Starting phenix.real_space_refine on Thu Mar 5 17:12:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7swl_25474/03_2026/7swl_25474.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swl_25474/03_2026/7swl_25474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7swl_25474/03_2026/7swl_25474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swl_25474/03_2026/7swl_25474.map" model { file = "/net/cci-nas-00/data/ceres_data/7swl_25474/03_2026/7swl_25474.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swl_25474/03_2026/7swl_25474.cif" } resolution = 2.88 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 ------------------------------------------------------------------------------- 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= 0.049 sd= 0.336 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 29 5.49 5 Mg 9 5.21 5 S 115 5.16 5 C 14929 2.51 5 N 4252 2.21 5 O 4573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23907 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4238 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 523} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 4262 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 551, 4246 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 522} Chain breaks: 4 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 551, 4246 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 522} Chain breaks: 4 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4294 Chain: "C" Number of atoms: 4320 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 559, 4306 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 530} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 559, 4306 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 530} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 4357 Chain: "D" Number of atoms: 4259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4259 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 525} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 3652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3652 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 456} Chain breaks: 6 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2684 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 329} Chain breaks: 7 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 177 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.64, per 1000 atoms: 0.28 Number of scatterers: 23907 At special positions: 0 Unit cell: (127.595, 146.575, 158.175, 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 115 16.00 P 29 15.00 Mg 9 11.99 O 4573 8.00 N 4252 7.00 C 14929 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: 1.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5698 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 11 sheets defined 61.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 207 through 218 removed outlier: 3.844A pdb=" N LYS A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.983A pdb=" N CYS A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 removed outlier: 3.585A pdb=" N GLY A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 removed outlier: 4.297A pdb=" N ILE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 269 through 273' Processing helix chain 'A' and resid 276 through 294 removed outlier: 4.274A pdb=" N GLU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.965A pdb=" N VAL A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 331 " --> pdb=" O MET A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 407 through 423 Processing helix chain 'A' and resid 423 through 438 removed outlier: 3.682A pdb=" N LEU A 430 " --> pdb=" O ASN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 460 removed outlier: 3.977A pdb=" N HIS A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.711A pdb=" N PHE A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 517 through 523 Processing helix chain 'A' and resid 523 through 529 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.646A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 606 Processing helix chain 'A' and resid 614 through 632 removed outlier: 4.380A pdb=" N SER A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG A 620 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 650 removed outlier: 3.647A pdb=" N ILE A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.772A pdb=" N ARG A 656 " --> pdb=" O ALA A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.658A pdb=" N VAL A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 725 removed outlier: 3.586A pdb=" N GLU A 720 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 729 Processing helix chain 'A' and resid 732 through 755 Processing helix chain 'A' and resid 755 through 760 Processing helix chain 'A' and resid 776 through 786 removed outlier: 3.578A pdb=" N LYS A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 786 " --> pdb=" O LYS A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 799 removed outlier: 4.323A pdb=" N TYR A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 798 " --> pdb=" O PRO A 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 207 through 218 removed outlier: 4.201A pdb=" N LYS B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 removed outlier: 3.531A pdb=" N LEU B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 231 removed outlier: 3.578A pdb=" N CYS B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 270 through 273 Processing helix chain 'B' and resid 278 through 294 removed outlier: 3.658A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 316 through 337 removed outlier: 3.682A pdb=" N SER B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.650A pdb=" N LYS B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 423 Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.697A pdb=" N LEU B 430 " --> pdb=" O ASN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 472 through 483 Processing helix chain 'B' and resid 485 through 489 Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 517 through 523 Processing helix chain 'B' and resid 523 through 531 removed outlier: 3.504A pdb=" N PHE B 527 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 Processing helix chain 'B' and resid 577 through 593 Processing helix chain 'B' and resid 603 through 606 Processing helix chain 'B' and resid 618 through 630 Processing helix chain 'B' and resid 646 through 650 Processing helix chain 'B' and resid 670 through 684 removed outlier: 3.834A pdb=" N VAL B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 725 Processing helix chain 'B' and resid 726 through 729 Processing helix chain 'B' and resid 732 through 761 Processing helix chain 'B' and resid 776 through 784 removed outlier: 3.521A pdb=" N TRP B 780 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 798 Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.533A pdb=" N ILE C 204 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 218 removed outlier: 4.089A pdb=" N LYS C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 224 removed outlier: 3.511A pdb=" N LEU C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.524A pdb=" N CYS C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 259 removed outlier: 3.507A pdb=" N GLY C 258 " --> pdb=" O HIS C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 273 Processing helix chain 'C' and resid 278 through 294 removed outlier: 3.697A pdb=" N ILE C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 317 through 337 removed outlier: 4.173A pdb=" N ARG C 334 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR C 337 " --> pdb=" O ILE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.506A pdb=" N GLN C 379 " --> pdb=" O ARG C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 407 through 423 Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.572A pdb=" N LEU C 430 " --> pdb=" O ASN C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 459 Processing helix chain 'C' and resid 472 through 483 removed outlier: 3.903A pdb=" N SER C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 489 Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 506 through 517 Processing helix chain 'C' and resid 517 through 523 Processing helix chain 'C' and resid 523 through 530 removed outlier: 3.785A pdb=" N PHE C 527 " --> pdb=" O ASN C 523 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 559 Processing helix chain 'C' and resid 577 through 593 Processing helix chain 'C' and resid 603 through 606 Processing helix chain 'C' and resid 615 through 630 removed outlier: 3.868A pdb=" N VAL C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 622 " --> pdb=" O SER C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 650 Processing helix chain 'C' and resid 670 through 684 removed outlier: 3.649A pdb=" N VAL C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 676 " --> pdb=" O GLU C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 725 Processing helix chain 'C' and resid 726 through 729 Processing helix chain 'C' and resid 732 through 761 Processing helix chain 'C' and resid 776 through 785 removed outlier: 3.572A pdb=" N LYS C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 799 removed outlier: 4.167A pdb=" N TYR C 797 " --> pdb=" O ASP C 793 