Starting phenix.real_space_refine on Sun Feb 8 03:35:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m3z_63612/02_2026/9m3z_63612.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m3z_63612/02_2026/9m3z_63612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m3z_63612/02_2026/9m3z_63612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m3z_63612/02_2026/9m3z_63612.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m3z_63612/02_2026/9m3z_63612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m3z_63612/02_2026/9m3z_63612.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 195 5.16 5 C 24473 2.51 5 N 6883 2.21 5 O 7631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39218 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5938 Classifications: {'peptide': 761} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 723} Chain: "B" Number of atoms: 5938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5938 Classifications: {'peptide': 761} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 723} Chain: "C" Number of atoms: 5938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5938 Classifications: {'peptide': 761} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 723} Chain: "D" Number of atoms: 5938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5938 Classifications: {'peptide': 761} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 723} Chain: "E" Number of atoms: 5938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5938 Classifications: {'peptide': 761} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 723} Chain: "F" Number of atoms: 5938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5938 Classifications: {'peptide': 761} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 723} Chain: "G" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3236 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 18, 'TRANS': 394} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.08, per 1000 atoms: 0.23 Number of scatterers: 39218 At special positions: 0 Unit cell: (177.173, 178.346, 165.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 195 16.00 P 30 15.00 Mg 6 11.99 O 7631 8.00 N 6883 7.00 C 24473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.9 seconds 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9244 Finding SS restraints... Secondary structure from input PDB file: 235 helices and 37 sheets defined 49.5% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 124 through 127 removed outlier: 4.036A pdb=" N VAL A 127 " --> pdb=" O ASP A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 127' Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 195 through 201 removed outlier: 4.469A pdb=" N ARG A 200 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 removed outlier: 4.295A pdb=" N LEU A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix Processing helix chain 'A' and resid 229 through 237 removed outlier: 4.024A pdb=" N PHE A 233 " --> pdb=" O HIS A 229 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.740A pdb=" N GLY A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.646A pdb=" N ILE A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.290A pdb=" N ASN A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 338 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.813A pdb=" N ARG A 361 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 362 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 388 Processing helix chain 'A' and resid 398 through 406 Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 485 through 497 Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 502 through 510 removed outlier: 3.630A pdb=" N PHE A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 509 " --> pdb=" O LYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 538 Processing helix chain 'A' and resid 547 through 557 Processing helix chain 'A' and resid 561 through 572 Processing helix chain 'A' and resid 582 through 585 Processing helix chain 'A' and resid 595 through 616 removed outlier: 3.795A pdb=" N ASN A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 633 removed outlier: 3.627A pdb=" N ILE A 632 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.648A pdb=" N ARG A 639 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.575A pdb=" N LEU A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 719 Processing helix chain 'A' and resid 736 through 745 removed outlier: 3.643A pdb=" N LYS A 745 " --> pdb=" O GLU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 765 Processing helix chain 'A' and resid 769 through 773 Processing helix chain 'B' and resid 15 through 19 removed outlier: 4.290A pdb=" N THR B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 195 through 200 removed outlier: 3.682A pdb=" N ARG B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 224 Processing helix chain 'B' and resid 229 through 237 removed outlier: 4.213A pdb=" N PHE B 233 " --> pdb=" O HIS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 274 through 280 removed outlier: 4.055A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 298 removed outlier: 3.720A pdb=" N ARG B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 4.068A pdb=" N ILE B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 320 Processing helix chain 'B' and resid 321 through 337 Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.881A pdb=" N ARG B 362 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 388 Processing helix chain 'B' and resid 398 through 406 removed outlier: 3.558A pdb=" N ILE B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 429 removed outlier: 3.616A pdb=" N LYS B 429 " --> pdb=" O CYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 Processing helix chain 'B' and resid 451 through 461 removed outlier: 3.545A pdb=" N PHE B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 502 removed outlier: 4.658A pdb=" N TYR B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Proline residue: B 499 - end of helix Processing helix chain 'B' and resid 502 through 510 removed outlier: 4.191A pdb=" N PHE B 506 " --> pdb=" O HIS B 502 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU B 507 " --> pdb=" O PRO B 503 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE B 509 " --> pdb=" O LYS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 539 removed outlier: 3.597A pdb=" N ALA B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 558 removed outlier: 3.851A pdb=" N PHE B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 571 Processing helix chain 'B' and resid 581 through 585 removed outlier: 3.636A pdb=" N SER B 584 " --> pdb=" O GLU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 616 removed outlier: 4.028A pdb=" N GLY B 598 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY B 614 " --> pdb=" O THR B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.597A pdb=" N LEU B 637 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 666 Processing helix chain 'B' and resid 675 through 683 Processing helix chain 'B' and resid 688 through 720 removed outlier: 3.729A pdb=" N THR B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 745 removed outlier: 3.650A pdb=" N PHE B 740 " --> pdb=" O LYS B 736 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS B 745 " --> pdb=" O GLU B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 767 Processing helix chain 'B' and resid 768 through 773 removed outlier: 4.113A pdb=" N GLY B 771 " --> pdb=" O GLN B 768 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 773 " --> pdb=" O ARG B 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 19 removed outlier: 3.860A pdb=" N THR C 18 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 removed outlier: 3.880A pdb=" N LYS C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 53' Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 124 through 127 removed outlier: 3.851A pdb=" N VAL C 127 " --> pdb=" O ASP C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 124 through 127' Processing helix chain 'C' and resid 133 through 143 removed outlier: 4.880A pdb=" N LYS C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Proline residue: C 141 - end of helix Processing helix chain 'C' and resid 194 through 201 Processing helix chain 'C' and resid 213 through 229 removed outlier: 4.368A pdb=" N LEU C 225 " --> pdb=" O GLU C 221 " (cutoff:3.500A) Proline residue: C 226 - end of helix Processing helix chain 'C' and resid 229 through 237 removed outlier: 4.537A pdb=" N PHE C 233 " --> pdb=" O HIS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 283 through 299 Processing helix chain 'C' and resid 308 through 313 removed outlier: 3.821A pdb=" N ILE C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 338 Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.597A pdb=" N ILE C 356 " --> pdb=" O PRO C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 3.519A pdb=" N ARG C 361 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG C 362 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 388 Processing helix chain 'C' and resid 398 through 406 removed outlier: 3.574A pdb=" N ILE C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 428 Processing helix chain 'C' and resid 441 through 447 removed outlier: 3.706A pdb=" N LEU C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 461 Processing helix chain 'C' and resid 478 through 482 Processing helix chain 'C' and resid 485 through 502 removed outlier: 4.823A pdb=" N TYR C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Proline residue: C 499 - end of helix Processing helix chain 'C' and resid 503 through 510 removed outlier: 3.860A pdb=" N GLU C 507 " --> pdb=" O PRO C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 539 Processing helix chain 'C' and resid 546 through 555 removed outlier: 4.153A pdb=" N LEU C 550 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 551 " --> pdb=" O GLY C 547 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 572 removed outlier: 4.703A pdb=" N ARG C 563 " --> pdb=" O GLU C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 603 through 613 Processing helix chain 'C' and resid 634 through 638 removed outlier: 3.583A pdb=" N LEU C 637 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 666 Processing helix chain 'C' and resid 675 through 683 Processing helix chain 'C' and resid 687 through 720 Processing helix chain 'C' and resid 736 through 745 removed outlier: 3.760A pdb=" N LYS C 745 " --> pdb=" O GLU C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 767 Processing helix chain 'C' and resid 769 through 