Starting phenix.real_space_refine on Wed Jul 30 20:01:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6feq_4246/07_2025/6feq_4246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6feq_4246/07_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_4246/07_2025/6feq_4246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6feq_4246/07_2025/6feq_4246.map" model { file = "/net/cci-nas-00/data/ceres_data/6feq_4246/07_2025/6feq_4246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6feq_4246/07_2025/6feq_4246.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.96, per 1000 atoms: 0.64 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: 2.86 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.49 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: 4.07 Time building geometry restraints manager: 3.44 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 654 or resid 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: 1.180 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.850 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.030 0.003 TRP F 109 HIS 0.015 0.003 HIS B 583 PHE 0.030 0.003 PHE E 98 TYR 0.024 0.003 TYR F 51 ARG 0.009 0.001 ARG A 96 Details of bonding type rmsd link_NAG-ASN : bond 0.01048 ( 2) link_NAG-ASN : angle 5.22645 ( 6) hydrogen bonds : bond 0.28892 ( 539) hydrogen bonds : angle 9.28319 ( 1587) SS BOND : bond 0.01263 ( 7) SS BOND : angle 2.07149 ( 14) covalent geometry : bond 0.01077 (12677) covalent geometry : angle 1.04691 (17178) *********************** 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 : 1.526 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: 0.8407 (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: 0.8629 (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: 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: 0.8676 (mm110) 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: 0.3054 time to fit residues: 107.1887 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 : 1.390 ------------------------------------------------------------------------------- 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 130 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 62 optimal weight: 0.0570 chunk 120 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS A 391 ASN A 425 ASN A 436 ASN A 437 GLN A 583 HIS B 41 ASN B 68 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 375 HIS B 391 ASN B 425 ASN B 437 GLN B 457 HIS B 583 HIS C 6 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN F 40 GLN F 53 ASN F 77 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.088303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.066173 restraints weight = 34124.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.068550 restraints weight = 16475.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070060 restraints weight = 10207.630| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12686 Z= 0.141 Angle : 0.700 9.507 17198 Z= 0.354 Chirality : 0.043 0.191 1954 Planarity : 0.005 0.055 2141 Dihedral : 8.552 86.501 1769 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.33 % Allowed : 8.07 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.20), residues: 1558 helix: -0.50 (0.18), residues: 642 sheet: -1.23 (0.30), residues: 270 loop : -1.99 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 564 HIS 0.005 0.001 HIS A 243 PHE 0.015 0.002 PHE A 489 TYR 0.019 0.002 TYR B 336 ARG 0.007 0.001 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 2) link_NAG-ASN : angle 2.72154 ( 6) hydrogen bonds : bond 0.05252 ( 539) hydrogen bonds : angle 5.23220 ( 1587) SS BOND : bond 0.00435 ( 7) SS BOND : angle 0.98218 ( 14) covalent geometry : bond 0.00298 (12677) covalent geometry : angle 0.69814 (17178) *********************** 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 193 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.9094 (mttt) cc_final: 0.8526 (tptm) REVERT: A 182 PHE cc_start: 0.8242 (m-80) cc_final: 0.7525 (t80) REVERT: A 266 PHE cc_start: 0.7251 (t80) cc_final: 0.6831 (t80) REVERT: A 334 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8786 (mm-30) REVERT: A 344 GLU cc_start: 0.8996 (tp30) cc_final: 0.8416 (tp30) REVERT: A 345 THR cc_start: 0.9013 (m) cc_final: 0.8811 (p) REVERT: A 391 ASN cc_start: 0.9083 (t0) cc_final: 0.8693 (t0) REVERT: B 164 VAL cc_start: 0.9445 (t) cc_final: 0.9213 (p) REVERT: B 172 LYS cc_start: 0.8934 (mttt) cc_final: 0.8369 (tmtt) REVERT: B 226 LEU cc_start: 0.9054 (mt) cc_final: 0.8728 (tp) REVERT: B 351 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: B 393 GLN cc_start: 0.5890 (mm-40) cc_final: 0.5618 (tp40) REVERT: B 402 THR cc_start: 0.9171 (m) cc_final: 0.8898 (p) REVERT: B 515 MET cc_start: 0.9261 (mmm) cc_final: 0.9036 (mmp) REVERT: C 55 GLU cc_start: 0.8486 (tp30) cc_final: 0.8156 (tp30) REVERT: C 79 GLN cc_start: 0.8336 (mm110) cc_final: 0.8054 (mm110) REVERT: E 79 GLN cc_start: 0.8999 (mm110) cc_final: 0.8570 (mm110) REVERT: E 82 ASP cc_start: 0.8230 (m-30) cc_final: 0.7822 (m-30) REVERT: F 55 ASP cc_start: 0.8608 (p0) cc_final: 0.8140 (p0) outliers start: 18 outliers final: 7 residues processed: 189 average time/residue: 0.2515 time to fit residues: 70.4578 Evaluate side-chains 129 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 105 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 243 HIS A 457 HIS B 76 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.086881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064895 restraints weight = 34356.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.067120 restraints weight = 16853.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068633 restraints weight = 10606.013| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12686 Z= 0.153 Angle : 0.661 9.920 17198 Z= 0.330 Chirality : 0.042 0.175 1954 Planarity : 0.004 0.057 2141 Dihedral : 7.976 85.782 1767 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.37 % Allowed : 10.37 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.21), residues: 1558 helix: 0.48 (0.20), residues: 648 sheet: -0.87 (0.31), residues: 262 loop : -1.74 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.007 0.001 HIS A 243 PHE 0.017 0.001 PHE F 79 TYR 0.015 0.001 TYR A 336 ARG 0.006 0.000 ARG A 163 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 2) link_NAG-ASN : angle 2.27590 ( 6) hydrogen bonds : bond 0.04056 ( 539) hydrogen bonds : angle 4.74367 ( 1587) SS BOND : bond 0.00441 ( 7) SS BOND : angle 1.18433 ( 14) covalent geometry : bond 0.00350 (12677) covalent geometry : angle 0.65872 (17178) *********************** 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 166 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8299 (mmm) cc_final: 0.8012 (mmm) REVERT: A 172 LYS cc_start: 0.9054 (mttt) cc_final: 0.8504 (tptm) REVERT: A 182 PHE cc_start: 0.8324 (m-80) cc_final: 0.7453 (t80) REVERT: A 265 MET cc_start: 0.7801 (mtp) cc_final: 0.7568 (mtt) REVERT: A 266 PHE cc_start: 0.7223 (t80) cc_final: 0.6934 (t80) REVERT: A 274 LEU cc_start: 0.8475 (tp) cc_final: 0.8265 (pp) REVERT: A 334 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8813 (mm-30) REVERT: A 344 GLU cc_start: 0.8961 (tp30) cc_final: 0.8359 (tp30) REVERT: A 345 THR cc_start: 0.8989 (m) cc_final: 0.8758 (p) REVERT: A 391 ASN cc_start: 0.9162 (t0) cc_final: 0.8689 (t0) REVERT: B 152 MET cc_start: 0.8292 (ttm) cc_final: 0.7946 (mpp) REVERT: B 172 LYS cc_start: 0.8996 (mttt) cc_final: 0.8408 (tmtt) REVERT: B 226 LEU cc_start: 0.9129 (mt) cc_final: 0.8753 (tp) REVERT: B 393 GLN cc_start: 0.6164 (mm-40) cc_final: 0.5789 (tp40) REVERT: B 402 THR cc_start: 0.9166 (m) cc_final: 0.8881 (p) REVERT: B 515 MET cc_start: 0.9289 (mmm) cc_final: 0.8983 (mmt) REVERT: C 55 GLU cc_start: 0.8504 (tp30) cc_final: 0.8141 (tp30) REVERT: E 79 GLN cc_start: 0.8979 (mm110) cc_final: 0.8502 (mm110) REVERT: E 82 ASP cc_start: 0.8221 (m-30) cc_final: 0.7781 (m-30) REVERT: F 55 ASP cc_start: 0.8616 (p0) cc_final: 0.8183 (p0) outliers start: 32 outliers final: 14 residues processed: 159 average time/residue: 0.2043 time to fit residues: 50.0640 Evaluate side-chains 130 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 493 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 543 ILE 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 51 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 63 optimal weight: 9.9990 chunk 117 optimal weight: 0.0970 chunk 45 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN D 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.087936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.065634 restraints weight = 34179.