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS C 799 " --> pdb=" O GLU C 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 207 through 218 removed outlier: 3.662A pdb=" N LEU D 211 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 248 through 261 removed outlier: 3.527A pdb=" N GLY D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 removed outlier: 4.238A pdb=" N ILE D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 269 through 273' Processing helix chain 'D' and resid 278 through 294 removed outlier: 3.609A pdb=" N ILE D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 317 through 337 removed outlier: 3.526A pdb=" N ILE D 333 " --> pdb=" O GLY D 329 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN D 335 " --> pdb=" O ASP D 331 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 407 through 423 Processing helix chain 'D' and resid 424 through 435 removed outlier: 3.679A pdb=" N LEU D 430 " --> pdb=" O ASN D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 460 Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.554A pdb=" N SER D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 489 removed outlier: 3.625A pdb=" N ARG D 489 " --> pdb=" O ALA D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 506 through 517 Processing helix chain 'D' and resid 517 through 523 Processing helix chain 'D' and resid 523 through 530 removed outlier: 3.895A pdb=" N VAL D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.514A pdb=" N VAL D 555 " --> pdb=" O VAL D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 593 removed outlier: 3.603A pdb=" N VAL D 583 " --> pdb=" O SER D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 606 Processing helix chain 'D' and resid 618 through 630 Processing helix chain 'D' and resid 646 through 650 Processing helix chain 'D' and resid 670 through 684 removed outlier: 3.737A pdb=" N VAL D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS D 676 " --> pdb=" O GLU D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 725 removed outlier: 3.561A pdb=" N GLU D 720 " --> pdb=" O ASP D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 729 Processing helix chain 'D' and resid 732 through 754 Processing helix chain 'D' and resid 776 through 787 removed outlier: 3.910A pdb=" N ASN D 785 " --> pdb=" O GLU D 781 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 786 " --> pdb=" O LYS D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 799 removed outlier: 3.722A pdb=" N HIS D 799 " --> pdb=" O GLU D 795 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 204 Processing helix chain 'E' and resid 207 through 218 removed outlier: 3.727A pdb=" N LEU E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 224 removed outlier: 3.550A pdb=" N LEU E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 232 removed outlier: 4.187A pdb=" N CYS E 228 " --> pdb=" O GLY E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 261 removed outlier: 3.717A pdb=" N GLY E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'E' and resid 278 through 294 Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 316 through 336 Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 356 through 362 removed outlier: 3.849A pdb=" N ARG E 362 " --> pdb=" O ALA E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 402 removed outlier: 3.849A pdb=" N LEU E 399 " --> pdb=" O ASN E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 422 Processing helix chain 'E' and resid 472 through 483 removed outlier: 3.738A pdb=" N PHE E 476 " --> pdb=" O THR E 472 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER E 481 " --> pdb=" O ARG E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 503 Processing helix chain 'E' and resid 506 through 517 removed outlier: 3.550A pdb=" N MET E 515 " --> pdb=" O LYS E 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 523 removed outlier: 3.517A pdb=" N LYS E 522 " --> pdb=" O ILE E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 530 removed outlier: 3.639A pdb=" N VAL E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 560 Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 577 through 593 removed outlier: 3.731A pdb=" N VAL E 583 " --> pdb=" O SER E 579 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE E 587 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER E 588 " --> pdb=" O ARG E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 606 Processing helix chain 'E' and resid 616 through 629 removed outlier: 3.631A pdb=" N VAL E 621 " --> pdb=" O ALA E 617 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL E 622 " --> pdb=" O SER E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 632 No H-bonds generated for 'chain 'E' and resid 630 through 632' Processing helix chain 'E' and resid 646 through 650 removed outlier: 3.846A pdb=" N ILE E 650 " --> pdb=" O PRO E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 651 through 656 removed outlier: 3.704A pdb=" N ARG E 656 " --> pdb=" O ALA E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 683 Processing helix chain 'E' and resid 716 through 724 removed outlier: 3.598A pdb=" N VAL E 722 " --> pdb=" O ASP E 718 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 723 " --> pdb=" O LEU E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 750 removed outlier: 3.851A pdb=" N GLY E 737 " --> pdb=" O GLY E 733 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN E 741 " --> pdb=" O GLY E 737 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 746 " --> pdb=" O ALA E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 777 through 785 removed outlier: 4.255A pdb=" N GLU E 781 " --> pdb=" O MET E 777 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS E 782 " --> pdb=" O GLU E 778 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA E 783 " --> pdb=" O ASP E 779 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN E 785 " --> pdb=" O GLU E 781 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 385 removed outlier: 4.243A pdb=" N GLN F 379 " --> pdb=" O ARG F 375 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 380 " --> pdb=" O ALA F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 402 removed outlier: 3.522A pdb=" N MET F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 436 removed outlier: 3.889A pdb=" N TYR F 413 " --> pdb=" O SER F 409 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN F 426 " --> pdb=" O SER F 422 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA F 436 " --> pdb=" O ALA F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 460 removed outlier: 3.959A pdb=" N HIS F 459 " --> pdb=" O LEU F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 483 removed outlier: 3.560A pdb=" N SER F 481 " --> pdb=" O ARG F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 489 Processing helix chain 'F' and resid 506 through 517 removed outlier: 3.980A pdb=" N LYS F 511 " --> pdb=" O GLU F 507 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS F 512 " --> pdb=" O ASP F 508 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET F 515 " --> pdb=" O LYS F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.996A pdb=" N LYS F 522 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN F 523 " --> pdb=" O GLY F 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 518 through 523' Processing helix chain 'F' and resid 526 through 531 Processing helix chain 'F' and resid 547 through 559 Processing helix chain 'F' and resid 567 through 572 Processing helix chain 'F' and resid 580 through 593 removed outlier: 3.549A pdb=" N ARG F 584 " --> pdb=" O GLU F 580 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE F 587 " --> pdb=" O VAL F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 602 through 606 Processing helix chain 'F' and resid 620 through 631 removed outlier: 3.680A pdb=" N LEU F 626 " --> pdb=" O VAL F 622 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 628 " --> pdb=" O THR F 624 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP F 630 " --> pdb=" O LEU F 626 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLY F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 670 through 685 removed outlier: 4.002A pdb=" N LYS F 676 " --> pdb=" O GLU F 672 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU F 681 " --> pdb=" O ILE F 677 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN F 684 " --> pdb=" O THR F 680 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR F 685 " --> pdb=" O LEU F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 723 removed outlier: 3.762A pdb=" N ALA F 723 " --> pdb=" O LEU F 719 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 754 removed outlier: 3.583A pdb=" N GLY F 737 " --> pdb=" O GLY F 733 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN F 738 " --> pdb=" O ALA F 734 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU F 739 " --> pdb=" O ASP F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 776 through 785 removed outlier: 3.552A pdb=" N TRP F 780 " --> pdb=" O THR F 776 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS F 782 " --> pdb=" O GLU F 778 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA F 783 " --> pdb=" O ASP F 779 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN F 785 " --> pdb=" O GLU F 781 