773 Processing helix chain 'D' and resid 46 through 53 Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 124 through 127 removed outlier: 3.853A pdb=" N VAL D 127 " --> pdb=" O ASP D 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 124 through 127' Processing helix chain 'D' and resid 133 through 138 Processing helix chain 'D' and resid 138 through 144 removed outlier: 3.890A pdb=" N TYR D 142 " --> pdb=" O TYR D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 201 removed outlier: 4.115A pdb=" N GLU D 199 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG D 200 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 212 through 229 removed outlier: 4.421A pdb=" N LEU D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Proline residue: D 226 - end of helix Processing helix chain 'D' and resid 253 through 266 Processing helix chain 'D' and resid 274 through 280 removed outlier: 3.664A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 299 Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.797A pdb=" N ILE D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 322 through 336 Processing helix chain 'D' and resid 337 through 339 No H-bonds generated for 'chain 'D' and resid 337 through 339' Processing helix chain 'D' and resid 357 through 362 removed outlier: 3.567A pdb=" N ARG D 361 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG D 362 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 388 removed outlier: 3.759A pdb=" N GLU D 382 " --> pdb=" O ILE D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 406 removed outlier: 3.957A pdb=" N ILE D 402 " --> pdb=" O ASP D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 429 removed outlier: 3.630A pdb=" N LYS D 429 " --> pdb=" O CYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 448 Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.614A pdb=" N ASP D 481 " --> pdb=" O SER D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 502 removed outlier: 3.641A pdb=" N GLU D 494 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Proline residue: D 499 - end of helix Processing helix chain 'D' and resid 502 through 510 removed outlier: 3.908A pdb=" N PHE D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 538 Processing helix chain 'D' and resid 547 through 557 Processing helix chain 'D' and resid 559 through 572 removed outlier: 4.464A pdb=" N ARG D 563 " --> pdb=" O GLU D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 595 through 615 removed outlier: 5.421A pdb=" N ALA D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP D 602 " --> pdb=" O GLY D 598 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 614 " --> pdb=" O THR D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 639 removed outlier: 3.578A pdb=" N LEU D 638 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 665 removed outlier: 3.599A pdb=" N LEU D 665 " --> pdb=" O PHE D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 683 removed outlier: 4.097A pdb=" N LEU D 679 " --> pdb=" O ASP D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 719 Processing helix chain 'D' and resid 736 through 746 Processing helix chain 'D' and resid 752 through 767 Processing helix chain 'E' and resid 18 through 22 Processing helix chain 'E' and resid 48 through 53 removed outlier: 4.044A pdb=" N LYS E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU E 53 " --> pdb=" O THR E 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 53' Processing helix chain 'E' and resid 89 through 96 Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.708A pdb=" N VAL E 127 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU E 128 " --> pdb=" O ASP E 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 124 through 128' Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 194 through 201 removed outlier: 3.651A pdb=" N GLU E 199 " --> pdb=" O GLU E 196 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU E 201 " --> pdb=" O GLU E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 229 removed outlier: 4.417A pdb=" N LEU E 225 " --> pdb=" O GLU E 221 " (cutoff:3.500A) Proline residue: E 226 - end of helix Processing helix chain 'E' and resid 229 through 237 removed outlier: 4.213A pdb=" N PHE E 233 " --> pdb=" O HIS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 266 removed outlier: 3.505A pdb=" N GLY E 266 " --> pdb=" O ALA E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 283 through 299 removed outlier: 3.653A pdb=" N ASN E 299 " --> pdb=" O GLU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 313 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 321 through 337 Processing helix chain 'E' and resid 338 through 341 Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 376 through 389 removed outlier: 3.797A pdb=" N LYS E 389 " --> pdb=" O ARG E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 406 removed outlier: 3.722A pdb=" N ILE E 402 " --> pdb=" O ASP E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 429 removed outlier: 3.504A pdb=" N THR E 419 " --> pdb=" O ALA E 415 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS E 429 " --> pdb=" O CYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 447 removed outlier: 3.762A pdb=" N LEU E 445 " --> pdb=" O ASP E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 461 removed outlier: 3.581A pdb=" N PHE E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 502 removed outlier: 4.516A pdb=" N TYR E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Proline residue: E 499 - end of helix Processing helix chain 'E' and resid 502 through 510 removed outlier: 4.345A pdb=" N PHE E 506 " --> pdb=" O HIS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 538 Processing helix chain 'E' and resid 547 through 557 removed outlier: 4.076A pdb=" N PHE E 555 " --> pdb=" O LEU E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 571 removed outlier: 3.963A pdb=" N ARG E 563 " --> pdb=" O GLU E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 removed outlier: 3.941A pdb=" N SER E 584 " --> pdb=" O GLU E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 600 Processing helix chain 'E' and resid 600 through 616 removed outlier: 3.814A pdb=" N VAL E 604 " --> pdb=" O ALA E 600 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN E 606 " --> pdb=" O ASP E 602 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY E 614 " --> pdb=" O THR E 610 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN E 616 " --> pdb=" O MET E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 639 removed outlier: 3.693A pdb=" N ARG E 639 " --> pdb=" O ALA E 636 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 665 removed outlier: 3.733A pdb=" N LEU E 665 " --> pdb=" O PHE E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 683 removed outlier: 3.847A pdb=" N LEU E 679 " --> pdb=" O ASP E 675 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA E 680 " --> pdb=" O ILE E 676 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS E 681 " --> pdb=" O GLY E 677 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 720 Processing helix chain 'E' and resid 736 through 744 removed outlier: 3.621A pdb=" N PHE E 740 " --> pdb=" O LYS E 736 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 767 Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 46 through 53 Processing helix chain 'F' and resid 66 through 68 No H-bonds generated for 'chain 'F' and resid 66 through 68' Processing helix chain 'F' and resid 89 through 96 removed outlier: 3.626A pdb=" N ARG F 93 " --> pdb=" O ASN F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 127 removed outlier: 3.751A pdb=" N VAL F 127 " --> pdb=" O ASP F 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 124 through 127' Processing helix chain 'F' and resid 133 through 138 Processing helix chain 'F' and resid 138 through 143 removed outlier: 3.745A pdb=" N TYR F 142 " --> pdb=" O TYR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 201 removed outlier: 3.775A pdb=" N GLU F 199 " --> pdb=" O GLU F 196 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG F 200 " --> pdb=" O ASP F 197 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU F 201 " --> pdb=" O GLU F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 229 removed outlier: 4.547A pdb=" N LEU F 225 " --> pdb=" O GLU F 221 " (cutoff:3.500A) Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 229 through 237 removed outlier: 4.176A pdb=" N PHE F 233 " --> pdb=" O HIS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 265 removed outlier: 4.107A pdb=" N THR F 265 " --> pdb=" O VAL F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 279 Processing helix chain 'F' and resid 283 through 298 removed outlier: 3.682A pdb=" N SER F 287 " --> pdb=" O GLY F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 319 removed outlier: 3.574A pdb=" N THR F 319 " --> pdb=" O ARG F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 337 removed outlier: 3.652A pdb=" N ASP F 336 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY F 337 " --> pdb=" O THR F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 352 through 356 removed outlier: 3.649A pdb=" N ILE F 356 " --> pdb=" O PRO F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 362 removed outlier: 3.876A pdb=" N ARG F 362 " --> pdb=" O ALA F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 388 removed outlier: 3.686A pdb=" N ARG F 385 " --> pdb=" O LEU F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 406 removed outlier: 3.928A pdb=" N ILE F 402 " --> pdb=" O ASP F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 428 removed outlier: 3.612A pdb=" N GLU F 428 " --> pdb=" O GLN F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 447 Processing helix chain 'F' and resid 451 through 462 removed outlier: 3.512A pdb=" N PHE F 455 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 502 removed outlier: 3.658A pdb=" N GLU F 494 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR F 498 " --> pdb=" O GLU F 494 " (cutoff:3.500A) Proline residue: F 499 - end of helix Processing helix chain 'F' and resid 502 through 510 removed outlier: 4.346A pdb=" N PHE F 506 " --> pdb=" O HIS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 526 through 539 Processing helix chain 'F' and resid 547 through 557 Processing helix chain 'F' and resid 560 through 572 removed outlier: 3.710A pdb=" N GLU F 564 " --> pdb=" O ALA F 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 removed outlier: 3.942A pdb=" N SER F 584 " --> pdb=" O GLU F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 600 removed outlier: 4.152A pdb=" N