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.067974 restraints weight = 16725.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.069496 restraints weight = 10478.594| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12686 Z= 0.119 Angle : 0.615 10.046 17198 Z= 0.306 Chirality : 0.041 0.195 1954 Planarity : 0.004 0.054 2141 Dihedral : 7.688 87.024 1767 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.63 % Allowed : 11.11 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.22), residues: 1558 helix: 1.03 (0.21), residues: 650 sheet: -0.68 (0.31), residues: 266 loop : -1.54 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 564 HIS 0.007 0.001 HIS A 243 PHE 0.014 0.001 PHE A 545 TYR 0.016 0.001 TYR A 336 ARG 0.004 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00114 ( 2) link_NAG-ASN : angle 2.17707 ( 6) hydrogen bonds : bond 0.03517 ( 539) hydrogen bonds : angle 4.38071 ( 1587) SS BOND : bond 0.00867 ( 7) SS BOND : angle 1.04495 ( 14) covalent geometry : bond 0.00269 (12677) covalent geometry : angle 0.61311 (17178) *********************** 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 152 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.613 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8344 (mmm) cc_final: 0.8052 (mmm) REVERT: A 172 LYS cc_start: 0.9058 (mttt) cc_final: 0.8505 (tptm) REVERT: A 182 PHE cc_start: 0.8392 (m-80) cc_final: 0.7517 (t80) REVERT: A 201 ILE cc_start: 0.9373 (mm) cc_final: 0.9121 (mt) REVERT: A 259 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8466 (tp) REVERT: A 344 GLU cc_start: 0.8965 (tp30) cc_final: 0.8317 (tp30) REVERT: A 345 THR cc_start: 0.8997 (m) cc_final: 0.8763 (p) REVERT: A 391 ASN cc_start: 0.9116 (t0) cc_final: 0.8586 (t0) REVERT: B 172 LYS cc_start: 0.9012 (mttt) cc_final: 0.8390 (tmtt) REVERT: B 226 LEU cc_start: 0.9103 (mt) cc_final: 0.8756 (tp) REVERT: B 336 TYR cc_start: 0.9056 (t80) cc_final: 0.8569 (t80) REVERT: B 515 MET cc_start: 0.9227 (mmm) cc_final: 0.8954 (mmt) REVERT: C 55 GLU cc_start: 0.8479 (tp30) cc_final: 0.8102 (tp30) REVERT: E 55 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8124 (tp30) REVERT: E 79 GLN cc_start: 0.8938 (mm110) cc_final: 0.8481 (mm-40) REVERT: E 82 ASP cc_start: 0.8193 (m-30) cc_final: 0.7724 (m-30) REVERT: F 55 ASP cc_start: 0.8618 (p0) cc_final: 0.8243 (p0) outliers start: 22 outliers final: 9 residues processed: 147 average time/residue: 0.2429 time to fit residues: 55.7728 Evaluate side-chains 122 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 295 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 92 optimal weight: 7.9990 chunk 79 optimal weight: 30.0000 chunk 100 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN 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 = 0.3452 r_free = 0.3452 target = 0.084254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.062353 restraints weight = 35131.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.064521 restraints weight = 17274.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.065943 restraints weight = 10857.183| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12686 Z= 0.323 Angle : 0.772 12.492 17198 Z= 0.384 Chirality : 0.046 0.194 1954 Planarity : 0.004 0.056 2141 Dihedral : 8.079 82.982 1767 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.37 % Allowed : 11.