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.630A pdb=" N ALA A 263 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE A 300 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A 265 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP A 302 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 267 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N CYS A 297 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU A 346 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE A 299 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA A 348 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 301 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 240 " --> pdb=" O ILE A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 562 through 567 removed outlier: 6.531A pdb=" N CYS A 596 " --> pdb=" O TYR A 639 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 641 " --> pdb=" O CYS A 596 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU A 598 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ALA A 643 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE A 600 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 536 " --> pdb=" O ILE A 638 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.655A pdb=" N ALA B 263 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE B 300 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE B 265 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASP B 302 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 267 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N CYS B 297 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 346 " --> pdb=" O CYS B 297 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ILE B 299 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA B 348 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 301 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 562 through 567 removed outlier: 6.305A pdb=" N CYS B 596 " --> pdb=" O TYR B 639 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE B 641 " --> pdb=" O CYS B 596 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU B 598 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA B 643 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE B 600 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 536 " --> pdb=" O ILE B 638 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.391A pdb=" N CYS C 297 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU C 346 " --> pdb=" O CYS C 297 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE C 299 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA C 348 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU C 301 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY C 238 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE C 367 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 240 " --> pdb=" O ILE C 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 562 through 567 removed outlier: 6.322A pdb=" N CYS C 596 " --> pdb=" O TYR C 639 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE C 641 " --> pdb=" O CYS C 596 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU C 598 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA C 643 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE C 600 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 536 " --> pdb=" O ILE C 638 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY C 537 " --> pdb=" O THR C 662 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE C 664 " --> pdb=" O GLY C 537 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 539 " --> pdb=" O ILE C 664 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 263 through 268 removed outlier: 6.487A pdb=" N CYS D 297 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU D 346 " --> pdb=" O CYS D 297 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE D 299 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA D 348 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU D 301 " --> pdb=" O ALA D 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 562 through 567 removed outlier: 6.352A pdb=" N CYS D 596 " --> pdb=" O TYR D 639 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE D 641 " --> pdb=" O CYS D 596 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU D 598 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA D 643 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE D 600 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY D 537 " --> pdb=" O THR D 662 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE D 664 " --> pdb=" O GLY D 537 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU D 539 " --> pdb=" O ILE D 664 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.369A pdb=" N CYS E 297 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU E 346 " --> pdb=" O CYS E 297 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE E 299 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA E 348 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU E 301 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 562 through 566 removed outlier: 6.472A pdb=" N ASN E 562 " --> pdb=" O ILE E 597 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N PHE E 599 " --> pdb=" O ASN E 562 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE E 564 " --> pdb=" O PHE E 599 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP E 601 " --> pdb=" O ILE E 564 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE E 566 " --> pdb=" O ASP E 601 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE E 538 " --> pdb=" O GLY E 642 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR E 644 " --> pdb=" O ILE E 538 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU E 540 " --> pdb=" O THR E 644 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR E 662 " --> pdb=" O GLY E 537 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 492 through 493 removed outlier: 6.386A pdb=" N ASN F 562 " --> pdb=" O ILE F 597 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE F 599 " --> pdb=" O ASN F 562 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE F 564 " --> pdb=" O PHE F 599 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N CYS F 596 " --> pdb=" O TYR F 639 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE F 641 " --> pdb=" O CYS F 596 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU F 598 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA F 643 " --> pdb=" O LEU F 598 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE F 600 " --> pdb=" O ALA F 643 " (cutoff:3.500A) 1172 hydrogen bonds defined for protein. 3272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.13 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8024 1.34 - 1.46: 4124 1.46 - 1.58: 11891 1.58 - 1.69: 48 1.69 - 1.81: 192 Bond restraints: 24279 Sorted by residual: bond pdb=" O5' ATP E 902 " pdb=" PA ATP E 902 " ideal model delta sigma weight residual 1.579 1.610 -0.031 1.10e-02 8.26e+03 7.98e+00 bond pdb=" O5' ATP A 901 " pdb=" PA ATP A 901 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.43e+00 bond pdb=" O5' ATP A 902 " pdb=" PA ATP A 902 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.36e+00 bond pdb=" O5' ATP D 901 " pdb=" PA ATP D 901 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.33e+00 bond pdb=" O5' ATP B 901 " pdb=" PA ATP B 901 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.24e+00 ... (remaining 24274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 32534 2.09 - 4.18: 271 4.18 - 6.27: 49 6.27 - 8.36: 12 8.36 - 10.45: 7 Bond angle restraints: 32873 Sorted by residual: angle pdb=" PB ATP E 902 " pdb=" O3B ATP E 902 " pdb=" PG ATP E 902 " ideal model delta sigma weight residual 139.87 129.42 10.45 1.00e+00 1.00e+00 1.09e+02 angle pdb=" PB ATP B 901 " pdb=" O3B ATP B 901 " pdb=" PG ATP B 901 " ideal model delta sigma weight residual 139.87 129.59 10.28 1.00e+00 1.00e+00 1.06e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 129.89 9.98 1.00e+00 1.00e+00 9.95e+01 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 130.23 9.64 1.00e+00 1.00e+00 9.30e+01 angle pdb=" PB ATP D 902 " pdb=" O3B ATP D 902 " pdb=" PG ATP D 902 " ideal model delta sigma weight residual 139.87 130.92 8.95 1.00e+00 1.00e+00 8.01e+01 ... (remaining 32868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 14690 24.83 - 49.65: 329 49.65 - 74.48: 85 74.48 - 99.31: 9 99.31 - 124.13: 1 Dihedral angle restraints: 15114 sinusoidal: 6318 harmonic: 8796 Sorted by residual: dihedral pdb=" C5' ADP E 901 " pdb=" O5' ADP E 901 " pdb=" PA ADP E 901 " pdb=" O2A ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 175.87 124.13 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" O2A ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PA ADP E 901 " pdb=" PB ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 -134.83 74.83 1 2.00e+01 2.50e-03 1.77e+01 dihedral pdb=" CA ARG D 635 " pdb=" CB ARG D 635 " pdb=" CG ARG D 635 " pdb=" CD ARG D 635 " ideal model delta sinusoidal sigma weight residual 60.00 118.64 -58.64 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 15111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2259 0.029 - 0.058: 1036 0.058 - 0.087: 220 0.087 - 0.116: 211 0.116 - 0.144: 36 Chirality restraints: 3762 Sorted by residual: chirality