GLY F 598 " --> pdb=" O GLY F 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA F 600 " --> pdb=" O GLY F 597 " (cutoff:3.500A) Processing helix chain 'F' and resid 602 through 616 removed outlier: 3.522A pdb=" N GLY F 614 " --> pdb=" O THR F 610 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN F 616 " --> pdb=" O MET F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 629 through 633 removed outlier: 3.591A pdb=" N ILE F 633 " --> pdb=" O PRO F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 638 removed outlier: 3.630A pdb=" N LEU F 637 " --> pdb=" O ASP F 634 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU F 638 " --> pdb=" O SER F 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 634 through 638' Processing helix chain 'F' and resid 653 through 665 Processing helix chain 'F' and resid 675 through 683 Processing helix chain 'F' and resid 687 through 720 Processing helix chain 'F' and resid 738 through 745 removed outlier: 3.775A pdb=" N GLU F 742 " --> pdb=" O ALA F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 766 Processing helix chain 'F' and resid 767 through 773 removed outlier: 3.561A pdb=" N ARG F 770 " --> pdb=" O GLN F 767 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY F 771 " --> pdb=" O GLN F 768 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY F 773 " --> pdb=" O ARG F 770 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 36 Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'G' and resid 55 through 62 removed outlier: 3.833A pdb=" N PHE G 62 " --> pdb=" O ASP G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 3.517A pdb=" N THR G 66 " --> pdb=" O PHE G 62 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP G 67 " --> pdb=" O THR G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 67' Processing helix chain 'G' and resid 72 through 76 Processing helix chain 'G' and resid 110 through 118 Processing helix chain 'G' and resid 136 through 149 Processing helix chain 'G' and resid 192 through 206 Processing helix chain 'G' and resid 218 through 224 Processing helix chain 'G' and resid 229 through 243 Processing helix chain 'G' and resid 273 through 282 Processing helix chain 'G' and resid 346 through 357 Processing helix chain 'G' and resid 361 through 366 Processing helix chain 'G' and resid 368 through 377 Processing helix chain 'G' and resid 383 through 395 Processing helix chain 'G' and resid 399 through 411 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 34 removed outlier: 7.789A pdb=" N ILE A 86 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 31 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N MET A 88 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP A 33 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP A 59 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 122 removed outlier: 6.980A pdb=" N HIS A 119 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 151 removed outlier: 3.932A pdb=" N ARG A 148 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 269 removed outlier: 6.964A pdb=" N PHE A 268 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE A 305 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE A 272 " --> pdb=" O ASP A 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 268 through 269 removed outlier: 6.964A pdb=" N PHE A 268 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE A 305 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER A 302 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N MET A 347 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 304 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 543 through 546 removed outlier: 6.570A pdb=" N ILE A 543 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP A 580 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL A 545 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS A 575 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A 624 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU A 577 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA A 626 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE A 579 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLY A 516 " --> pdb=" O GLN A 645 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE A 647 " --> pdb=" O GLY A 516 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A 518 " --> pdb=" O ILE A 647 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.617A pdb=" N SER B 105 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 119 through 122 removed outlier: 3.649A pdb=" N GLU B 171 " --> pdb=" O HIS B 119 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU B 121 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL B 169 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 149 through 151 Processing sheet with id=AB1, first strand: chain 'B' and resid 244 through 247 Processing sheet with id=AB2, first strand: chain 'B' and resid 344 through 348 removed outlier: 6.627A pdb=" N PHE B 268 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE B 305 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE B 270 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASP B 307 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 272 " --> pdb=" O ASP B 307 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET G 109 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 541 through 546 removed outlier: 3.677A pdb=" N ILE B 543 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 517 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N THR B 627 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE B 519 " --> pdb=" O THR B 627 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 34 removed outlier: 6.348A pdb=" N VAL C 43 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP C 59 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.265A pdb=" N LEU C 121 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL C 169 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 149 through 151 Processing sheet with id=AB7, first strand: chain 'C' and resid 268 through 272 removed outlier: 6.636A pdb=" N PHE C 268 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE C 305 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE C 270 " --> pdb=" O PHE C 305 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASP C 307 " --> pdb=" O PHE C 270 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 272 " --> pdb=" O ASP C 307 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 544 through 545 removed outlier: 6.134A pdb=" N CYS C 575 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE C 624 " --> pdb=" O CYS C 575 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU C 577 " --> pdb=" O ILE C 624 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ALA C 626 " --> pdb=" O LEU C 577 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE C 579 " --> pdb=" O ALA C 626 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU C 518 " --> pdb=" O ILE C 647 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 30 through 34 removed outlier: 5.820A pdb=" N VAL D 31 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N MET D 88 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASP D 33 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP D 59 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 105 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 117 through 122 removed outlier: 4.201A pdb=" N ARG D 117 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU D 121 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL D 169 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 149 through 151 Processing sheet with id=AC3, first strand: chain 'D' and resid 243 through 244 removed outlier: 3.597A pdb=" N ILE D 303 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE D 305 " --> pdb=" O PHE D 270 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 541 through 546 removed outlier: 3.652A pdb=" N ILE D 543 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU D 518 " --> pdb=" O ILE D 647 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 29 through 31 removed outlier: 4.401A pdb=" N SER E 105 " --> pdb=" O LYS E 64 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL E 43 " --> pdb=" O LEU E 76 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 114 through 115 Processing sheet with id=AC7, first strand: chain 'E' and resid 119 through 122 removed outlier: 6.616A pdb=" N HIS E 119 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 268 through 272 removed outlier: 7.728A pdb=" N SER E 302 " --> pdb=" O ILE E 345 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N MET E 347 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE E 304 " --> pdb=" O MET E 347 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ALA E 349 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE E 306 " --> pdb=" O ALA E 349 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 541 through 546 removed outlier: 6.400A pdb=" N CYS E 575 " --> pdb=" O PHE E 622 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE E 624 " --> pdb=" O CYS E 575 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU E 577 " --> pdb=" O ILE E 624 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL E 517 " --> pdb=" O GLY E 625 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY E 516 " --> pdb=" O GLN E 645 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE E 647 " --> pdb=" O GLY E 516 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU E 518 " --> pdb=" O ILE E 647 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 29 through 31 Processing sheet with id=AD2, first strand: chain 'F' and resid 118 through 122 removed outlier: 6.435A pdb=" N LEU F 121 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL F 169 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 149 through 151 Processing sheet with id=AD4, first strand: chain 'F' and resid 244 through 246 removed outlier: 6.962A pdb=" N ILE F 244 " --> pdb=" O GLY F 348 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA F 349 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE F 305 " --> pdb=" O PHE F 270 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 543 through 546 removed outlier: 3.616A pdb=" N ILE F 543 " --> pdb=" O VAL F 576 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N CYS F 575 " --> pdb=" O PHE F 622 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE F 624 " --> pdb=" O CYS F 575 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU F 577 " --> pdb=" O ILE F 624 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ALA F 626 " --> pdb=" O LEU F 577 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE F 579 " --> pdb=" O ALA F 626 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL F 517 " --> pdb=" O GLY F 625 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N THR F 627 " --> pdb=" O VAL F 517 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE F 519 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 12 through 17 removed outlier: 3.999A pdb=" N SER G 81 " --> pdb=" O MET G 3 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 120 through 121 Processing sheet with id=AD8, first strand: chain 'G' and resid 320 through 322 removed outlier: 9.555A pdb=" N VAL G 249 " --> pdb=" O ARG G 209 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL G 211 " --> pdb=" O VAL G 249 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA G 251 " --> pdb=" O VAL G 211 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE G 213 " --> pdb=" O ALA G 251 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL G 253 " --> pdb=" O PHE G 213 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE G 215 " --> pdb=" O VAL G 253 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N LEU G 255 " --> pdb=" O PHE G 215 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ARG G 210 " --> pdb=" O GLY G 162 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLY G 162 " --> pdb=" O ARG G 210 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE G 159 " --> pdb=" O ILE G 175 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE G 175 " --> pdb=" O PHE G 159 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR G 161 " --> pdb=" O ASP G 173 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER G 131 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL G 172 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER G 133 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE G 174 " --> pdb=" O SER G 133 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ASP G 135 " --> pdb=" O PHE G 174 " (cutoff:3.500A) removed outlier: 11.762A pdb=" N TYR G 176 " --> pdb=" O ASP G 135 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 180 through 182 Processing sheet with id=AE1, first strand: chain 'G' and resid 297 through 298 1672 hydrogen bonds defined for protein. 4722 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: 9.25 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13412 1.34 - 1.46: 6543 1.46 - 1.58: 19558 1.58 - 1.69: 40 1.69 - 1.81: 316 Bond restraints: 39869 Sorted by residual: bond pdb=" N TYR D 759 " pdb=" CA TYR D 759 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.63e+00 bond pdb=" N GLU B 324 " pdb=" CA GLU B 324 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.62e+00 bond pdb=" CB PRO A 652 " pdb=" CG PRO A 652 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.32e+00 bond pdb=" N THR A 172 " pdb=" CA THR A 172 " ideal model delta sigma weight residual 1.454 1.473 -0.019 1.31e-02 5.83e+03 2.12e+00 bond pdb=" C MET D 347 " pdb=" N GLY D 348 " ideal model delta sigma weight residual 1.332 1.326 0.006 5.00e-03 4.00e+04 1.37e+00 ... (remaining 39864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 52680 1.41 - 2.82: 870 2.82 - 4.24: 233 4.24 - 5.65: 64 5.65 - 7.06: 13 Bond angle restraints: 53860 Sorted by residual: angle pdb=" C SER F 558 " pdb=" CA SER F 558 " pdb=" CB SER F 558 " ideal model delta sigma weight residual 115.89 110.50 5.39 1.32e+00 5.74e-01 1.67e+01 angle pdb=" N PRO A 652 " pdb=" CA PRO A 652 " pdb=" C PRO A 652 " ideal model delta sigma weight residual 112.47 118.78 -6.31 2.06e+00 2.36e-01 9.38e+00 angle pdb=" N ALA A 175 " pdb=" CA ALA A 175 " pdb=" C ALA A 175 " ideal model delta sigma weight residual 110.97 114.02 -3.05 1.09e+00 8.42e-01 7.83e+00 angle pdb=" CA THR A 172 " pdb=" C THR A 172 " pdb=" O THR A 172 " ideal model delta sigma weight residual 121.47 118.27 3.20 1.15e+00 7.56e-01 7.72e+00 angle pdb=" N VAL F 127 " pdb=" CA VAL F 127 " pdb=" C VAL F 127 " ideal model delta sigma weight residual 111.91 109.46 2.45 8.90e-01 1.26e+00 7.58e+00 ... (remaining 53855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.62: 23844 24.62 - 49.24: 750 49.24 - 73.86: 112 73.86 - 98.48: 18 98.48 - 123.10: 3 Dihedral angle restraints: 24727 sinusoidal: 10414 harmonic: 14313 Sorted by residual: dihedral pdb=" O1B ADP C 903 " pdb=" O3A ADP C 903 " pdb=" PB ADP C 903 " pdb=" PA ADP C 903 " ideal model delta sinusoidal sigma weight residual -60.00 63.10 -123.10 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" C5' ADP A 903 " pdb=" O5' ADP A 903 " pdb=" PA ADP A 903 " pdb=" O2A ADP A 903 " ideal model delta sinusoidal sigma weight residual -60.00 -174.31 114.31 1 2.00e+01 2.50e-03 3.39e+01 dihedral pdb=" C5' ADP B 903 " pdb=" O5' ADP B 903 " pdb=" PA ADP B 903 " pdb=" O2A ADP B 903 " ideal model delta sinusoidal sigma weight residual -60.00 46.14 -106.14 1 2.00e+01 2.50e-03 3.07e+01 ... (remaining 24724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4516 0.043 - 0.086: 1036 0.086 - 0.130: 432 0.130 - 0.173: 12 0.173 - 0.216: 1 Chirality restraints: 5997 Sorted by residual: chirality pdb=" CA PRO A 652 " pdb=" N PRO A 652 " pdb=" C PRO A 652 " pdb=" CB PRO A 652 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE F 74 " pdb=" N ILE F 74 " pdb=" C ILE F 74 " pdb=" CB ILE F 74 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE D 272 " pdb=" N ILE D 272 " pdb=" C ILE D 272 " pdb=" CB ILE D 272 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 5994 not shown) Planarity restraints: 7086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 651 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A 652 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 652 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 652 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 651 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C LEU A 651 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU A 651 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO A 652 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 547 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO E 548 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 548 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 548 " -0.024 5.00e-02 4.00e+02 ... (remaining 7083 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 345 2.51 - 3.11: 29288 3.11 - 3.71: 60591 3.71 - 4.30: 81363 4.30 - 4.90: 136960 Nonbonded interactions: 308547 Sorted by model distance: nonbonded pdb=" OD2 ASP E 307 " pdb="MG MG E 902 " model vdw 1.916 2.170 nonbonded pdb=" OG1 THR F 255 " pdb="MG MG F 902 " model vdw 1.946 2.170 nonbonded pdb=" O2B ANP A 901 " pdb="MG MG A 902 " model vdw 1.952 2.170 nonbonded pdb=" O1G ANP C 901 " pdb="MG MG C 902 " model vdw 1.961 2.170 nonbonded pdb=" O2B ANP C 901 " pdb="MG MG C 902 " model vdw 1.962 2.170 ... (remaining 308542 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 3.520 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 37.600 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 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 : 0.002 0.076 39869 Z= 0.116 Angle : 0.522 7.062 53860 Z= 0.270 Chirality : 0.042 0.216 5997 Planarity : 0.004 0.114 7086 Dihedral : 12.047 123.100 15483 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.71 % Favored : 95.27 % Rotamer: Outliers : 2.22 % Allowed : 6.65 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.12), residues: 4965 helix: 0.98 (0.12), residues: 2084 sheet: -0.84 (0.20), residues: 682 loop : -0.46 (0.14), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 427 TYR 0.015 0.001 TYR C 520 PHE 0.013 0.001 PHE G 174 TRP 0.005 0.001 TRP B 479 HIS 0.003 0.000 HIS F 456 Details of bonding type rmsd covalent geometry : bond 0.00246 (39869) covalent geometry : angle 0.52190 (53860) hydrogen bonds : bond 0.15996 ( 1672) hydrogen bonds : angle 5.90429 ( 4722) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 401 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 ILE cc_start: 0.9051 (tp) cc_final: 0.8683 (tp) REVERT: A 703 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8967 (tt) REVERT: A 707 ILE cc_start: 0.7774 (tp) cc_final: 0.7421 (tt) REVERT: A 724 MET cc_start: 0.6416 (pmm) cc_final: 0.5428 (tpt) REVERT: B 229 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.7653 (m90) REVERT: B 307 ASP cc_start: 0.7834 (t0) cc_final: 0.7630 (t0) REVERT: B 338 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7889 (mm) REVERT: C 352 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7172 (ptt-90) REVERT: C 553 MET cc_start: 0.6640 (mmp) cc_final: 0.5525 (mtt) REVERT: D 452 ASN cc_start: 0.7187 (OUTLIER) cc_final: 0.6862 (t0) REVERT: D 456 HIS cc_start: 0.7636 (OUTLIER) cc_final: 0.6901 (t-90) REVERT: D 622 PHE cc_start: 0.8133 (m-80) cc_final: 0.7803 (m-80) REVERT: D 665 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7673 (pp) REVERT: F 273 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7512 (m-40) REVERT: F 334 LEU cc_start: 0.8265 (mt) cc_final: 0.7991 (mt) REVERT: F 613 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8251 (m-30) REVERT: F 682 TYR cc_start: 0.5441 (OUTLIER) cc_final: 0.4966 (t80) REVERT: F 739 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7382 (t70) REVERT: G 160 MET cc_start: 0.2734 (mmm) cc_final: 0.2382 (tpp) REVERT: G 300 MET cc_start: 0.5414 (mtt) cc_final: 0.5128 (mtp) outliers start: 94 outliers final: 35 residues processed: 483 average time/residue: 0.2409 time to fit residues: 191.1828 Evaluate side-chains 314 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 268 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 661 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 456 HIS Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 288 ASN Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 713 LYS Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 613 ASP Chi-restraints excluded: chain F residue 682 TYR Chi-restraints excluded: chain F residue 739 HIS Chi-restraints excluded: chain F residue 744 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 315 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 494 optimal weight: 0.0980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 588 GLN A 645 GLN A 696 GLN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN B 541 ASN B 588 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 46 HIS C 330 GLN C 493 GLN C 588 GLN C 607 GLN D 218 GLN D 288 ASN D 452 ASN D 539 GLN D 696 GLN D 768 GLN ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 HIS E 493 GLN E 588 GLN E 607 GLN E 767 GLN F 561 ASN F 571 GLN F 588 GLN F 606 ASN F 645 GLN G 143 GLN G 235 GLN G 240 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.214231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.197146 restraints weight = 59776.