176 ( 14) hydrogen bonds : bond 0.03464 ( 539) hydrogen bonds : angle 4.34257 ( 1587) link_NAG-ASN : bond 0.00474 ( 2) link_NAG-ASN : angle 2.25788 ( 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 146 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8519 (mmm) cc_final: 0.8209 (mmm) REVERT: A 172 LYS cc_start: 0.8992 (mttt) cc_final: 0.8557 (tptm) REVERT: A 182 PHE cc_start: 0.8231 (m-80) cc_final: 0.7467 (t80) REVERT: A 266 PHE cc_start: 0.6870 (t80) cc_final: 0.6547 (t80) REVERT: A 334 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8752 (mm-30) REVERT: A 391 ASN cc_start: 0.9060 (t0) cc_final: 0.8559 (t0) REVERT: A 437 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7947 (mt0) REVERT: B 71 MET cc_start: 0.8289 (mtm) cc_final: 0.7860 (mtm) REVERT: B 172 LYS cc_start: 0.9038 (mttt) cc_final: 0.8419 (tmtt) REVERT: B 226 LEU cc_start: 0.9075 (mt) cc_final: 0.8801 (tp) REVERT: B 402 THR cc_start: 0.9152 (m) cc_final: 0.8940 (p) REVERT: B 515 MET cc_start: 0.9236 (mmm) cc_final: 0.8902 (mmt) REVERT: C 55 GLU cc_start: 0.8342 (tp30) cc_final: 0.7979 (tp30) REVERT: E 70 ASP cc_start: 0.8425 (m-30) cc_final: 0.8202 (m-30) REVERT: E 79 GLN cc_start: 0.8870 (mm110) cc_final: 0.8566 (mm-40) REVERT: F 55 ASP cc_start: 0.8442 (p0) cc_final: 0.8161 (p0) outliers start: 33 outliers final: 21 residues processed: 137 average time/residue: 0.0742 time to fit residues: 16.1790 Evaluate side-chains 129 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 437 GLN 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 33 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: 0.9990 chunk 131 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 162 ASN B 393 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.087199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.065529 restraints weight = 34303.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.067820 restraints weight = 16403.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069284 restraints weight = 10153.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.070227 restraints weight = 7380.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.070781 restraints weight = 5980.013| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3677 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= 0.123 Angle : 0.635 11.918 17198 Z= 0.314 Chirality : 0.042 0.236 1954 Planarity : 0.003 0.050 2141 Dihedral : 7.481 88.089 1767 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.78 % Allowed : 13.04 % Favored : 85.19 % 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 aren not related in a simple way. whole: 0.15 (0.22), residues: 1558 helix: 1.60 (0.21), residues: 654 sheet: -0.32 (0.32), residues: 270 loop : -1.31 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 230 TYR 0.012 0.001 TYR A 336 PHE 0.020 0.001 PHE B 545 TRP 0.008 0.001 TRP F 35 HIS 0.016 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00283 (12677) covalent geometry : angle 0.63393 (17178) SS BOND : bond 0.00396 ( 7) SS BOND : angle 0.87814 ( 14) hydrogen bonds : bond 0.03228 ( 539) hydrogen bonds : angle 4.16577 ( 1587) link_NAG-ASN : bond 0.00083 ( 2) link_NAG-ASN : angle 2.17799 ( 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 144 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.297 Fit side-chains REVERT: A 172 LYS cc_start: 0.9013 (mttt) cc_final: 0.8552 (tptm) REVERT: A 182 PHE cc_start: 0.8313 (m-80) cc_final: 0.7555 (t80) REVERT: A 266 PHE cc_start: 0.6637 (t80) cc_final: 0.6354 (t80) REVERT: A 334 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8743 (mm-30) REVERT: A 391 ASN cc_start: 0.9047 (t0) cc_final: 0.8532 (t0) REVERT: B 172 LYS cc_start: 0.9064 (mttt) cc_final: 0.8422 (tmtt) REVERT: B 226 LEU cc_start: 0.9057 (mt) cc_final: 0.8773 (tp) REVERT: B 231 MET cc_start: 0.8814 (ptp) cc_final: 0.8540 (ptp) REVERT: B 402 THR cc_start: 0.9179 (m) cc_final: 0.8940 (p) REVERT: B 515 MET cc_start: 0.9240 (mmm) cc_final: 0.8878 (mmt) REVERT: C 55 GLU cc_start: 0.8332 (tp30) cc_final: 