pdb=" C3' ATP D 902 " pdb=" C2' ATP D 902 " pdb=" C4' ATP D 902 " pdb=" O3' ATP D 902 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" C3' ATP E 902 " pdb=" C2' ATP E 902 " pdb=" C4' ATP E 902 " pdb=" O3' ATP E 902 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" C3' ATP A 901 " pdb=" C2' ATP A 901 " pdb=" C4' ATP A 901 " pdb=" O3' ATP A 901 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 3759 not shown) Planarity restraints: 4214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 356 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 357 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 357 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 357 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 519 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.43e+00 pdb=" N PRO A 520 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 520 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 220 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO D 221 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " -0.016 5.00e-02 4.00e+02 ... (remaining 4211 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 172 2.54 - 3.13: 18071 3.13 - 3.72: 36542 3.72 - 4.31: 53475 4.31 - 4.90: 89334 Nonbonded interactions: 197594 Sorted by model distance: nonbonded pdb=" O1B ATP B 901 " pdb="MG MG B 903 " model vdw 1.953 2.170 nonbonded pdb=" O1B ATP C 902 " pdb="MG MG C 904 " model vdw 1.970 2.170 nonbonded pdb=" O1B ATP D 902 " pdb="MG MG D 904 " model vdw 1.993 2.170 nonbonded pdb=" O2G ATP D 901 " pdb="MG MG D 903 " model vdw 1.994 2.170 nonbonded pdb=" O2G ATP C 902 " pdb="MG MG C 904 " model vdw 1.995 2.170 ... (remaining 197589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 200 through 302 or resid 304 through 388 or resid 394 thro \ ugh 425 or resid 470 through 483 or (resid 484 and (name N or name CA or name C \ or name O or name CB )) or resid 485 through 487 or resid 494 through 588 or res \ id 590 through 634 or (resid 635 and (name N or name CA or name C or name O or n \ ame CB )) or resid 636 through 654 or resid 656 through 726 or resid 732 through \ 751 or resid 775 through 788 or resid 904)) selection = (chain 'B' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 388 or resid 394 through 425 or resid 470 through 483 or (resid 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 through 487 or res \ id 494 through 588 or resid 590 through 634 or (resid 635 and (name N or name CA \ or name C or name O or name CB )) or resid 636 through 654 or resid 656 through \ 726 or resid 732 through 751 or resid 775 through 788 or resid 904)) selection = (chain 'C' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 388 or resid 394 through 425 or resid 470 through 483 or (resid 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 through 487 or res \ id 494 through 588 or resid 590 through 634 or (resid 635 and (name N or name CA \ or name C or name O or name CB )) or resid 636 through 654 or resid 656 through \ 726 or resid 732 through 751 or resid 775 through 788 or resid 904)) selection = (chain 'D' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 388 or resid 394 through 425 or resid 470 through 483 or (resid 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 through 487 or res \ id 494 through 588 or resid 590 through 634 or (resid 635 and (name N or name CA \ or name C or name O or name CB )) or resid 636 through 654 or resid 656 through \ 726 or resid 732 through 751 or resid 775 through 788 or resid 904)) selection = (chain 'E' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 588 or resid 590 through 654 or resid 656 through 788 or resid 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.260 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.003 0.053 24279 Z= 0.152 Angle : 0.509 10.455 32873 Z= 0.305 Chirality : 0.040 0.144 3762 Planarity : 0.003 0.035 4214 Dihedral : 11.234 124.134 9416 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 0.95 % Allowed : 2.88 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.12 (0.16), residues: 3006 helix: -0.21 (0.13), residues: 1583 sheet: 0.79 (0.28), residues: 365 loop : 0.65 (0.21), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 377 TYR 0.009 0.001 TYR B 406 PHE 0.008 0.001 PHE C 264 TRP 0.005 0.001 TRP E 541 HIS 0.003 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00323 (24279) covalent geometry : angle 0.50948 (32873) hydrogen bonds : bond 0.27120 ( 1172) hydrogen bonds : angle 7.44932 ( 3272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 541 time to evaluate : 0.914 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8647 (tp) REVERT: A 208 ASP cc_start: 0.7875 (m-30) cc_final: 0.7465 (m-30) REVERT: A 401 LYS cc_start: 0.8407 (mtmt) cc_final: 0.8180 (tptt) REVERT: A 735 ASP cc_start: 0.8623 (m-30) cc_final: 0.8321 (m-30) REVERT: B 351 ARG cc_start: 0.7899 (mmt-90) cc_final: 0.7691 (mmt90) REVERT: B 649 MET cc_start: 0.8070 (mmm) cc_final: 0.7754 (mmp) REVERT: B 777 MET cc_start: 0.8479 (tpt) cc_final: 0.8260 (tpt) REVERT: C 286 ASP cc_start: 0.7882 (m-30) cc_final: 0.7607 (m-30) REVERT: C 635 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7989 (ppt170) REVERT: C 757 GLN cc_start: 0.6926 (tt0) cc_final: 0.6534 (mt0) REVERT: D 401 LYS cc_start: 0.8520 (mtmt) cc_final: 0.8220 (tttp) REVERT: D 778 GLU cc_start: 0.8054 (pt0) cc_final: 0.7683 (tp30) REVERT: E 416 LYS cc_start: 0.7499 (mttt) cc_final: 0.7083 (mmtt) REVERT: E 472 THR cc_start: 0.7282 (OUTLIER) cc_final: 0.7080 (t) REVERT: E 473 MET cc_start: 0.6010 (tmm) cc_final: 0.5747 (ppp) REVERT: E 475 GLN cc_start: 0.6054 (mt0) cc_final: 0.5675 (mt0) REVERT: E 526 LEU cc_start: 0.8078 (tp) cc_final: 0.7530 (tp) REVERT: E 639 TYR cc_start: 0.7789 (m-80) cc_final: 0.7388 (m-80) REVERT: E 776 THR cc_start: 0.6000 (p) cc_final: 0.5736 (t) REVERT: F 424 GLN cc_start: 0.7342 (tp40) cc_final: 0.6571 (tt0) REVERT: F 586 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7038 (mp) REVERT: F 601 ASP cc_start: 0.6872 (p0) cc_final: 0.6355 (t0) REVERT: F 649 MET cc_start: 0.6171 (mmm) cc_final: 0.5468 (mmm) REVERT: F 754 GLN cc_start: 0.6943 (mt0) cc_final: 0.6285 (pp30) REVERT: F 782 LYS cc_start: 0.6716 (ptpp) cc_final: 0.6147 (tttp) outliers start: 24 outliers final: 7 residues processed: 559 average time/residue: 0.7877 time to fit residues: 491.5988 Evaluate side-chains 339 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 328 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain G residue 18 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN C 424 GLN C 438 HIS C 459 HIS C 562 ASN C 585 GLN D 433 GLN D 741 GLN E 335 GLN E 523 ASN E 602 GLN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 745 GLN F 433 GLN F 484 GLN F 785 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.171197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131393 restraints weight = 54113.570| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 4.16 r_work: 0.3140 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24279 Z= 0.135 Angle : 0.554 8.796 32873 Z= 0.286 Chirality : 0.043 0.269 3762 Planarity : 0.004 0.049 4214 Dihedral : 11.388 102.783 3662 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.80 % Rotamer: Outliers : 2.37 % Allowed : 10.96 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.71 (0.16), residues: 3006 helix: 0.50 (0.13), residues: 1614 sheet: 0.51 (0.27), residues: 381 loop : 0.74 (0.22), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 609 TYR 0.013 0.001 TYR A 752 PHE 0.019 0.001 PHE E 527 TRP 0.010 0.001 TRP F 466 HIS 0.002 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00280 (24279) covalent geometry : angle 0.55394 (32873) hydrogen bonds : bond 0.05197 ( 1172) hydrogen bonds : angle 4.74658 ( 3272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 396 time to evaluate : 0.963 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 223 ARG cc_start: 0.6337 (tpm170) cc_final: 0.6123 (tpt170) REVERT: A 351 ARG cc_start: 0.7194 (mmp-170) cc_final: 0.6533 (tpp-160) REVERT: A 354 PHE cc_start: 0.7454 (m-10) cc_final: 0.7128 (m-10) REVERT: A 355 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6901 (mp) REVERT: A 401 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8246 (tptt) REVERT: A 560 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8865 (mttp) REVERT: A 716 ASP cc_start: 0.7965 (t0) cc_final: 0.7227 (m-30) REVERT: A 735 ASP cc_start: 0.9025 (m-30) cc_final: 0.8685 (m-30) REVERT: A 781 GLU cc_start: 0.8116 (tp30) cc_final: 0.7771 (tt0) REVERT: A 796 LYS cc_start: 0.5486 (tmtp) cc_final: 0.4865 (mmpt) REVERT: B 320 SER cc_start: 0.8548 (t) cc_final: 0.8319 (m) REVERT: B 325 GLU cc_start: 0.8116 (tp30) cc_final: 0.7638 (tp30) REVERT: B 335 GLN cc_start: 0.8156 (mt0) cc_final: 0.7938 (mt0) REVERT: B 433 GLN cc_start: 0.7802 (tp40) cc_final: 0.7400 (tm-30) REVERT: B 477 ARG cc_start: 0.8217 (mtt90) cc_final: 0.7938 (mtt90) REVERT: B 515 MET cc_start: 0.8991 (tpt) cc_final: 0.8773 (tpp) REVERT: B 755 ARG cc_start: 0.6494 (ttp-170) cc_final: 0.6269 (ttp80) REVERT: B 777 MET cc_start: 0.8798 (tpt) cc_final: 0.8565 (tpt) REVERT: C 286 ASP cc_start: 0.8265 (m-30) cc_final: 0.7954 (m-30) REVERT: C 635 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8566 (ppt-90) REVERT: C 757 