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1558 helix: 1.13 (0.21), residues: 654 sheet: -0.72 (0.31), residues: 270 loop : -1.57 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 92 HIS 0.007 0.002 HIS B 630 PHE 0.027 0.002 PHE F 79 TYR 0.018 0.002 TYR E 86 ARG 0.008 0.001 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00788 ( 2) link_NAG-ASN : angle 2.36569 ( 6) hydrogen bonds : bond 0.04008 ( 539) hydrogen bonds : angle 4.69984 ( 1587) SS BOND : bond 0.00703 ( 7) SS BOND : angle 1.58173 ( 14) covalent geometry : bond 0.00735 (12677) covalent geometry : angle 0.76977 (17178) *********************** 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 145 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8479 (mmm) cc_final: 0.8182 (mmm) REVERT: A 172 LYS cc_start: 0.9053 (mttt) cc_final: 0.8558 (tptm) REVERT: A 182 PHE cc_start: 0.8268 (m-80) cc_final: 0.7493 (t80) REVERT: A 266 PHE cc_start: 0.6906 (t80) cc_final: 0.6505 (t80) REVERT: A 274 LEU cc_start: 0.8615 (tp) cc_final: 0.8362 (pp) REVERT: A 344 GLU cc_start: 0.8920 (tp30) cc_final: 0.8235 (tp30) REVERT: A 345 THR cc_start: 0.9006 (m) cc_final: 0.8740 (p) REVERT: A 391 ASN cc_start: 0.9140 (t0) cc_final: 0.8638 (t0) REVERT: B 172 LYS cc_start: 0.9075 (mttt) cc_final: 0.8419 (tmtt) REVERT: B 226 LEU cc_start: 0.9115 (mt) cc_final: 0.8790 (tp) REVERT: B 402 THR cc_start: 0.9161 (m) cc_final: 0.8898 (p) REVERT: B 437 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8005 (mm-40) REVERT: B 515 MET cc_start: 0.9265 (mmm) cc_final: 0.8960 (mmt) REVERT: C 55 GLU cc_start: 0.8479 (tp30) cc_final: 0.8061 (tp30) REVERT: E 55 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8129 (tp30) REVERT: E 79 GLN cc_start: 0.8951 (mm110) cc_final: 0.8624 (mm-40) REVERT: F 55 ASP cc_start: 0.8499 (p0) cc_final: 0.8224 (p0) outliers start: 32 outliers final: 21 residues processed: 138 average time/residue: 0.1978 time to fit residues: 42.9255 Evaluate side-chains 127 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 348 GLU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 636 MET 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 548 MET 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 46 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 46 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 140 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 13 optimal weight: 0.0770 chunk 123 optimal weight: 6.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.087217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.065273 restraints weight = 34962.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.067607 restraints weight = 16884.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.069098 restraints weight = 10487.785| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12686 Z= 0.114 Angle : 0.619 10.623 17198 Z= 0.307 Chirality : 0.041 0.215 1954 Planarity : 0.004 0.055 2141 Dihedral : 7.701 89.415 1767 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.37 % Allowed : 11.78 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1558 helix: 1.46 (0.21), residues: 654 sheet: -0.49 (0.31), residues: 270 loop : -1.39 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 624 HIS 0.003 0.001 HIS A 243 PHE 0.011 0.001 PHE F 79 TYR 0.019 0.001 TYR A 336 ARG 0.003 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 2) link_NAG-ASN : angle 2.27103 ( 6) hydrogen bonds : bond 0.03291 ( 539) hydrogen bonds : angle 4.22747 ( 1587) SS BOND : bond 0.00383 ( 7) SS BOND : angle 0.86378 ( 14) covalent geometry : bond 0.00257 (12677) covalent geometry : angle 0.61775 (17178) *********************** 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 159 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8455 (mmm) cc_final: 0.8157 (mmm) REVERT: A 172 LYS cc_start: 0.9053 (mttt) cc_final: 0.8549 (tptm) REVERT: A 182 PHE cc_start: 0.8340 (m-80) cc_final: 0.7526 (t80) REVERT: A 201 ILE cc_start: 0.9433 (mm) cc_final: 0.9205 (mt) REVERT: A 266 PHE cc_start: 0.6762 (t80) cc_final: 0.6408 (t80) REVERT: A 344 GLU cc_start: 0.8899 (tp30) cc_final: 0.8189 (tp30) REVERT: A 345 THR cc_start: 0.8978 (m) cc_final: 0.8712 (p) REVERT: A 391 ASN cc_start: 0.9118 (t0) cc_final: 0.8599 (t0) REVERT: B 164 VAL cc_start: 0.9365 (t) cc_final: 0.9148 (p) REVERT: B 172 LYS cc_start: 0.9079 (mttt) cc_final: 0.8372 (tmtt) REVERT: B 226 LEU cc_start: 0.9094 (mt) cc_final: 0.8764 (tp) REVERT: B 336 TYR cc_start: 0.8932 (t80) cc_final: 0.8107 (t80) REVERT: B 402 THR cc_start: 0.9138 (m) cc_final: 0.8919 (p) REVERT: B 437 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7897 (mm-40) REVERT: B 515 MET cc_start: 0.9223 (mmm) cc_final: 0.8868 (mmt) REVERT: C 55 GLU cc_start: 0.8379 (tp30) cc_final: 0.8020 (tp30) REVERT: D 5 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7788 (tm-30) REVERT: E 79 GLN cc_start: 0.8876 (mm110) cc_final: 0.8434 (mm-40) REVERT: F 55 ASP cc_start: 0.8433 (p0) cc_final: 0.8053 (p0) outliers start: 32 outliers final: 14 residues processed: 146 average time/residue: 0.2015 time to fit residues: 45.9207 Evaluate side-chains 129 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 76 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 15 optimal weight: 0.0980 chunk 120 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS B 393 GLN ** 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 = 0.3520 r_free = 0.3520 target = 0.087854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.066140 restraints weight = 34098.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068389 restraints weight = 16335.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.069917 restraints weight = 10183.195| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12686 Z= 0.109 Angle : 0.626 11.615 17198 Z= 0.308 Chirality : 0.041 0.223 1954 Planarity : 0.004 0.054 2141 Dihedral : 7.372 88.914 1767 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.70 % Allowed : 12.44 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1558 helix: 1.57 (0.21), residues: 654 sheet: -0.35 (0.32), residues: 270 loop : -1.30 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 564 HIS 0.002 0.000 HIS A 267 PHE 0.011 0.001 PHE A 545 TYR 0.013 0.001 TYR A 336 ARG 0.003 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00011 ( 2) link_NAG-ASN : angle 2.18954 ( 6) hydrogen bonds : bond 0.03148 ( 539) hydrogen bonds : angle 4.13456 ( 1587) SS BOND : bond 0.00365 ( 7) SS BOND : angle 0.88491 ( 14) covalent geometry : bond 0.00249 (12677) covalent geometry : angle 0.62460 (17178) *********************** 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 148 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.388 Fit side-chains REVERT: A 71 MET cc_start: 0.8523 (mmm) cc_final: 0.8221 (mmm) REVERT: A 172 LYS cc_start: 0.9039 (mttt) cc_final: 0.8551 (tptm) REVERT: A 182 PHE cc_start: 0.8360 (m-80) cc_final: 0.7511 (t80) REVERT: A 201 ILE cc_start: 0.9421 (mm) cc_final: 0.9201 (mt) REVERT: A 266 PHE cc_start: 0.6638 (t80) cc_final: 0.6287 (t80) REVERT: A 334 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8764 (mm-30) REVERT: A 344 GLU cc_start: 0.8920 (tp30) cc_final: 0.8225 (tp30) REVERT: A 345 THR cc_start: 0.9036 (m) cc_final: 0.8755 (p) REVERT: A 391 ASN cc_start: 0.9088 (t0) cc_final: 0.8551 (t0) REVERT: B 164 VAL cc_start: 0.9347 (t) cc_final: 0.9127 (p) REVERT: B 172 LYS cc_start: 0.9055 (mttt) cc_final: 0.8359 (tmtt) REVERT: B 226 LEU cc_start: 0.9093 (mt) cc_final: 0.8837 (tp) REVERT: B 336 TYR cc_start: 0.8911 (t80) cc_final: 0.8704 (t80) REVERT: B 402 THR cc_start: 0.9172 (m) cc_final: 0.8919 (p) REVERT: C 55 GLU cc_start: 0.8373 (tp30) cc_final: 0.8023 (tp30) REVERT: D 5 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7863 (tm-30) REVERT: E 79 GLN cc_start: 0.8846 (mm110) cc_final: 0.8578 (mm-40) REVERT: F 55 ASP cc_start: 0.8489 (p0) cc_final: 0.8140 (p0) outliers start: 23 outliers final: 15 residues processed: 141 average time/residue: 0.1960 time to fit residues: 43.5408 Evaluate side-chains 130 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 259 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 252 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 69 optimal weight: 8.9990 chunk 104 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 23 optimal weight: 0.0980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.088495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.067025 restraints weight = 34335.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.069382 restraints weight = 16358.