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.190440 restraints weight = 138627.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.185490 restraints weight = 99208.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.185549 restraints weight = 120906.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.185901 restraints weight = 73482.979| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 39869 Z= 0.136 Angle : 0.582 8.065 53860 Z= 0.285 Chirality : 0.044 0.231 5997 Planarity : 0.004 0.114 7086 Dihedral : 8.424 128.951 5746 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.77 % Favored : 95.21 % Rotamer: Outliers : 2.06 % Allowed : 9.53 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.12), residues: 4965 helix: 0.98 (0.12), residues: 2111 sheet: -0.84 (0.20), residues: 697 loop : -0.44 (0.14), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 341 TYR 0.020 0.001 TYR G 226 PHE 0.021 0.001 PHE C 555 TRP 0.024 0.002 TRP A 554 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00308 (39869) covalent geometry : angle 0.58166 (53860) hydrogen bonds : bond 0.04090 ( 1672) hydrogen bonds : angle 4.74036 ( 4722) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 317 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 MET cc_start: 0.8824 (mmm) cc_final: 0.8251 (tpt) REVERT: A 512 SER cc_start: 0.8543 (t) cc_final: 0.8319 (m) REVERT: A 534 ILE cc_start: 0.9012 (tp) cc_final: 0.8652 (tp) REVERT: A 707 ILE cc_start: 0.7734 (tp) cc_final: 0.7491 (tt) REVERT: A 724 MET cc_start: 0.6380 (pmm) cc_final: 0.5769 (tpp) REVERT: B 96 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8610 (mm) REVERT: B 229 HIS cc_start: 0.7817 (OUTLIER) cc_final: 0.7311 (m-70) REVERT: B 298 LYS cc_start: 0.7300 (ttmt) cc_final: 0.7094 (ttmm) REVERT: B 338 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7703 (mm) REVERT: C 107 HIS cc_start: 0.4496 (m90) cc_final: 0.4040 (m90) REVERT: C 352 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6944 (ptt-90) REVERT: C 553 MET cc_start: 0.6604 (mmp) cc_final: 0.5581 (mtt) REVERT: C 613 ASP cc_start: 0.7240 (m-30) cc_final: 0.6334 (m-30) REVERT: D 123 VAL cc_start: 0.4714 (OUTLIER) cc_final: 0.4454 (t) REVERT: D 353 PRO cc_start: 0.8064 (Cg_exo) cc_final: 0.7844 (Cg_endo) REVERT: D 456 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.6941 (t-90) REVERT: D 665 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7589 (pp) REVERT: F 273 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7630 (m-40) REVERT: F 278 MET cc_start: 0.7943 (mmm) cc_final: 0.7732 (tpp) REVERT: F 334 LEU cc_start: 0.8197 (mt) cc_final: 0.7958 (mt) REVERT: F 580 ASP cc_start: 0.8936 (t0) cc_final: 0.8614 (t70) REVERT: F 613 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8075 (m-30) REVERT: F 682 TYR cc_start: 0.5552 (OUTLIER) cc_final: 0.5181 (t80) REVERT: G 160 MET cc_start: 0.2566 (mmm) cc_final: 0.1787 (tpp) REVERT: G 409 MET cc_start: -0.1306 (ptt) cc_final: -0.1758 (ptt) outliers start: 87 outliers final: 49 residues processed: 390 average time/residue: 0.2329 time to fit residues: 152.0150 Evaluate side-chains 329 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 270 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 661 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 456 HIS Chi-restraints excluded: chain D residue 476 ASN Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 512 SER Chi-restraints excluded: chain E residue 575 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 613 ASP Chi-restraints excluded: chain F residue 682 TYR Chi-restraints excluded: chain F residue 739 HIS Chi-restraints excluded: chain F residue 744 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 315 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 434 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 18 optimal weight: 0.0370 chunk 303 optimal weight: 6.9990 chunk 443 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 342 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 363 optimal weight: 0.7980 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 HIS ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** D 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.208476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.192829 restraints weight = 58857.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.191092 restraints weight = 134481.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.187337 restraints weight = 85322.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.186266 restraints weight = 116737.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.185973 restraints weight = 73569.903| |-----------------------------------------------------------------------------| r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 39869 Z= 0.138 Angle : 0.571 10.812 53860 Z= 0.278 Chirality : 0.043 0.228 5997 Planarity : 0.004 0.113 7086 Dihedral : 7.697 129.761 5731 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.61 % Favored : 95.37 % Rotamer: Outliers : 2.46 % Allowed : 10.19 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.12), residues: 4965 helix: 0.98 (0.12), residues: 2116 sheet: -0.89 (0.20), residues: 694 loop : -0.45 (0.14), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 757 TYR 0.016 0.001 TYR C 746 PHE 0.027 0.001 PHE E 268 TRP 0.032 0.002 TRP A 554 HIS 0.003 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00322 (39869) covalent geometry : angle 0.57150 (53860) hydrogen bonds : bond 0.03795 ( 1672) hydrogen bonds : angle 4.54677 ( 4722) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 291 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 ILE cc_start: 0.9006 (tp) cc_final: 0.8650 (tp) REVERT: A 555 PHE cc_start: 0.6696 (m-80) cc_final: 0.6469 (m-80) REVERT: A 724 MET cc_start: 0.5826 (pmm) cc_final: 0.5532 (tpp) REVERT: B 229 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7464 (m-70) REVERT: B 338 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7767 (mm) REVERT: B 445 LEU cc_start: 0.7852 (mm) cc_final: 0.7596 (tp) REVERT: C 107 HIS cc_start: 0.4202 (m90) cc_final: 0.3756 (m90) REVERT: C 553 MET cc_start: 0.6550 (mmp) cc_final: 0.5570 (mtt) REVERT: C 613 ASP cc_start: 0.7174 (m-30) cc_final: 0.6323 (m-30) REVERT: D 123 VAL cc_start: 0.4783 (OUTLIER) cc_final: 0.4502 (t) REVERT: D 371 ASP cc_start: 0.7597 (t0) cc_final: 0.7017 (p0) REVERT: D 456 HIS cc_start: 0.7718 (OUTLIER) cc_final: 0.7008 (t-90) REVERT: D 665 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7643 (pp) REVERT: E 256 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8352 (tm) REVERT: F 216 MET cc_start: 0.8717 (tpp) cc_final: 0.8445 (tpp) REVERT: F 273 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7656 (m-40) REVERT: F 334 LEU cc_start: 0.8246 (mt) cc_final: 0.7959 (mt) REVERT: F 580 ASP cc_start: 0.8910 (t0) cc_final: 0.8650 (t70) REVERT: F 613 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8147 (m-30) REVERT: F 682 TYR cc_start: 0.5784 (OUTLIER) cc_final: 0.5292 (t80) REVERT: G 160 MET cc_start: 0.2002 (mmm) cc_final: 0.1648 (mmt) REVERT: G 409 MET cc_start: -0.1361 (ptt) cc_final: -0.1685 (ptt) outliers start: 104 outliers final: 61 residues processed: 375 average time/residue: 0.2212 time to fit residues: 140.1227 Evaluate side-chains 330 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 260 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 661 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 456 HIS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 476 ASN Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 512 SER Chi-restraints excluded: chain E residue 553 MET Chi-restraints excluded: chain E residue 575 CYS Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 713 LYS Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 613 ASP Chi-restraints excluded: chain F residue 644 ASP Chi-restraints excluded: chain F residue 682 TYR Chi-restraints excluded: chain F residue 739 HIS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 228 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 122 optimal weight: 5.9990 chunk 274 optimal weight: 0.9990 chunk 466 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 406 optimal weight: 2.9990 chunk 280 optimal weight: 0.0770 chunk 207 optimal weight: 4.9990 chunk 433 optimal weight: 0.8980 chunk 330 optimal weight: 0.9980 chunk 379 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** D 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 HIS F 606 ASN G 411 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.219059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.205382 restraints weight = 57829.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.199565 restraints weight = 118725.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.196363 restraints weight = 100214.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.196578 restraints weight = 104921.