GLN cc_start: 0.6710 (tt0) cc_final: 0.6311 (mt0) REVERT: D 234 ARG cc_start: 0.7844 (ttm110) cc_final: 0.7513 (ttm110) REVERT: D 421 GLU cc_start: 0.7779 (tp30) cc_final: 0.7164 (tp30) REVERT: D 533 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8133 (mptp) REVERT: D 778 GLU cc_start: 0.8361 (pt0) cc_final: 0.7517 (tp30) REVERT: D 781 GLU cc_start: 0.7518 (mp0) cc_final: 0.7158 (mp0) REVERT: E 223 ARG cc_start: 0.8103 (tpm170) cc_final: 0.7884 (mmt-90) REVERT: E 231 MET cc_start: 0.5415 (ptp) cc_final: 0.5203 (ptm) REVERT: E 234 ARG cc_start: 0.7538 (mtt90) cc_final: 0.7257 (ttm-80) REVERT: E 282 LYS cc_start: 0.7633 (tttt) cc_final: 0.7018 (tmtm) REVERT: E 318 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7067 (ttt) REVERT: E 320 SER cc_start: 0.7398 (t) cc_final: 0.7100 (m) REVERT: E 416 LYS cc_start: 0.7077 (mttt) cc_final: 0.6687 (mmtt) REVERT: E 472 THR cc_start: 0.7063 (OUTLIER) cc_final: 0.6675 (t) REVERT: E 475 GLN cc_start: 0.5390 (mt0) cc_final: 0.5091 (mm-40) REVERT: E 477 ARG cc_start: 0.7001 (mtm180) cc_final: 0.6361 (mtm110) REVERT: E 478 LYS cc_start: 0.6613 (tptp) cc_final: 0.6211 (mmtp) REVERT: E 507 GLU cc_start: 0.7107 (mp0) cc_final: 0.6712 (tm-30) REVERT: E 515 MET cc_start: 0.8401 (ttp) cc_final: 0.8095 (tpp) REVERT: E 567 LYS cc_start: 0.7796 (tptp) cc_final: 0.7556 (tptp) REVERT: E 649 MET cc_start: 0.7769 (mmm) cc_final: 0.7285 (tmt) REVERT: E 741 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6376 (tt0) REVERT: E 750 ARG cc_start: 0.4906 (ttp80) cc_final: 0.3872 (tpt90) REVERT: F 424 GLN cc_start: 0.7090 (tp40) cc_final: 0.6319 (tt0) REVERT: F 604 ASP cc_start: 0.7472 (p0) cc_final: 0.6777 (p0) REVERT: F 754 GLN cc_start: 0.6571 (mt0) cc_final: 0.6021 (pp30) REVERT: F 782 LYS cc_start: 0.6448 (ptpp) cc_final: 0.6189 (tttp) REVERT: F 786 GLU cc_start: 0.6007 (mp0) cc_final: 0.5038 (mt-10) REVERT: G 17 LEU cc_start: 0.8343 (mp) cc_final: 0.8045 (mp) outliers start: 60 outliers final: 18 residues processed: 431 average time/residue: 0.7846 time to fit residues: 378.6496 Evaluate side-chains 363 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 338 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 741 GLN Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 182 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 289 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 424 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS ** E 623 ASN ** 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 = 0.3973 r_free = 0.3973 target = 0.166976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126724 restraints weight = 48249.315| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.86 r_work: 0.3105 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 24279 Z= 0.227 Angle : 0.605 8.730 32873 Z= 0.304 Chirality : 0.046 0.195 3762 Planarity : 0.005 0.047 4214 Dihedral : 11.605 93.248 3653 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 2.80 % Allowed : 12.15 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.62 (0.16), residues: 3006 helix: 0.55 (0.13), residues: 1616 sheet: 0.27 (0.26), residues: 379 loop : 0.55 (0.22), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 609 TYR 0.015 0.002 TYR B 406 PHE 0.024 0.002 PHE E 527 TRP 0.011 0.001 TRP F 466 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00556 (24279) covalent geometry : angle 0.60526 (32873) hydrogen bonds : bond 0.04812 ( 1172) hydrogen bonds : angle 4.51724 ( 3272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 347 time to evaluate : 0.965 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 351 ARG cc_start: 0.7458 (mmp-170) cc_final: 0.6865 (tpp-160) REVERT: A 371 MET cc_start: 0.8962 (mtt) cc_final: 0.8610 (mtt) REVERT: A 392 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7173 (m-30) REVERT: A 474 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: A 560 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8936 (mttp) REVERT: A 735 ASP cc_start: 0.9052 (m-30) cc_final: 0.8683 (m-30) REVERT: A 796 LYS cc_start: 0.6166 (tmtp) cc_final: 0.5472 (mmpt) REVERT: B 320 SER cc_start: 0.8473 (t) cc_final: 0.8251 (m) REVERT: B 325 GLU cc_start: 0.8163 (tp30) cc_final: 0.7604 (tp30) REVERT: B 335 GLN cc_start: 0.8137 (mt0) cc_final: 0.7905 (mt0) REVERT: B 433 GLN cc_start: 0.7797 (tp40) cc_final: 0.7421 (tm-30) REVERT: B 755 ARG cc_start: 0.6531 (ttp-170) cc_final: 0.6322 (ttp80) REVERT: B 777 MET cc_start: 0.8838 (tpt) cc_final: 0.8523 (mmm) REVERT: C 286 ASP cc_start: 0.8227 (m-30) cc_final: 0.7705 (m-30) REVERT: C 635 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8581 (ppt-90) REVERT: C 757 GLN cc_start: 0.6490 (tt0) cc_final: 0.6189 (mt0) REVERT: D 330 MET cc_start: 0.9083 (mtp) cc_final: 0.8859 (mtm) REVERT: D 421 GLU cc_start: 0.7811 (tp30) cc_final: 0.7259 (tp30) REVERT: D 533 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8090 (mptp) REVERT: D 781 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7306 (mp0) REVERT: E 282 LYS cc_start: 0.7423 (tttt) cc_final: 0.7131 (tptp) REVERT: E 318 MET cc_start: 0.7424 (ttp) cc_final: 0.7055 (ttt) REVERT: E 320 SER cc_start: 0.7723 (t) cc_final: 0.7394 (m) REVERT: E 477 ARG cc_start: 0.6836 (mtm180) cc_final: 0.6359 (mtp-110) REVERT: E 478 LYS cc_start: 0.6573 (tptp) cc_final: 0.6155 (mmtp) REVERT: E 526 LEU cc_start: 0.8075 (tp) cc_final: 0.7857 (tp) REVERT: E 585 GLN cc_start: 0.8315 (tt0) cc_final: 0.8035 (mm-40) REVERT: E 602 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7596 (tt0) REVERT: E 639 TYR cc_start: 0.8290 (m-80) cc_final: 0.8009 (m-80) REVERT: E 741 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6492 (tt0) REVERT: F 424 GLN cc_start: 0.7161 (tp40) cc_final: 0.6322 (tt0) REVERT: F 473 MET cc_start: 0.6198 (tpt) cc_final: 0.5997 (mmm) REVERT: F 539 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7064 (tm) REVERT: F 603 MET cc_start: 0.6425 (OUTLIER) cc_final: 0.6124 (ptm) REVERT: F 754 GLN cc_start: 0.6918 (mt0) cc_final: 0.6206 (pt0) REVERT: F 782 LYS cc_start: 0.6762 (ptpp) cc_final: 0.6258 (tttp) REVERT: G 17 LEU cc_start: 0.8405 (mp) cc_final: 0.8076 (mp) outliers start: 71 outliers final: 32 residues processed: 386 average time/residue: 0.7813 time to fit residues: 337.0492 Evaluate side-chains 362 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 322 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 741 GLN Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 603 MET Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 195 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 267 optimal weight: 8.9990 chunk 243 optimal weight: 1.9990 chunk 25 optimal weight: 30.0000 chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS C 523 ASN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.169885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.130199 restraints weight = 51436.791| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 4.03 r_work: 0.3128 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24279 Z= 0.123 Angle : 0.525 9.037 32873 Z= 0.261 Chirality : 0.042 0.170 3762 Planarity : 0.004 0.041 4214 Dihedral : 11.261 90.245 3650 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 2.33 % Allowed : 13.53 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.16), residues: 3006 helix: 0.91 (0.13), residues: 1617 sheet: 0.19 (0.26), residues: 378 loop : 0.64 (0.22), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 375 TYR 0.010 0.001 TYR A 752 PHE 0.021 0.001 PHE E 527 TRP 0.015 0.001 TRP F 466 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00288 (24279) covalent geometry : angle 0.52488 (32873) hydrogen bonds : bond 0.03626 ( 1172) hydrogen bonds : angle 4.20298 ( 3272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 353 time to evaluate : 0.895 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 351 ARG cc_start: 0.7316 (mmp-170) cc_final: 0.6788 (tpp-160) REVERT: A 490 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: A 560 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8977 (mttp) REVERT: A 735 ASP cc_start: 0.9046 (m-30) cc_final: 0.8693 (m-30) REVERT: A 795 GLU cc_start: 0.7327 (pp20) cc_final: 0.7114 (pp20) REVERT: A 796 LYS cc_start: 0.6211 (tmtp) cc_final: 0.5472 (mmpt) REVERT: B 325 GLU cc_start: 0.8116 (tp30) cc_final: 0.7595 (tp30) REVERT: B 335 GLN cc_start: 0.8050 (mt0) cc_final: 0.7799 (mt0) REVERT: B 433 GLN cc_start: 0.7698 (tp40) cc_final: 0.7384 (tm-30) REVERT: B 755 ARG cc_start: 0.6544 (ttp-170) cc_final: 0.6312 (ttp80) REVERT: B 777 MET cc_start: 0.8796 (tpt) cc_final: 0.8473 (mmm) REVERT: C 223 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7692 (mpt180) REVERT: C 231 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7533 (ptm) REVERT: C 286 ASP cc_start: 0.8177 (m-30) cc_final: 0.7855 (m-30) REVERT: C 421 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: C 435 ARG cc_start: 0.6901 (mtt90) cc_final: 0.6510 (mtt90) REVERT: C 635 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8321 (ppt170) REVERT: D 421 GLU cc_start: 0.7735 (tp30) cc_final: 0.7141 (tp30) REVERT: D 778 GLU cc_start: 0.8382 (pt0) cc_final: 0.7555 (tp30) REVERT: E 223 ARG cc_start: 0.8111 (tpm170) cc_final: 0.7774 (mmt-90) REVERT: E 234 ARG cc_start: 0.7605 (mtt90) cc_final: 0.7181 (ttp-110) REVERT: E 318 