0.7990 (tp30) REVERT: E 55 GLU cc_start: 0.8274 (tp30) cc_final: 0.8021 (tp30) REVERT: E 79 GLN cc_start: 0.8852 (mm110) cc_final: 0.8415 (mm-40) REVERT: F 55 ASP cc_start: 0.8488 (p0) cc_final: 0.8204 (p0) outliers start: 24 outliers final: 19 residues processed: 137 average time/residue: 0.0673 time to fit residues: 14.8086 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 : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 155 HIS 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 565 LEU 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 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: 10.0000 chunk 122 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 HIS B 120 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.083777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.061731 restraints weight = 35110.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.063927 restraints weight = 17191.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.065326 restraints weight = 10806.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.066257 restraints weight = 7946.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.066840 restraints weight = 6475.751| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 12686 Z= 0.331 Angle : 0.778 13.188 17198 Z= 0.387 Chirality : 0.047 0.247 1954 Planarity : 0.004 0.051 2141 Dihedral : 7.835 86.623 1767 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.78 % Allowed : 13.11 % Favored : 85.11 % 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 aren not related in a simple way. whole: -0.19 (0.22), residues: 1558 helix: 1.25 (0.21), residues: 670 sheet: -0.47 (0.31), residues: 280 loop : -1.50 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 18 TYR 0.017 0.002 TYR E 86 PHE 0.024 0.002 PHE F 79 TRP 0.013 0.002 TRP F 37 HIS 0.009 0.002 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00757 (12677) covalent geometry : angle 0.77591 (17178) SS BOND : bond 0.00750 ( 7) SS BOND : angle 1.35595 ( 14) hydrogen bonds : bond 0.03842 ( 539) hydrogen bonds : angle 4.63155 ( 1587) link_NAG-ASN : bond 0.00714 ( 2) link_NAG-ASN : angle 2.35176 ( 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 130 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.9018 (mttt) cc_final: 0.8586 (tptm) REVERT: A 182 PHE cc_start: 0.8230 (m-80) cc_final: 0.7563 (t80) REVERT: A 266 PHE cc_start: 0.6804 (t80) cc_final: 0.6469 (t80) REVERT: A 334 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8767 (mm-30) REVERT: A 391 ASN cc_start: 0.9077 (t0) cc_final: 0.8570 (t0) REVERT: B 71 MET cc_start: 0.8327 (mtm) cc_final: 0.8038 (mtm) REVERT: B 226 LEU cc_start: 0.9090 (mt) cc_final: 0.8802 (tp) REVERT: B 391 ASN cc_start: 0.9058 (t0) cc_final: 0.8531 (m-40) REVERT: B 402 THR cc_start: 0.9168 (m) cc_final: 0.8940 (p) REVERT: B 515 MET cc_start: 0.9243 (mmm) cc_final: 0.8903 (mmt) REVERT: C 55 GLU cc_start: 0.8373 (tp30) cc_final: 0.7979 (tp30) REVERT: E 79 GLN cc_start: 0.8859 (mm110) cc_final: 0.8533 (mm-40) REVERT: E 82 ASP cc_start: 0.8178 (m-30) cc_final: 0.7793 (m-30) REVERT: F 55 ASP cc_start: 0.8419 (p0) cc_final: 0.8168 (p0) outliers start: 24 outliers final: 21 residues processed: 127 average time/residue: 0.0799 time to fit residues: 15.9073 Evaluate side-chains 121 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 155 HIS 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 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 29 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3504 r_free = 0.3504 target = 0.087107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.065709 restraints weight = 34615.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068007 restraints weight = 16386.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.069465 restraints weight = 10069.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070417 restraints weight = 7297.