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.196226 restraints weight = 66491.598| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 39869 Z= 0.119 Angle : 0.549 15.246 53860 Z= 0.266 Chirality : 0.043 0.230 5997 Planarity : 0.004 0.112 7086 Dihedral : 7.134 129.409 5719 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.45 % Favored : 95.53 % Rotamer: Outliers : 2.58 % Allowed : 10.86 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.12), residues: 4965 helix: 1.04 (0.12), residues: 2122 sheet: -0.85 (0.20), residues: 694 loop : -0.42 (0.14), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 120 TYR 0.012 0.001 TYR C 520 PHE 0.019 0.001 PHE G 280 TRP 0.029 0.002 TRP G 248 HIS 0.003 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00274 (39869) covalent geometry : angle 0.54871 (53860) hydrogen bonds : bond 0.03403 ( 1672) hydrogen bonds : angle 4.35890 ( 4722) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 278 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.6828 (mmp) cc_final: 0.6353 (mmm) REVERT: A 430 MET cc_start: 0.8468 (tpp) cc_final: 0.8198 (ttm) REVERT: A 534 ILE cc_start: 0.9030 (tp) cc_final: 0.8721 (tp) REVERT: A 724 MET cc_start: 0.5903 (pmm) cc_final: 0.5655 (tpp) REVERT: B 96 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8510 (mm) REVERT: B 229 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7543 (m-70) REVERT: B 338 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7886 (mm) REVERT: C 107 HIS cc_start: 0.4242 (m90) cc_final: 0.3800 (m90) REVERT: C 352 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7311 (ptt-90) REVERT: C 613 ASP cc_start: 0.7066 (m-30) cc_final: 0.6353 (m-30) REVERT: D 371 ASP cc_start: 0.7592 (t0) cc_final: 0.6947 (p0) REVERT: D 456 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7076 (t-90) REVERT: D 611 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6888 (mt-10) REVERT: D 665 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7703 (pp) REVERT: E 256 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8254 (tm) REVERT: F 273 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7632 (m-40) REVERT: F 334 LEU cc_start: 0.8257 (mt) cc_final: 0.7960 (mt) REVERT: F 682 TYR cc_start: 0.5669 (OUTLIER) cc_final: 0.5084 (t80) REVERT: G 2 MET cc_start: 0.2608 (tpp) cc_final: 0.2323 (mmm) REVERT: G 160 MET cc_start: 0.2210 (mmm) cc_final: 0.1814 (mmt) outliers start: 109 outliers final: 68 residues processed: 367 average time/residue: 0.2084 time to fit residues: 131.9520 Evaluate side-chains 331 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 253 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 661 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 456 HIS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 476 ASN Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 661 PHE Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 512 SER Chi-restraints excluded: chain E residue 575 CYS Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 713 LYS Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 618 LYS Chi-restraints excluded: chain F residue 644 ASP Chi-restraints excluded: chain F residue 682 TYR Chi-restraints excluded: chain F residue 739 HIS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 306 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 188 optimal weight: 0.0030 chunk 87 optimal weight: 6.9990 chunk 435 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 355 optimal weight: 0.0010 chunk 26 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 372 optimal weight: 2.9990 chunk 452 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 469 optimal weight: 7.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** E 387 HIS ** 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 = 0.4636 r_free = 0.4636 target = 0.214927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.190417 restraints weight = 59546.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.190547 restraints weight = 139911.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.187463 restraints weight = 74917.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.187061 restraints weight = 83380.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.187062 restraints weight = 65003.716| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 39869 Z= 0.146 Angle : 0.567 14.780 53860 Z= 0.274 Chirality : 0.043 0.228 5997 Planarity : 0.004 0.112 7086 Dihedral : 6.986 130.348 5715 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.99 % Favored : 94.98 % Rotamer: Outliers : 2.46 % Allowed : 11.90 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.12), residues: 4965 helix: 1.00 (0.12), residues: 2113 sheet: -0.92 (0.20), residues: 693 loop : -0.43 (0.14), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 120 TYR 0.016 0.001 TYR C 520 PHE 0.023 0.001 PHE D 363 TRP 0.036 0.002 TRP A 554 HIS 0.003 0.001 HIS F 456 Details of bonding type rmsd covalent geometry : bond 0.00343 (39869) covalent geometry : angle 0.56696 (53860) hydrogen bonds : bond 0.03617 ( 1672) hydrogen bonds : angle 4.36225 ( 4722) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 265 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 MET cc_start: 0.8905 (tpt) cc_final: 0.8493 (tpt) REVERT: A 512 SER cc_start: 0.8628 (t) cc_final: 0.8289 (m) REVERT: A 534 ILE cc_start: 0.9051 (tp) cc_final: 0.8742 (tp) REVERT: A 724 MET cc_start: 0.6278 (pmm) cc_final: 0.5804 (tpp) REVERT: B 229 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.7522 (m-70) REVERT: B 338 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7797 (mm) REVERT: C 107 HIS cc_start: 0.4262 (m90) cc_final: 0.3797 (m90) REVERT: C 352 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7581 (pmt-80) REVERT: C 613 ASP cc_start: 0.7045 (m-30) cc_final: 0.6243 (m-30) REVERT: D 456 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.6994 (t-90) REVERT: D 611 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6887 (mt-10) REVERT: D 665 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7781 (pp) REVERT: E 256 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8308 (tm) REVERT: F 216 MET cc_start: 0.8776 (tpp) cc_final: 0.8469 (tpp) REVERT: F 273 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7724 (m-40) REVERT: F 334 LEU cc_start: 0.8266 (mt) cc_final: 0.7953 (mt) REVERT: F 682 TYR cc_start: 0.5917 (OUTLIER) cc_final: 0.5235 (t80) REVERT: G 160 MET cc_start: 0.2289 (mmm) cc_final: 0.1837 (mmt) REVERT: G 409 MET cc_start: -0.1241 (ptt) cc_final: -0.1507 (ptt) outliers start: 104 outliers final: 78 residues processed: 349 average time/residue: 0.2131 time to fit residues: 127.9421 Evaluate side-chains 341 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 254 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 661 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 456 HIS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 476 ASN Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 553 MET Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 661 PHE Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 512 SER Chi-restraints excluded: chain E residue 553 MET Chi-restraints excluded: chain E residue 575 CYS Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 713 LYS Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 247 TYR Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 644 ASP Chi-restraints excluded: chain F residue 682 TYR Chi-restraints excluded: chain F residue 739 HIS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 306 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 334 optimal weight: 0.1980 chunk 140 optimal weight: 2.9990 chunk 423 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 411 optimal weight: 2.9990 chunk 378 optimal weight: 0.0070 chunk 355 optimal weight: 0.5980 chunk 321 optimal weight: 10.0000 chunk 409 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 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 = 0.4647 r_free = 0.4647 target = 0.210663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.190454 restraints weight = 60117.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.186874 restraints weight = 136105.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.181386 restraints weight = 93659.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.181758 restraints weight = 107849.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.181365 restraints weight = 77871.529| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 39869 Z= 0.117 Angle : 0.546 14.969 53860 Z= 0.263 Chirality : 0.043 0.229 5997 Planarity : 0.004 0.111 7086 Dihedral : 6.794 129.395 5715 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.31 % Favored : 95.67 % Rotamer: Outliers : 2.72 % Allowed : 12.13 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.12), residues: 4965 helix: 1.07 (0.12), residues: 2111 sheet: -0.81 (0.20), residues: 688 loop : -0.40 (0.14), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 120 TYR 0.014 0.001 TYR D 247 PHE 0.020 0.001 PHE C 555 TRP 0.028 0.002 TRP G 248 HIS 0.002 0.000 HIS F 456 Details of bonding type rmsd covalent geometry : bond 0.00269 (39869) covalent geometry : angle 0.54563 (53860) hydrogen bonds : bond 0.03266 ( 1672) hydrogen bonds : angle 4.23976 ( 4722) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 269 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.5740 (OUTLIER) cc_final: 0.5330 (m-40) REVERT: A 216 MET cc_start: 0.8931 (tpt) cc_final: 0.8598 (tpt) REVERT: A 278 MET cc_start: 0.6832 (mmp) cc_final: 0.6332 (mmm) REVERT: A 365 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8194 (mtm-85) REVERT: A 518 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8906 (tp) REVERT: A 534 ILE cc_start: 0.9013 (tp) cc_final: 0.8737 (tp) REVERT: A 724 MET cc_start: 0.6199 (pmm) cc_final: 0.5821 (tpp) REVERT: B 96 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8492 (mm) REVERT: B 229 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7503 (m-70) REVERT: B 338 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7858 (mm) REVERT: B 445 LEU cc_start: 0.8046 (mm) cc_final: 0.7754 (tp) REVERT: C 107 HIS cc_start: 0.4332 (m90) cc_final: 0.3882 (m90) REVERT: C 352 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7661 (pmt-80) REVERT: C 613 ASP cc_start: 0.7310 (m-30) cc_final: 0.6806 (m-30) REVERT: D 456 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7072 (t-90) REVERT: D 554 TRP cc_start: 0.7612 (t60) cc_final: 0.6588 (t60) REVERT: D 611 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6981 (mt-10) REVERT: D 665 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7743 (pp) REVERT: E 256 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8242 (tm) REVERT: E 615 MET cc_start: 0.7294 (tpp) cc_final: 0.6848 (tpp) REVERT: F 216 MET cc_start: 0.8696 (tpp) cc_final: 0.8420 (tpp) REVERT: F 247 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.8083 (p90) REVERT: F 273 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7630 (m-40) REVERT: F 334 LEU cc_start: 0.8248 (mt) cc_final: 0.7924 (mt) REVERT: F 682 TYR cc_start: 0.5628 (OUTLIER) cc_final: 0.5000 (t80) REVERT: F 696 GLN cc_start: 0.8290 (tp40) cc_final: 0.7866 (tp40) REVERT: G 82 MET cc_start: 0.5399 (mmm) cc_final: 0.4785 (ppp) REVERT: G 160 MET cc_start: 0.2353 (mmm) cc_final: 0.1862 (mmt) REVERT: G 208 MET cc_start: -0.0649 (ptp) cc_final: -0.0861 (ptp) REVERT: G 374 PHE cc_start: 0.4177 (t80) cc_final: 0.3929 (t80) outliers start: 115 outliers final: 76 residues processed: 366 average time/residue: 0.2202 time to fit residues: 137.5916 Evaluate side-chains 342 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 252 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 661 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 456 HIS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 476 ASN Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 553 MET Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 661 PHE Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 512 SER Chi-restraints excluded: chain E residue 553 MET Chi-restraints excluded: chain E residue 575 CYS Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 713 LYS Chi-restraints excluded: chain F residue 247 TYR Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 644 ASP Chi-restraints excluded: chain F residue 682 TYR Chi-restraints excluded: chain F residue 739 HIS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 306 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 111 optimal weight: 1.9990 chunk 213 optimal weight: 0.0370 chunk 269 optimal weight: 0.7980 chunk 370 optimal weight: 10.0000 chunk 242 optimal weight: 50.0000 chunk 150 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 271 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 453 optimal weight: 7.9990 chunk 168 optimal weight: 0.0040 overall best weight: 1.3674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN E 288 ASN ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.216744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.202438 restraints weight = 57392.