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6961 (ttt) REVERT: E 320 SER cc_start: 0.7542 (t) cc_final: 0.7248 (m) REVERT: E 477 ARG cc_start: 0.6652 (mtm180) cc_final: 0.6335 (mtm-85) REVERT: E 478 LYS cc_start: 0.6543 (tptp) cc_final: 0.6155 (mmtp) REVERT: E 526 LEU cc_start: 0.8070 (tp) cc_final: 0.7676 (tp) REVERT: E 550 LEU cc_start: 0.8160 (tp) cc_final: 0.7949 (tt) REVERT: E 585 GLN cc_start: 0.8294 (tt0) cc_final: 0.8039 (mm-40) REVERT: E 602 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7549 (tt0) REVERT: E 639 TYR cc_start: 0.8269 (m-80) cc_final: 0.7955 (m-80) REVERT: E 741 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6798 (mm-40) REVERT: F 424 GLN cc_start: 0.7041 (tp40) cc_final: 0.6217 (tt0) REVERT: F 539 LEU cc_start: 0.7160 (tm) cc_final: 0.6875 (tm) REVERT: F 603 MET cc_start: 0.6339 (OUTLIER) cc_final: 0.6125 (ptp) REVERT: F 740 MET cc_start: 0.7127 (ttp) cc_final: 0.6641 (tmm) REVERT: F 741 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6532 (tp40) REVERT: F 754 GLN cc_start: 0.6652 (mt0) cc_final: 0.6087 (pt0) REVERT: F 782 LYS cc_start: 0.6818 (ptpp) cc_final: 0.6439 (tttp) REVERT: F 786 GLU cc_start: 0.5993 (mp0) cc_final: 0.5058 (mt-10) REVERT: G 17 LEU cc_start: 0.8372 (mp) cc_final: 0.8026 (mp) outliers start: 59 outliers final: 24 residues processed: 386 average time/residue: 0.7983 time to fit residues: 344.8122 Evaluate side-chains 350 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 316 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 523 ASN Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 741 GLN Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 557 ASN Chi-restraints excluded: chain F residue 603 MET Chi-restraints excluded: chain F residue 604 ASP Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 741 GLN Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 165 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 278 optimal weight: 50.0000 chunk 99 optimal weight: 6.9990 chunk 74 optimal weight: 0.0670 chunk 225 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS E 502 HIS ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.169609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.129973 restraints weight = 53712.419| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 4.16 r_work: 0.3126 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24279 Z= 0.127 Angle : 0.521 8.112 32873 Z= 0.258 Chirality : 0.042 0.159 3762 Planarity : 0.004 0.042 4214 Dihedral : 11.187 89.531 3650 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 2.64 % Allowed : 14.31 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.06 (0.16), residues: 3006 helix: 1.05 (0.13), residues: 1616 sheet: 0.14 (0.26), residues: 376 loop : 0.64 (0.22), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 375 TYR 0.009 0.001 TYR A 752 PHE 0.022 0.001 PHE E 527 TRP 0.011 0.001 TRP F 466 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00304 (24279) covalent geometry : angle 0.52076 (32873) hydrogen bonds : bond 0.03507 ( 1172) hydrogen bonds : angle 4.10512 ( 3272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 323 time to evaluate : 0.769 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 351 ARG cc_start: 0.7510 (mmp-170) cc_final: 0.6976 (tpp-160) REVERT: A 490 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: A 560 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8966 (mttp) REVERT: A 735 ASP cc_start: 0.9029 (m-30) cc_final: 0.8654 (m-30) REVERT: A 795 GLU cc_start: 0.7373 (pp20) cc_final: 0.7142 (pp20) REVERT: A 796 LYS cc_start: 0.6267 (tmtp) cc_final: 0.5524 (mmpt) REVERT: B 325 GLU cc_start: 0.8128 (tp30) cc_final: 0.7602 (tp30) REVERT: B 335 GLN cc_start: 0.8022 (mt0) cc_final: 0.7818 (mt0) REVERT: B 433 GLN cc_start: 0.7700 (tp40) cc_final: 0.7415 (tm-30) REVERT: B 755 ARG cc_start: 0.6579 (ttp-170) cc_final: 0.6313 (ttp80) REVERT: B 777 MET cc_start: 0.8833 (tpt) cc_final: 0.8519 (mmm) REVERT: C 231 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7533 (ptm) REVERT: C 286 ASP cc_start: 0.8091 (m-30) cc_final: 0.7775 (m-30) REVERT: C 435 ARG cc_start: 0.6881 (mtt90) cc_final: 0.6498 (mtt90) REVERT: C 635 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8299 (ppt170) REVERT: D 421 GLU cc_start: 0.7682 (tp30) cc_final: 0.7124 (tp30) REVERT: E 212 GLN cc_start: 0.8188 (tt0) cc_final: 0.7911 (mt0) REVERT: E 223 ARG cc_start: 0.8103 (tpm170) cc_final: 0.7787 (mmt-90) REVERT: E 234 ARG cc_start: 0.7610 (mtt90) cc_final: 0.7341 (ttp-110) REVERT: E 318 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7000 (ttt) REVERT: E 320 SER cc_start: 0.7606 (t) cc_final: 0.7323 (m) REVERT: E 477 ARG cc_start: 0.6586 (mtm180) cc_final: 0.6281 (mtm-85) REVERT: E 478 LYS cc_start: 0.6568 (tptp) cc_final: 0.6153 (mmtm) REVERT: E 526 LEU cc_start: 0.8048 (tp) cc_final: 0.7847 (tp) REVERT: E 550 LEU cc_start: 0.8193 (tp) cc_final: 0.7967 (tt) REVERT: E 567 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7600 (tptp) REVERT: E 585 GLN cc_start: 0.8331 (tt0) cc_final: 0.8067 (mm-40) REVERT: E 602 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7586 (tt0) REVERT: E 639 TYR cc_start: 0.8320 (m-80) cc_final: 0.8020 (m-80) REVERT: E 741 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6816 (mm-40) REVERT: F 424 GLN cc_start: 0.7073 (tp40) cc_final: 0.6222 (tt0) REVERT: F 539 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6924 (tm) REVERT: F 740 MET cc_start: 0.7031 (ttp) cc_final: 0.6706 (tmm) REVERT: F 741 GLN cc_start: 0.6873 (OUTLIER) cc_final: 0.6536 (tp40) REVERT: F 754 GLN cc_start: 0.6563 (mt0) cc_final: 0.6104 (pt0) REVERT: F 782 LYS cc_start: 0.6748 (ptpp) cc_final: 0.6268 (tttp) REVERT: G 17 LEU cc_start: 0.8393 (mp) cc_final: 0.8067 (mp) outliers start: 67 outliers final: 30 residues processed: 366 average time/residue: 0.7577 time to fit residues: 311.2879 Evaluate side-chains 347 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 308 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain E residue 741 GLN Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 557 ASN Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 741 GLN Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 27 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 171 optimal weight: 10.0000 chunk 293 optimal weight: 0.3980 chunk 117 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 247 optimal weight: 3.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN C 459 HIS E 502 HIS ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.169363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129670 restraints weight = 53201.382| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 4.13 r_work: 0.3117 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24279 Z= 0.133 Angle : 0.525 8.789 32873 Z= 0.259 Chirality : 0.043 0.160 3762 Planarity : 0.004 0.042 4214 Dihedral : 11.166 89.284 3650 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 2.29 % Allowed : 14.91 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.11 (0.16), residues: 3006 helix: 1.12 (0.13), residues: 1613 sheet: 0.10 (0.26), residues: 376 loop : 0.61 (0.21), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 609 TYR 0.009 0.001 TYR B 406 PHE 0.014 0.001 PHE E 527 TRP 0.011 0.001 TRP F 466 HIS 0.003 0.001 HIS C 459 Details of bonding type rmsd covalent geometry : bond 0.00323 (24279) covalent geometry : angle 0.52539 (32873) hydrogen bonds : bond 0.03430 ( 1172) hydrogen bonds : angle 4.05128 ( 3272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 324 time to evaluate : 0.711 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 351 ARG cc_start: 0.7505 (mmp-170) cc_final: 0.6947 (tpp-160) REVERT: A 474 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: A 560 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8965 (mttp) REVERT: A 735 ASP cc_start: 0.9037 (m-30) cc_final: 0.8625 (m-30) REVERT: A 795 GLU cc_start: 0.7387 (pp20) cc_final: 0.7102 (pp20) REVERT: A 796 LYS cc_start: 0.6237 (tmtp) cc_final: 0.5490 (mmpt) REVERT: B 325 GLU cc_start: 0.8140 (tp30) cc_final: 0.7609 (tp30) REVERT: B 335 GLN cc_start: 0.7997 (mt0) cc_final: 0.7763 (mt0) REVERT: B 433 GLN cc_start: 0.7587 (tp40) cc_final: 0.7333 (tm-30) REVERT: B 755 ARG cc_start: 0.6573 (ttp-170) cc_final: 0.6301 (ttp80) REVERT: B 777 MET cc_start: 0.8831 (tpt) cc_final: 0.8521 (mmm) REVERT: C 231 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7558 (ptm) REVERT: C 286 ASP cc_start: 0.8114 (m-30) cc_final: 0.7795 (m-30) REVERT: C 435 ARG cc_start: 0.6810 (mtt90) cc_final: 0.6435 (mtt90) REVERT: D 421 GLU cc_start: 0.7702 (tp30) cc_final: 0.7166 (tp30) REVERT: D 778 GLU cc_start: 0.8353 (pt0) cc_final: 0.7553 (tp30) REVERT: E 212 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7886 (mt0) REVERT: E 223 ARG cc_start: 0.8078 (tpm170) cc_final: 0.7769 (mmt-90) REVERT: E 234 ARG cc_start: 0.7578 (mtt90) cc_final: 0.7287 (ttp-110) REVERT: E 318 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6964 (ttt) REVERT: E 320 SER cc_start: 0.7597 (t) cc_final: 0.7325 (m) REVERT: E 550 LEU cc_start: 0.8174 (tp) cc_final: 0.7952 (tt) REVERT: E 567 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7490 (tptp) REVERT: E 585 GLN cc_start: 0.8337 (tt0) cc_final: 0.8064 (mm-40) REVERT: E 639 