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.070865 restraints weight = 10019.374| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12686 Z= 0.105 Angle : 0.620 11.528 17198 Z= 0.303 Chirality : 0.041 0.236 1954 Planarity : 0.003 0.053 2141 Dihedral : 7.016 87.088 1767 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.41 % Allowed : 13.19 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.22), residues: 1558 helix: 1.65 (0.21), residues: 654 sheet: -0.29 (0.32), residues: 280 loop : -1.23 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 35 HIS 0.003 0.001 HIS A 243 PHE 0.011 0.001 PHE E 98 TYR 0.012 0.001 TYR F 51 ARG 0.003 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00049 ( 2) link_NAG-ASN : angle 2.14859 ( 6) hydrogen bonds : bond 0.03026 ( 539) hydrogen bonds : angle 4.03532 ( 1587) SS BOND : bond 0.00349 ( 7) SS BOND : angle 0.82781 ( 14) covalent geometry : bond 0.00238 (12677) covalent geometry : angle 0.61901 (17178) *********************** 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 145 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 2.415 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.9027 (mttt) cc_final: 0.8540 (tptm) REVERT: A 182 PHE cc_start: 0.8346 (m-80) cc_final: 0.7528 (t80) REVERT: A 201 ILE cc_start: 0.9459 (mm) cc_final: 0.9240 (mt) REVERT: A 266 PHE cc_start: 0.6690 (t80) cc_final: 0.6381 (t80) REVERT: A 334 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8741 (mm-30) REVERT: A 391 ASN cc_start: 0.9006 (t0) cc_final: 0.8426 (t0) REVERT: B 172 LYS cc_start: 0.9044 (mttt) cc_final: 0.8412 (tmtt) REVERT: B 226 LEU cc_start: 0.9081 (mt) cc_final: 0.8767 (tp) REVERT: B 402 THR cc_start: 0.9152 (m) cc_final: 0.8901 (p) REVERT: B 437 GLN cc_start: 0.8308 (mm-40) cc_final: 0.8015 (mm-40) REVERT: C 55 GLU cc_start: 0.8366 (tp30) cc_final: 0.8022 (tp30) REVERT: D 5 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7839 (tm-30) REVERT: F 55 ASP cc_start: 0.8475 (p0) cc_final: 0.8135 (p0) outliers start: 19 outliers final: 13 residues processed: 140 average time/residue: 0.2700 time to fit residues: 59.5308 Evaluate side-chains 128 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 72 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.084686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.062479 restraints weight = 35044.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064700 restraints weight = 17152.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.066123 restraints weight = 10790.738| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 12686 Z= 0.291 Angle : 0.747 12.671 17198 Z= 0.370 Chirality : 0.045 0.245 1954 Planarity : 0.004 0.053 2141 Dihedral : 7.626 83.258 1767 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.33 % Allowed : 13.78 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1558 helix: 1.56 (0.21), residues: 646 sheet: -0.36 (0.31), residues: 280 loop : -1.32 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 35 HIS 0.005 0.001 HIS B 630 PHE 0.022 0.002 PHE F 79 TYR 0.016 0.002 TYR A 413 ARG 0.004 0.001 ARG D 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 2) link_NAG-ASN : angle 2.24273 ( 6) hydrogen bonds : bond 0.03662 ( 539) hydrogen bonds : angle 4.47822 ( 1587) SS BOND : bond 0.00697 ( 7) SS BOND : angle 1.39460 ( 14) covalent geometry : bond 0.00661 (12677) covalent geometry : angle 0.74501 (17178) *********************** 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 123 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.593 Fit side-chains REVERT: A 172 LYS cc_start: 0.9035 (mttt) cc_final: 0.8572 (tptm) REVERT: A 182 PHE cc_start: 0.8363 (m-80) cc_final: 0.7649 (t80) REVERT: A 266 PHE cc_start: 0.6757 (t80) cc_final: 0.6405 (t80) REVERT: A 334 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8753 (mm-30) REVERT: A 391 ASN cc_start: 0.9070 (t0) cc_final: 0.8541 (t0) REVERT: B 172 LYS cc_start: 0.9100 (mttt) cc_final: 0.8419 (tmtt) REVERT: B 226 LEU cc_start: 0.9133 (mt) cc_final: 0.8794 (tp) REVERT: B 402 THR cc_start: 0.9168 (m) cc_final: 0.8910 (p) REVERT: C 55 GLU cc_start: 0.8442 (tp30) cc_final: 0.8022 (tp30) REVERT: D 5 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7899 (tm-30) REVERT: E 79 GLN cc_start: 0.8882 (mm110) cc_final: 0.8508 (mm-40) REVERT: E 82 ASP cc_start: 0.8530 (m-30) cc_final: 0.7766 (m-30) REVERT: F 16 GLN cc_start: 0.7862 (tt0) cc_final: 0.7369 (pp30) REVERT: F 55 ASP cc_start: 0.8368 (p0) cc_final: 0.8050 (p0) outliers start: 18 outliers final: 16 residues processed: 122 average time/residue: 0.2460 time to fit residues: 47.3211 Evaluate side-chains 118 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 64 LEU 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 81 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 99 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 48 optimal weight: 0.0030 chunk 49 optimal weight: 0.9990 chunk 137 optimal weight: 0.1980 chunk 111 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.088252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.066713 restraints weight = 33905.