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.070993 restraints weight = 5903.926| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12686 Z= 0.113 Angle : 0.646 12.531 17198 Z= 0.321 Chirality : 0.042 0.259 1954 Planarity : 0.003 0.050 2141 Dihedral : 7.261 89.154 1767 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.19 % Allowed : 13.63 % Favored : 85.19 % 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 aren not related in a simple way. whole: 0.28 (0.22), residues: 1558 helix: 1.66 (0.21), residues: 654 sheet: -0.28 (0.32), residues: 278 loop : -1.18 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 263 TYR 0.013 0.001 TYR F 51 PHE 0.022 0.001 PHE B 545 TRP 0.012 0.001 TRP A 624 HIS 0.006 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00255 (12677) covalent geometry : angle 0.64493 (17178) SS BOND : bond 0.00318 ( 7) SS BOND : angle 0.74909 ( 14) hydrogen bonds : bond 0.03186 ( 539) hydrogen bonds : angle 4.17649 ( 1587) link_NAG-ASN : bond 0.00036 ( 2) link_NAG-ASN : angle 2.22836 ( 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 134 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.390 Fit side-chains REVERT: A 172 LYS cc_start: 0.8995 (mttt) cc_final: 0.8557 (tptm) REVERT: A 182 PHE cc_start: 0.8315 (m-80) cc_final: 0.7612 (t80) REVERT: A 266 PHE cc_start: 0.6581 (t80) cc_final: 0.6303 (t80) REVERT: A 334 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8730 (mm-30) REVERT: A 391 ASN cc_start: 0.9056 (t0) cc_final: 0.8536 (t0) REVERT: B 71 MET cc_start: 0.8301 (mtm) cc_final: 0.7852 (mtm) REVERT: B 172 LYS cc_start: 0.9078 (mttt) cc_final: 0.8375 (tmtt) REVERT: B 226 LEU cc_start: 0.9063 (mt) cc_final: 0.8773 (tp) REVERT: C 55 GLU cc_start: 0.8290 (tp30) cc_final: 0.7942 (tp30) REVERT: E 79 GLN cc_start: 0.8800 (mm110) cc_final: 0.8510 (mm-40) REVERT: E 82 ASP cc_start: 0.8032 (m-30) cc_final: 0.7724 (m-30) REVERT: F 55 ASP cc_start: 0.8475 (p0) cc_final: 0.8167 (p0) outliers start: 16 outliers final: 15 residues processed: 130 average time/residue: 0.0787 time to fit residues: 16.3844 Evaluate side-chains 126 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 155 HIS 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 153 THR 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 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=1.00 ------------------------------------------------------------------------------- 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: 3.9990 chunk 113 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 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 = 0.3451 r_free = 0.3451 target = 0.084281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.062322 restraints weight = 34934.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.064534 restraints weight = 17012.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.065947 restraints weight = 10684.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.066859 restraints weight = 7866.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.067391 restraints weight = 6436.969| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 12686 Z= 0.290 Angle : 0.756 13.131 17198 Z= 0.376 Chirality : 0.046 0.260 1954 Planarity : 0.004 0.051 2141 Dihedral : 7.510 83.829 1767 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.41 % Allowed : 13.85 % Favored : 84.74 % 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 aren not related in a simple way. whole: 0.10 (0.22), residues: 1558 helix: 1.49 (0.21), residues: 654 sheet: -0.37 (0.32), residues: 280 loop : -1.25 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 72 TYR 0.016 0.002 TYR A 413 PHE 0.020 0.002 PHE F 79 TRP 0.012 0.001 TRP F 37 HIS 0.010 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00662 (12677) covalent geometry : angle 0.75438 (17178) SS BOND : bond 0.00685 ( 7) SS BOND : angle 1.28246 ( 14) hydrogen bonds : bond 0.03674 ( 539) hydrogen bonds : angle 4.51680 ( 1587) link_NAG-ASN : bond 0.00544 ( 2) link_NAG-ASN : angle 2.28150 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1558.80 seconds wall clock time: 27 minutes 58.15 seconds (1678.15 seconds total)