TYR cc_start: 0.8396 (m-80) cc_final: 0.8069 (m-80) REVERT: F 424 GLN cc_start: 0.7091 (tp40) cc_final: 0.6241 (tt0) REVERT: F 539 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6899 (tm) REVERT: F 741 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6169 (tp40) REVERT: F 754 GLN cc_start: 0.6537 (mt0) cc_final: 0.6122 (pt0) REVERT: F 782 LYS cc_start: 0.6794 (ptpp) cc_final: 0.6516 (tttm) REVERT: F 786 GLU cc_start: 0.6381 (mp0) cc_final: 0.5378 (mt-10) REVERT: G 17 LEU cc_start: 0.8360 (mp) cc_final: 0.8046 (mp) REVERT: G 25 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8743 (tt) outliers start: 58 outliers final: 34 residues processed: 355 average time/residue: 0.7529 time to fit residues: 299.9790 Evaluate side-chains 351 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 308 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 796 LYS Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 557 ASN Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 741 GLN Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 297 optimal weight: 30.0000 chunk 74 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 230 optimal weight: 8.9990 chunk 168 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 289 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS E 502 HIS E 602 GLN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 645 ASN F 433 GLN F 741 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.167840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126278 restraints weight = 40019.588| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.77 r_work: 0.3166 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24279 Z= 0.172 Angle : 0.552 9.171 32873 Z= 0.272 Chirality : 0.044 0.160 3762 Planarity : 0.004 0.042 4214 Dihedral : 11.287 87.875 3650 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.53 % Favored : 96.40 % Rotamer: Outliers : 2.56 % Allowed : 14.91 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.05 (0.16), residues: 3006 helix: 1.06 (0.13), residues: 1616 sheet: 0.03 (0.26), residues: 378 loop : 0.63 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 609 TYR 0.012 0.001 TYR B 406 PHE 0.015 0.002 PHE E 527 TRP 0.010 0.001 TRP E 500 HIS 0.004 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00423 (24279) covalent geometry : angle 0.55219 (32873) hydrogen bonds : bond 0.03638 ( 1172) hydrogen bonds : angle 4.08874 ( 3272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 319 time to evaluate : 0.836 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 351 ARG cc_start: 0.7485 (mmp-170) cc_final: 0.7069 (tpp-160) REVERT: A 474 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7190 (mm-30) REVERT: A 560 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8918 (mttp) REVERT: A 735 ASP cc_start: 0.8989 (m-30) cc_final: 0.8608 (m-30) REVERT: A 796 LYS cc_start: 0.6307 (tmtp) cc_final: 0.5543 (mmpt) REVERT: B 325 GLU cc_start: 0.8058 (tp30) cc_final: 0.7519 (tp30) REVERT: B 335 GLN cc_start: 0.7968 (mt0) cc_final: 0.7714 (mt0) REVERT: B 433 GLN cc_start: 0.7550 (tp40) cc_final: 0.7349 (tm-30) REVERT: B 618 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7880 (m) REVERT: B 755 ARG cc_start: 0.6567 (ttp-170) cc_final: 0.6322 (ttp80) REVERT: B 777 MET cc_start: 0.8780 (tpt) cc_final: 0.8473 (mmm) REVERT: C 231 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7471 (ptm) REVERT: C 286 ASP cc_start: 0.8008 (m-30) cc_final: 0.7692 (m-30) REVERT: C 333 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7787 (pt) REVERT: C 435 ARG cc_start: 0.6751 (mtt90) cc_final: 0.6388 (mtt90) REVERT: C 726 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8339 (mm) REVERT: D 421 GLU cc_start: 0.7586 (tp30) cc_final: 0.7098 (tp30) REVERT: E 212 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: E 234 ARG cc_start: 0.7575 (mtt90) cc_final: 0.7304 (ttp-110) REVERT: E 318 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.6980 (ttt) REVERT: E 320 SER cc_start: 0.7630 (t) cc_final: 0.7342 (m) REVERT: E 477 ARG cc_start: 0.6468 (mtm-85) cc_final: 0.5997 (mtm180) REVERT: E 550 LEU cc_start: 0.8161 (tp) cc_final: 0.7941 (tt) REVERT: E 567 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7530 (tptp) REVERT: E 585 GLN cc_start: 0.8223 (tt0) cc_final: 0.8017 (mm-40) REVERT: E 602 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7596 (tt0) REVERT: E 639 TYR cc_start: 0.8305 (m-80) cc_final: 0.7948 (m-80) REVERT: F 424 GLN cc_start: 0.7057 (tp40) cc_final: 0.6212 (tt0) REVERT: F 539 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6829 (tm) REVERT: F 754 GLN cc_start: 0.6539 (mt0) cc_final: 0.6207 (pt0) REVERT: F 782 LYS cc_start: 0.6781 (ptpp) cc_final: 0.6238 (tttp) outliers start: 65 outliers final: 37 residues processed: 361 average time/residue: 0.7609 time to fit residues: 308.7823 Evaluate side-chains 356 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 309 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 796 LYS Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 751 VAL Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 557 ASN Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 59 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 286 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 40.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 ASN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS E 502 HIS ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 741 GLN F 433 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.170174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129167 restraints weight = 45610.454| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.25 r_work: 0.3189 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24279 Z= 0.102 Angle : 0.523 12.264 32873 Z= 0.256 Chirality : 0.041 0.158 3762 Planarity : 0.004 0.044 4214 Dihedral : 10.978 89.317 3650 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 1.81 % Allowed : 15.85 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.32 (0.16), residues: 3006 helix: 1.33 (0.13), residues: 1614 sheet: 0.11 (0.26), residues: 374 loop : 0.68 (0.22), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 755 TYR 0.007 0.001 TYR C 406 PHE 0.018 0.001 PHE E 527 TRP 0.011 0.001 TRP F 780 HIS 0.003 0.001 HIS C 459 Details of bonding type rmsd covalent geometry : bond 0.00235 (24279) covalent geometry : angle 0.52285 (32873) hydrogen bonds : bond 0.03035 ( 1172) hydrogen bonds : angle 3.95120 ( 3272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 339 time to evaluate : 0.883 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 351 ARG cc_start: 0.7454 (mmp-170) cc_final: 0.7046 (tpp-160) REVERT: A 456 LEU cc_start: 0.8558 (mt) cc_final: 0.8356 (mt) REVERT: A 735 ASP cc_start: 0.8985 (m-30) cc_final: 0.8575 (m-30) REVERT: A 795 GLU cc_start: 0.7347 (pp20) cc_final: 0.7137 (pp20) REVERT: A 796 LYS cc_start: 0.6387 (tmtp) cc_final: 0.5667 (mmpt) REVERT: B 325 GLU cc_start: 0.8000 (tp30) cc_final: 0.7467 (tp30) REVERT: B 755 ARG cc_start: 0.6610 (ttp-170) cc_final: 0.6333 (ttp80) REVERT: B 777 MET cc_start: 0.8775 (tpt) cc_final: 0.8424 (mmm) REVERT: C 231 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7437 (ptm) REVERT: C 333 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7791 (pt) REVERT: C 526 LEU cc_start: 0.9065 (tp) cc_final: 0.8795 (tp) REVERT: C 635 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8214 (ppt170) REVERT: D 421 GLU cc_start: 0.7693 (tp30) cc_final: 0.7325 (tp30) REVERT: E 212 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: E 223 ARG cc_start: 0.8062 (tpm170) cc_final: 0.7703 (mmt-90) REVERT: E 233 TYR cc_start: 0.7724 (t80) cc_final: 0.7371 (t80) REVERT: E 234 ARG cc_start: 0.7576 (mtt90) cc_final: 0.7373 (ttp-110) REVERT: E 318 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6984 (ttt) REVERT: E 320 SER cc_start: 0.7448 (t) cc_final: 0.7199 (m) REVERT: E 341 LYS cc_start: 0.8313 (mptt) cc_final: 0.7713 (mmmt) REVERT: E 375 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7818 (tpt-90) REVERT: E 550 LEU cc_start: 0.8147 (tp) cc_final: 0.7937 (tt) REVERT: E 567 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7486 (tptp) REVERT: E 585 GLN cc_start: 0.8256 (tt0) cc_final: 0.8008 (mm-40) REVERT: E 639 TYR cc_start: 0.8317 (m-80) cc_final: 0.7989 (m-80) REVERT: E 649 MET cc_start: 0.7816 (mmt) cc_final: 0.7281 (ppp) REVERT: F 424 GLN cc_start: 0.7076 (tp40) cc_final: 0.6220 (tt0) REVERT: F 539 LEU cc_start: 0.7038 (tm) cc_final: 0.6777 (tm) REVERT: F 754 GLN cc_start: 0.6454 (mt0) cc_final: 0.6147 (pt0) REVERT: F 782 LYS cc_start: 0.6760 (ptpp) cc_final: 0.6379 (tttp) REVERT: F 786 GLU cc_start: 0.6214 (mp0) cc_final: 0.5210 (mt-10) outliers start: 46 outliers final: 27 residues processed: 369 average time/residue: 0.7476 time to fit residues: 309.3405 Evaluate side-chains 342 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 309 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 796 LYS Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 741 GLN Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 217 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 223 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 302 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN A 684 