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.195613 restraints weight = 124934.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.192144 restraints weight = 111869.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.192372 restraints weight = 110078.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.191956 restraints weight = 70998.821| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 39869 Z= 0.166 Angle : 0.597 15.402 53860 Z= 0.287 Chirality : 0.044 0.229 5997 Planarity : 0.004 0.116 7086 Dihedral : 6.812 130.837 5711 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.40 % Favored : 94.58 % Rotamer: Outliers : 2.72 % Allowed : 12.32 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.12), residues: 4965 helix: 0.95 (0.12), residues: 2108 sheet: -0.85 (0.20), residues: 664 loop : -0.45 (0.14), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 603 TYR 0.018 0.001 TYR C 520 PHE 0.020 0.001 PHE B 542 TRP 0.023 0.002 TRP G 248 HIS 0.004 0.001 HIS F 456 Details of bonding type rmsd covalent geometry : bond 0.00396 (39869) covalent geometry : angle 0.59733 (53860) hydrogen bonds : bond 0.03714 ( 1672) hydrogen bonds : angle 4.33995 ( 4722) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 264 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.5626 (OUTLIER) cc_final: 0.5184 (m-40) REVERT: A 216 MET cc_start: 0.8971 (tpt) cc_final: 0.8638 (tpt) REVERT: A 336 ASP cc_start: 0.6845 (m-30) cc_final: 0.6536 (m-30) REVERT: A 365 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8231 (mtm-85) REVERT: A 518 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8867 (tp) REVERT: B 96 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8612 (mm) REVERT: B 445 LEU cc_start: 0.7837 (mm) cc_final: 0.7541 (tp) REVERT: C 107 HIS cc_start: 0.4160 (m90) cc_final: 0.3713 (m90) REVERT: C 613 ASP cc_start: 0.7195 (m-30) cc_final: 0.6566 (m-30) REVERT: D 456 HIS cc_start: 0.7789 (OUTLIER) cc_final: 0.7062 (t-90) REVERT: D 554 TRP cc_start: 0.7649 (t60) cc_final: 0.6673 (t60) REVERT: D 611 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6906 (mt-10) REVERT: D 665 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7736 (pp) REVERT: E 326 ARG cc_start: 0.7016 (ttm110) cc_final: 0.6364 (mtm110) REVERT: F 50 MET cc_start: 0.4521 (mmm) cc_final: 0.3656 (mmm) REVERT: F 273 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7689 (m-40) REVERT: F 334 LEU cc_start: 0.8295 (mt) cc_final: 0.7954 (mt) REVERT: F 682 TYR cc_start: 0.5829 (OUTLIER) cc_final: 0.5159 (t80) REVERT: G 160 MET cc_start: 0.2378 (mmm) cc_final: 0.1888 (mmt) outliers start: 115 outliers final: 85 residues processed: 360 average time/residue: 0.2205 time to fit residues: 135.7410 Evaluate side-chains 352 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 258 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 642 ARG Chi-restraints excluded: chain C residue 661 PHE Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 456 HIS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 476 ASN Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 553 MET Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 661 PHE Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 512 SER Chi-restraints excluded: chain E residue 553 MET Chi-restraints excluded: chain E residue 575 CYS Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 713 LYS Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 247 TYR Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 644 ASP Chi-restraints excluded: chain F residue 682 TYR Chi-restraints excluded: chain F residue 739 HIS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 306 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 287 optimal weight: 0.6980 chunk 198 optimal weight: 0.6980 chunk 284 optimal weight: 0.0020 chunk 448 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 415 optimal weight: 1.9990 chunk 469 optimal weight: 20.0000 chunk 432 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN C 288 ASN ** E 387 HIS ** 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 = 0.4635 r_free = 0.4635 target = 0.212587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.188670 restraints weight = 59574.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.188459 restraints weight = 136260.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.185331 restraints weight = 71104.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.184684 restraints weight = 98835.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.185303 restraints weight = 65940.619| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 39869 Z= 0.108 Angle : 0.550 14.958 53860 Z= 0.264 Chirality : 0.042 0.228 5997 Planarity : 0.004 0.111 7086 Dihedral : 6.613 129.072 5709 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.15 % Favored : 95.83 % Rotamer: Outliers : 2.44 % Allowed : 12.72 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.12), residues: 4965 helix: 1.12 (0.12), residues: 2103 sheet: -0.74 (0.20), residues: 675 loop : -0.40 (0.14), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 603 TYR 0.015 0.001 TYR G 176 PHE 0.019 0.001 PHE C 555 TRP 0.027 0.002 TRP G 248 HIS 0.002 0.000 HIS C 739 Details of bonding type rmsd covalent geometry : bond 0.00248 (39869) covalent geometry : angle 0.54991 (53860) hydrogen bonds : bond 0.03140 ( 1672) hydrogen bonds : angle 4.19319 ( 4722) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 264 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.5702 (OUTLIER) cc_final: 0.5231 (m-40) REVERT: A 216 MET cc_start: 0.8870 (tpt) cc_final: 0.8504 (tpt) REVERT: A 278 MET cc_start: 0.6769 (mmp) cc_final: 0.6200 (mmm) REVERT: A 336 ASP cc_start: 0.6789 (m-30) cc_final: 0.6351 (m-30) REVERT: A 365 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8217 (mtm-85) REVERT: A 518 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8862 (tp) REVERT: A 534 ILE cc_start: 0.9052 (tp) cc_final: 0.8754 (tp) REVERT: B 96 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8536 (mm) REVERT: B 338 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7799 (mm) REVERT: C 50 MET cc_start: 0.5402 (ppp) cc_final: 0.5150 (ppp) REVERT: C 107 HIS cc_start: 0.4275 (m90) cc_final: 0.3829 (m90) REVERT: C 448 MET cc_start: 0.7590 (tpp) cc_final: 0.6584 (tpt) REVERT: C 613 ASP cc_start: 0.7296 (m-30) cc_final: 0.6701 (m-30) REVERT: D 456 HIS cc_start: 0.7708 (OUTLIER) cc_final: 0.7156 (t-90) REVERT: D 554 TRP cc_start: 0.7615 (t60) cc_final: 0.6658 (t60) REVERT: D 611 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7014 (mt-10) REVERT: D 665 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7688 (pp) REVERT: E 456 HIS cc_start: 0.6928 (OUTLIER) cc_final: 0.6675 (m-70) REVERT: E 615 MET cc_start: 0.7110 (tpp) cc_final: 0.6822 (tpp) REVERT: F 50 MET cc_start: 0.4286 (mmm) cc_final: 0.3374 (mmm) REVERT: F 216 MET cc_start: 0.8757 (tpp) cc_final: 0.8414 (tpp) REVERT: F 273 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7558 (m-40) REVERT: F 323 VAL cc_start: 0.7875 (OUTLIER) cc_final: 0.7436 (p) REVERT: F 334 LEU cc_start: 0.8234 (mt) cc_final: 0.7948 (mt) REVERT: F 682 TYR cc_start: 0.5720 (OUTLIER) cc_final: 0.4990 (t80) REVERT: F 696 GLN cc_start: 0.8141 (tp40) cc_final: 0.7692 (tp40) REVERT: G 82 MET cc_start: 0.5441 (mmm) cc_final: 0.4731 (ppp) REVERT: G 160 MET cc_start: 0.2279 (mmm) cc_final: 0.1758 (mmt) outliers start: 103 outliers final: 79 residues processed: 351 average time/residue: 0.2204 time to fit residues: 131.7996 Evaluate side-chains 346 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 255 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 642 ARG Chi-restraints excluded: chain C residue 661 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 456 HIS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 476 ASN Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 553 MET Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 661 PHE Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 456 HIS Chi-restraints excluded: chain E residue 512 SER Chi-restraints excluded: chain E residue 553 MET Chi-restraints excluded: chain E residue 575 CYS Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 713 LYS Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 682 TYR Chi-restraints excluded: chain F residue 739 HIS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 306 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 253 optimal weight: 3.9990 chunk 405 optimal weight: 3.9990 chunk 407 optimal weight: 0.9990 chunk 353 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 175 optimal weight: 0.5980 chunk 250 optimal weight: 0.0470 chunk 452 optimal weight: 6.9990 chunk 404 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 GLN A 760 GLN A 764 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN E 229 HIS ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.212751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.191492 restraints weight = 60189.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.191497 restraints weight = 143657.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.189056 restraints weight = 81555.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.188298 restraints weight = 93759.