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.069042 restraints weight = 16200.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.070516 restraints weight = 9998.791| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12686 Z= 0.106 Angle : 0.632 12.082 17198 Z= 0.310 Chirality : 0.041 0.262 1954 Planarity : 0.003 0.054 2141 Dihedral : 6.971 89.651 1767 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.89 % Allowed : 13.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1558 helix: 1.74 (0.21), residues: 652 sheet: -0.15 (0.32), residues: 274 loop : -1.11 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 624 HIS 0.003 0.001 HIS A 243 PHE 0.022 0.001 PHE B 545 TYR 0.013 0.001 TYR F 51 ARG 0.003 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 2) link_NAG-ASN : angle 2.28236 ( 6) hydrogen bonds : bond 0.03009 ( 539) hydrogen bonds : angle 4.05419 ( 1587) SS BOND : bond 0.00305 ( 7) SS BOND : angle 0.73122 ( 14) covalent geometry : bond 0.00242 (12677) covalent geometry : angle 0.63020 (17178) ********************** 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 133 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.733 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.9015 (mttt) cc_final: 0.8548 (tptm) REVERT: A 182 PHE cc_start: 0.8391 (m-80) cc_final: 0.7638 (t80) REVERT: A 266 PHE cc_start: 0.6616 (t80) cc_final: 0.6311 (t80) REVERT: A 334 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8730 (mm-30) REVERT: A 391 ASN cc_start: 0.9061 (t0) cc_final: 0.8503 (t0) REVERT: B 172 LYS cc_start: 0.9077 (mttt) cc_final: 0.8418 (tmtt) REVERT: B 226 LEU cc_start: 0.9093 (mt) cc_final: 0.8768 (tp) REVERT: B 402 THR cc_start: 0.9197 (m) cc_final: 0.8989 (p) REVERT: B 437 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7829 (mm-40) REVERT: C 55 GLU cc_start: 0.8366 (tp30) cc_final: 0.8028 (tp30) REVERT: F 55 ASP cc_start: 0.8478 (p0) cc_final: 0.8133 (p0) outliers start: 12 outliers final: 9 residues processed: 131 average time/residue: 0.2025 time to fit residues: 42.4564 Evaluate side-chains 122 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 25 optimal weight: 0.0370 chunk 146 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 131 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 overall best weight: 3.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** 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 = 0.3490 r_free = 0.3490 target = 0.086349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.064160 restraints weight = 34740.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.066442 restraints weight = 16919.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.067902 restraints weight = 10603.479| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12686 Z= 0.190 Angle : 0.669 12.715 17198 Z= 0.331 Chirality : 0.043 0.256 1954 Planarity : 0.004 0.053 2141 Dihedral : 7.081 88.273 1767 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.96 % Allowed : 14.07 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1558 helix: 1.74 (0.21), residues: 652 sheet: -0.23 (0.32), residues: 276 loop : -1.15 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 35 HIS 0.006 0.001 HIS A 243 PHE 0.016 0.001 PHE F 79 TYR 0.012 0.002 TYR A 413 ARG 0.002 0.000 ARG D 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 2) link_NAG-ASN : angle 2.08932 ( 6) hydrogen bonds : bond 0.03239 ( 539) hydrogen bonds : angle 4.20063 ( 1587) SS BOND : bond 0.00546 ( 7) SS BOND : angle 1.13416 ( 14) covalent geometry : bond 0.00438 (12677) covalent geometry : angle 0.66744 (17178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3847.51 seconds wall clock time: 69 minutes 22.46 seconds (4162.46 seconds total)