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS D 350 ASN D 426 ASN E 502 HIS ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN F 741 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.166603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.126236 restraints weight = 54227.946| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.87 r_work: 0.3105 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24279 Z= 0.218 Angle : 0.606 10.873 32873 Z= 0.298 Chirality : 0.045 0.170 3762 Planarity : 0.004 0.042 4214 Dihedral : 11.326 89.019 3648 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 2.01 % Allowed : 16.25 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.05 (0.16), residues: 3006 helix: 1.11 (0.13), residues: 1603 sheet: -0.05 (0.26), residues: 375 loop : 0.59 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 755 TYR 0.011 0.001 TYR D 639 PHE 0.027 0.002 PHE E 527 TRP 0.010 0.001 TRP C 219 HIS 0.004 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00536 (24279) covalent geometry : angle 0.60568 (32873) hydrogen bonds : bond 0.03843 ( 1172) hydrogen bonds : angle 4.11942 ( 3272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 313 time to evaluate : 0.619 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6632 (mtm110) cc_final: 0.6409 (mmp80) REVERT: A 351 ARG cc_start: 0.7560 (mmp-170) cc_final: 0.7076 (tpp-160) REVERT: A 474 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7224 (mm-30) REVERT: A 560 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8988 (mttp) REVERT: A 735 ASP cc_start: 0.9054 (m-30) cc_final: 0.8692 (m-30) REVERT: A 796 LYS cc_start: 0.6308 (tmtp) cc_final: 0.5517 (mmpt) REVERT: B 325 GLU cc_start: 0.8154 (tp30) cc_final: 0.7625 (tp30) REVERT: B 333 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8108 (pt) REVERT: B 755 ARG cc_start: 0.6655 (ttp-170) cc_final: 0.6373 (ttp80) REVERT: B 777 MET cc_start: 0.8860 (tpt) cc_final: 0.8568 (mmm) REVERT: C 231 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7519 (ptm) REVERT: C 333 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7869 (pt) REVERT: C 649 MET cc_start: 0.9026 (tpp) cc_final: 0.8785 (mmp) REVERT: D 421 GLU cc_start: 0.7805 (tp30) cc_final: 0.7324 (tp30) REVERT: E 212 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: E 223 ARG cc_start: 0.8129 (tpm170) cc_final: 0.7738 (mmt-90) REVERT: E 234 ARG cc_start: 0.7637 (mtt90) cc_final: 0.7334 (ttp-110) REVERT: E 318 MET cc_start: 0.7358 (ttp) cc_final: 0.7038 (ttt) REVERT: E 320 SER cc_start: 0.7754 (t) cc_final: 0.7468 (m) REVERT: E 550 LEU cc_start: 0.8213 (tp) cc_final: 0.7990 (tt) REVERT: E 567 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7553 (tptp) REVERT: E 585 GLN cc_start: 0.8345 (tt0) cc_final: 0.8113 (mm-40) REVERT: E 639 TYR cc_start: 0.8387 (m-80) cc_final: 0.8066 (m-80) REVERT: F 424 GLN cc_start: 0.7170 (tp40) cc_final: 0.6293 (tt0) REVERT: F 539 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6957 (tm) REVERT: F 754 GLN cc_start: 0.6536 (mt0) cc_final: 0.6200 (pt0) REVERT: F 782 LYS cc_start: 0.6905 (ptpp) cc_final: 0.6493 (tttp) REVERT: F 786 GLU cc_start: 0.6284 (mp0) cc_final: 0.5282 (mt-10) outliers start: 51 outliers final: 27 residues processed: 340 average time/residue: 0.7922 time to fit residues: 301.0079 Evaluate side-chains 340 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 305 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 557 ASN Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 281 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 242 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 238 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 233 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS D 350 ASN E 502 HIS E 602 GLN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 741 GLN F 433 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.168108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.126825 restraints weight = 48568.335| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.66 r_work: 0.3125 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24279 Z= 0.149 Angle : 0.572 11.762 32873 Z= 0.280 Chirality : 0.043 0.159 3762 Planarity : 0.004 0.053 4214 Dihedral : 11.220 87.607 3648 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 1.58 % Allowed : 16.88 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.12 (0.16), residues: 3006 helix: 1.18 (0.13), residues: 1612 sheet: -0.05 (0.26), residues: 376 loop : 0.61 (0.21), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 755 TYR 0.012 0.001 TYR A 752 PHE 0.026 0.002 PHE E 527 TRP 0.011 0.001 TRP F 780 HIS 0.004 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00364 (24279) covalent geometry : angle 0.57204 (32873) hydrogen bonds : bond 0.03435 ( 1172) hydrogen bonds : angle 4.05154 ( 3272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 314 time to evaluate : 0.874 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 351 ARG cc_start: 0.7480 (mmp-170) cc_final: 0.6966 (tpp-160) REVERT: A 474 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: A 560 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8945 (mttp) REVERT: A 673 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7953 (m-30) REVERT: A 735 ASP cc_start: 0.9065 (m-30) cc_final: 0.8687 (m-30) REVERT: A 796 LYS cc_start: 0.6219 (tmtp) cc_final: 0.5435 (mmpt) REVERT: B 325 GLU cc_start: 0.8094 (tp30) cc_final: 0.7567 (tp30) REVERT: B 333 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8092 (pt) REVERT: B 755 ARG cc_start: 0.6624 (ttp-170) cc_final: 0.6334 (ttp80) REVERT: B 777 MET cc_start: 0.8797 (tpt) cc_final: 0.8477 (mmm) REVERT: C 231 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7448 (ptm) REVERT: C 333 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7821 (pt) REVERT: C 649 MET cc_start: 0.9007 (tpp) cc_final: 0.8771 (mmp) REVERT: C 726 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8327 (mm) REVERT: D 369 MET cc_start: 0.8582 (mtp) cc_final: 0.8297 (mtp) REVERT: D 421 GLU cc_start: 0.7777 (tp30) cc_final: 0.7312 (tp30) REVERT: D 490 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8183 (mt-10) REVERT: E 212 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7887 (mt0) REVERT: E 234 ARG cc_start: 0.7602 (mtt90) cc_final: 0.7314 (ttp-110) REVERT: E 318 MET cc_start: 0.7288 (ttp) cc_final: 0.6979 (ttt) REVERT: E 320 SER cc_start: 0.7575 (t) cc_final: 0.7301 (m) REVERT: E 375 ARG cc_start: 0.8119 (tpp80) cc_final: 0.7917 (tpp80) REVERT: E 515 MET cc_start: 0.8544 (tpt) cc_final: 0.8261 (mmt) REVERT: E 550 LEU cc_start: 0.8137 (tp) cc_final: 0.7928 (tt) REVERT: E 567 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7576 (tptp) REVERT: E 585 GLN cc_start: 0.8311 (tt0) cc_final: 0.8027 (mm-40) REVERT: E 602 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7750 (mt0) REVERT: E 639 TYR cc_start: 0.8350 (m-80) cc_final: 0.7949 (m-80) REVERT: F 421 GLU cc_start: 0.7572 (tt0) cc_final: 0.7154 (tp30) REVERT: F 424 GLN cc_start: 0.7121 (tp40) cc_final: 0.5978 (tt0) REVERT: F 539 LEU cc_start: 0.7145 (tm) cc_final: 0.6888 (tm) REVERT: F 754 GLN cc_start: 0.6510 (mt0) cc_final: 0.6166 (pt0) REVERT: F 782 LYS cc_start: 0.6860 (ptpp) cc_final: 0.6460 (tttp) REVERT: F 786 GLU cc_start: 0.6025 (mp0) cc_final: 0.5061 (mt-10) outliers start: 40 outliers final: 27 residues processed: 337 average time/residue: 0.7975 time to fit residues: 300.2041 Evaluate side-chains 342 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 306 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 557 ASN Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 741 GLN Chi-restraints excluded: chain F residue 749 GLU Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 35 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 270 optimal weight: 0.5980 chunk 157 optimal weight: 8.9990 chunk 272 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 274 optimal weight: 10.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS D 350 ASN E 502 HIS ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 741 GLN F 433 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.167023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124548 restraints weight = 37426.180| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.43 r_work: 0.3190 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24279 Z= 0.168 Angle : 0.583 13.645 32873 Z= 0.285 Chirality : 0.044 0.160 3762 Planarity : 0.004 0.043 4214 Dihedral : 11.245 87.685 3648 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.70 % Favored : 96.24 % Rotamer: Outliers : 2.01 % Allowed : 16.48 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.09 (0.16), residues: 3006 helix: 1.17 (0.13), residues: 1611 sheet: -0.11 (0.25), residues: 375 loop : 0.58 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 755 TYR 0.011 0.001 TYR A 752 PHE 0.028 0.002 PHE E 527 TRP 0.011 0.001 TRP F 780 HIS 0.003 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00413 (24279) covalent geometry : angle 0.58303 (32873) hydrogen bonds : bond 0.03545 ( 1172) hydrogen bonds : angle 4.06858 ( 3272) =============================================================================== Job complete usr+sys time: 9118.80 seconds wall clock time: 155 minutes 22.95 seconds (9322.95 seconds total)