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.188212 restraints weight = 75801.094| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39869 Z= 0.113 Angle : 0.559 14.887 53860 Z= 0.268 Chirality : 0.043 0.226 5997 Planarity : 0.004 0.109 7086 Dihedral : 6.503 129.048 5706 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.55 % Favored : 95.43 % Rotamer: Outliers : 2.34 % Allowed : 12.84 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.12), residues: 4965 helix: 1.14 (0.12), residues: 2104 sheet: -0.74 (0.20), residues: 682 loop : -0.36 (0.14), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 657 TYR 0.013 0.001 TYR A 682 PHE 0.019 0.001 PHE C 555 TRP 0.029 0.002 TRP G 248 HIS 0.002 0.000 HIS C 456 Details of bonding type rmsd covalent geometry : bond 0.00260 (39869) covalent geometry : angle 0.55902 (53860) hydrogen bonds : bond 0.03145 ( 1672) hydrogen bonds : angle 4.17345 ( 4722) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 264 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.5600 (OUTLIER) cc_final: 0.5161 (m-40) REVERT: A 216 MET cc_start: 0.8896 (tpt) cc_final: 0.8530 (tpt) REVERT: A 278 MET cc_start: 0.6830 (mmp) cc_final: 0.6157 (mmm) REVERT: A 336 ASP cc_start: 0.6677 (m-30) cc_final: 0.6258 (m-30) REVERT: A 365 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8203 (mtm-85) REVERT: A 534 ILE cc_start: 0.9001 (tp) cc_final: 0.8715 (tp) REVERT: B 96 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8527 (mm) REVERT: B 338 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7819 (mm) REVERT: C 50 MET cc_start: 0.5293 (ppp) cc_final: 0.5066 (ppp) REVERT: C 107 HIS cc_start: 0.4140 (m90) cc_final: 0.3682 (m90) REVERT: C 448 MET cc_start: 0.7509 (tpp) cc_final: 0.6658 (tpt) REVERT: C 613 ASP cc_start: 0.7273 (m-30) cc_final: 0.6701 (m-30) REVERT: D 456 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7194 (t-90) REVERT: D 554 TRP cc_start: 0.7440 (t60) cc_final: 0.6578 (t60) REVERT: D 611 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6949 (mt-10) REVERT: D 665 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7756 (pp) REVERT: E 326 ARG cc_start: 0.6925 (ttm110) cc_final: 0.6278 (mtm110) REVERT: F 50 MET cc_start: 0.4359 (mmm) cc_final: 0.3505 (mmm) REVERT: F 216 MET cc_start: 0.8790 (tpp) cc_final: 0.8456 (tpp) REVERT: F 273 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7482 (m-40) REVERT: F 323 VAL cc_start: 0.7901 (OUTLIER) cc_final: 0.7450 (p) REVERT: F 334 LEU cc_start: 0.8267 (mt) cc_final: 0.7954 (mt) REVERT: F 682 TYR cc_start: 0.5683 (OUTLIER) cc_final: 0.5013 (t80) REVERT: F 696 GLN cc_start: 0.8132 (tp40) cc_final: 0.7688 (tp40) REVERT: G 82 MET cc_start: 0.5532 (mmm) cc_final: 0.4814 (ppp) REVERT: G 84 TYR cc_start: 0.2446 (m-10) cc_final: 0.2146 (m-10) REVERT: G 160 MET cc_start: 0.2341 (mmm) cc_final: 0.1749 (mmt) REVERT: G 300 MET cc_start: 0.4349 (mtt) cc_final: 0.2039 (ttt) outliers start: 99 outliers final: 81 residues processed: 349 average time/residue: 0.2244 time to fit residues: 132.5798 Evaluate side-chains 346 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 255 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 642 ARG Chi-restraints excluded: chain C residue 661 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 456 HIS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 476 ASN Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 553 MET Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 661 PHE Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 746 TYR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 512 SER Chi-restraints excluded: chain E residue 553 MET Chi-restraints excluded: chain E residue 575 CYS Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 713 LYS Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 682 TYR Chi-restraints excluded: chain F residue 739 HIS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 221 optimal weight: 4.9990 chunk 202 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 330 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 73 optimal weight: 7.9990 chunk 427 optimal weight: 0.7980 chunk 307 optimal weight: 1.9990 chunk 316 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 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 = 0.4651 r_free = 0.4651 target = 0.211736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.194974 restraints weight = 58027.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.192157 restraints weight = 141997.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.190029 restraints weight = 89671.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188822 restraints weight = 100464.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.189138 restraints weight = 62369.379| |-----------------------------------------------------------------------------| r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 39869 Z= 0.129 Angle : 0.578 14.705 53860 Z= 0.277 Chirality : 0.043 0.231 5997 Planarity : 0.004 0.109 7086 Dihedral : 6.511 129.687 5706 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.53 % Favored : 95.45 % Rotamer: Outliers : 2.27 % Allowed : 13.08 % Favored : 84.65 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.12), residues: 4965 helix: 1.09 (0.12), residues: 2106 sheet: -0.77 (0.20), residues: 684 loop : -0.36 (0.14), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 603 TYR 0.019 0.001 TYR G 176 PHE 0.018 0.001 PHE C 555 TRP 0.032 0.002 TRP G 248 HIS 0.003 0.000 HIS C 456 Details of bonding type rmsd covalent geometry : bond 0.00302 (39869) covalent geometry : angle 0.57839 (53860) hydrogen bonds : bond 0.03265 ( 1672) hydrogen bonds : angle 4.21061 ( 4722) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 263 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.5666 (OUTLIER) cc_final: 0.5196 (m-40) REVERT: A 216 MET cc_start: 0.8949 (tpt) cc_final: 0.8608 (tpt) REVERT: A 278 MET cc_start: 0.6993 (mmp) cc_final: 0.6136 (mmm) REVERT: A 336 ASP cc_start: 0.6766 (m-30) cc_final: 0.6472 (m-30) REVERT: A 365 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8275 (mtm-85) REVERT: A 534 ILE cc_start: 0.8990 (tp) cc_final: 0.8711 (tp) REVERT: B 96 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8538 (mm) REVERT: B 338 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7760 (mm) REVERT: C 50 MET cc_start: 0.5350 (ppp) cc_final: 0.5086 (ppp) REVERT: C 107 HIS cc_start: 0.4156 (m90) cc_final: 0.3708 (m90) REVERT: C 448 MET cc_start: 0.7437 (tpp) cc_final: 0.6689 (tpt) REVERT: C 613 ASP cc_start: 0.7334 (m-30) cc_final: 0.6755 (m-30) REVERT: D 456 HIS cc_start: 0.7812 (OUTLIER) cc_final: 0.7257 (t-90) REVERT: D 554 TRP cc_start: 0.7478 (t60) cc_final: 0.6585 (t60) REVERT: D 611 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6940 (mt-10) REVERT: D 665 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7744 (pp) REVERT: E 326 ARG cc_start: 0.6893 (ttm110) cc_final: 0.6246 (mtm110) REVERT: E 615 MET cc_start: 0.6969 (tpp) cc_final: 0.6598 (tpp) REVERT: F 50 MET cc_start: 0.4258 (mmm) cc_final: 0.3451 (mmm) REVERT: F 216 MET cc_start: 0.8823 (tpp) cc_final: 0.8475 (tpp) REVERT: F 247 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.8175 (p90) REVERT: F 273 ASN cc_start: 0.7978 (OUTLIER) cc_final: 0.7644 (m-40) REVERT: F 323 VAL cc_start: 0.7886 (OUTLIER) cc_final: 0.7427 (p) REVERT: F 334 LEU cc_start: 0.8323 (mt) cc_final: 0.7987 (mt) REVERT: F 682 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.4993 (t80) REVERT: F 696 GLN cc_start: 0.8155 (tp40) cc_final: 0.7692 (tp40) REVERT: G 82 MET cc_start: 0.5570 (mmm) cc_final: 0.4714 (ppp) REVERT: G 160 MET cc_start: 0.2108 (mmm) cc_final: 0.1551 (mmt) REVERT: G 300 MET cc_start: 0.4320 (mtt) cc_final: 0.2007 (ttt) outliers start: 96 outliers final: 80 residues processed: 347 average time/residue: 0.2239 time to fit residues: 132.9635 Evaluate side-chains 345 residues out of total 4228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 254 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 642 ARG Chi-restraints excluded: chain C residue 661 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 456 HIS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 476 ASN Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 553 MET Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 611 GLU Chi-restraints excluded: chain D residue 661 PHE Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 746 TYR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 512 SER Chi-restraints excluded: chain E residue 553 MET Chi-restraints excluded: chain E residue 575 CYS Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 713 LYS Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 247 TYR Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain F residue 682 TYR Chi-restraints excluded: chain F residue 739 HIS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 245 optimal weight: 30.0000 chunk 358 optimal weight: 7.9990 chunk 243 optimal weight: 5.9990 chunk 476 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 384 optimal weight: 20.0000 chunk 240 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 322 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 210 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS B 330 GLN B 497 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS ** C 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 ASN E 288 ASN ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 696 GLN F 606 ASN F 706 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.204471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.188947 restraints weight = 59164.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.183109 restraints weight = 136853.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.178550 restraints weight = 109896.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.178798 restraints weight = 119665.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.178748 restraints weight = 63539.389| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.099 39869 Z= 0.393 Angle : 0.870 17.910 53860 Z= 0.421 Chirality : 0.052 0.233 5997 Planarity : 0.006 0.113 7086 Dihedral : 7.494 137.219 5704 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.69 % Favored : 93.29 % Rotamer: Outliers : 2.39 % Allowed : 13.39 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.12), residues: 4965 helix: 0.16 (0.11), residues: 2123 sheet: -1.25 (0.21), residues: 628 loop : -0.78 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 352 TYR 0.035 0.002 TYR C 520 PHE 0.037 0.003 PHE D 542 TRP 0.035 0.004 TRP G 248 HIS 0.009 0.001 HIS F 343 Details of bonding type rmsd covalent geometry : bond 0.00948 (39869) covalent geometry : angle 0.86981 (53860) hydrogen bonds : bond 0.05706 ( 1672) hydrogen bonds : angle 5.04792 ( 4722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4933.59 seconds wall clock time: 87 minutes 8.95 seconds (5228.95 seconds total)