Starting phenix.real_space_refine on Sat Jul 4 22:59:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7swl_25474/07_2026/7swl_25474.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swl_25474/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7swl_25474/07_2026/7swl_25474.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7swl_25474/07_2026/7swl_25474.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7swl_25474/07_2026/7swl_25474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swl_25474/07_2026/7swl_25474.map" model { file = "/net/cci-nas-00/data/ceres_data/7swl_25474/07_2026/7swl_25474.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swl_25474/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 7.17, per 1000 atoms: 0.30 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: 2.17 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: 0.74 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: 4.60 Time building geometry restraints manager: 2.89 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: 14569 24.83 - 49.65: 248 49.65 - 74.48: 13 74.48 - 99.31: 4 99.31 - 124.13: 1 Dihedral angle restraints: 14835 sinusoidal: 6039 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 14832 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 25.390 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:9.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 9.227 124.134 9137 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/Z covalent geometry : bond 0.00323 / 0.15 (24279) covalent geometry : angle 0.50948 / 0.30 (32873) hydrogen bonds : bond 0.27120 / 18.05 ( 1172) hydrogen bonds : angle 7.44932 / 5.37 ( 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 : 0.944 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: 0.7929 time to fit residues: 496.7069 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 : 0.933 ------------------------------------------------------------------------------- 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... B 585 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN C 424 GLN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.170582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125626 restraints weight = 54232.519| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.22 r_work: 0.3167 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24279 Z= 0.125 Angle : 0.554 9.088 32873 Z= 0.283 Chirality : 0.042 0.261 3762 Planarity : 0.004 0.044 4214 Dihedral : 6.066 102.335 3383 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 2.37 % Allowed : 11.00 % Favored : 86.63 % 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: 0.70 (0.16), residues: 3006 helix: 0.49 (0.13), residues: 1607 sheet: 0.49 (0.27), residues: 381 loop : 0.75 (0.22), residues: 1018 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 0.021 0.001 PHE E 527 TRP 0.011 0.001 TRP F 466 HIS 0.002 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (24279) covalent geometry : angle 0.55423 / 0.28 (32873) hydrogen bonds : bond 0.04999 / 3.36 ( 1172) hydrogen bonds : angle 4.72321 / 3.43 ( 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 454 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 394 time to evaluate : 0.942 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 204 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 223 ARG cc_start: 0.6302 (tpm170) cc_final: 0.6084 (tpt170) REVERT: A 234 ARG cc_start: 0.6278 (ttm110) cc_final: 0.5962 (ttm110) REVERT: A 351 ARG cc_start: 0.7184 (mmp-170) cc_final: 0.6575 (tpp-160) REVERT: A 354 PHE cc_start: 0.7447 (m-10) cc_final: 0.7111 (m-10) REVERT: A 355 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6874 (mp) REVERT: A 401 LYS cc_start: 0.8634 (mtmt) cc_final: 0.8251 (tptt) REVERT: A 560 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8842 (mttp) REVERT: A 716 ASP cc_start: 0.7948 (t0) cc_final: 0.7213 (m-30) REVERT: A 735 ASP cc_start: 0.8980 (m-30) cc_final: 0.8632 (m-30) REVERT: A 781 GLU cc_start: 0.8061 (tp30) cc_final: 0.7752 (tt0) REVERT: A 795 GLU cc_start: 0.7175 (pp20) cc_final: 0.6901 (pp20) REVERT: A 796 LYS cc_start: 0.5471 (tmtp) cc_final: 0.4831 (mmpt) REVERT: B 320 SER cc_start: 0.8517 (t) cc_final: 0.8299 (m) REVERT: B 325 GLU cc_start: 0.8050 (tp30) cc_final: 0.7575 (tp30) REVERT: B 335 GLN cc_start: 0.8113 (mt0) cc_final: 0.7903 (mt0) REVERT: B 433 GLN cc_start: 0.7760 (tp40) cc_final: 0.7360 (tm-30) REVERT: B 477 ARG cc_start: 0.8194 (mtt90) cc_final: 0.7926 (mtt90) REVERT: B 652 GLU cc_start: 0.8294 (mp0) cc_final: 0.8092 (mp0) REVERT: B 755 ARG cc_start: 0.6471 (ttp-170) cc_final: 0.6250 (ttp80) REVERT: B 777 MET cc_start: 0.8753 (tpt) cc_final: 0.8517 (tpt) REVERT: C 286 ASP cc_start: 0.8202 (m-30) cc_final: 0.7731 (m-30) REVERT: C 635 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8549 (ppt-90) REVERT: C 757 GLN cc_start: 0.6723 (tt0) cc_final: 0.6355 (mt0) REVERT: D 234 ARG cc_start: 0.7853 (ttm110) cc_final: 0.7525 (ttm110) REVERT: D 421 GLU cc_start: 0.7709 (tp30) cc_final: 0.7105 (tp30) REVERT: D 490 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8143 (mt-10) REVERT: D 533 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8107 (mptp) REVERT: D 778 GLU cc_start: 0.8341 (pt0) cc_final: 0.7524 (tp30) REVERT: D 781 GLU cc_start: 0.7532 (mp0) cc_final: 0.7195 (mp0) REVERT: E 223 ARG cc_start: 0.8074 (tpm170) cc_final: 0.7846 (mmt-90) REVERT: E 234 ARG cc_start: 0.7517 (mtt90) cc_final: 0.7256 (ttm-80) REVERT: E 282 LYS cc_start: 0.7608 (tttt) cc_final: 0.6990 (tmtm) REVERT: E 318 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7052 (ttt) REVERT: E 320 SER cc_start: 0.7369 (t) cc_final: 0.7067 (m) REVERT: E 416 LYS cc_start: 0.7034 (mttt) cc_final: 0.6659 (mmtt) REVERT: E 472 THR cc_start: 0.7030 (OUTLIER) cc_final: 0.6643 (t) REVERT: E 475 GLN cc_start: 0.5369 (mt0) cc_final: 0.5052 (mm-40) REVERT: E 477 ARG cc_start: 0.6958 (mtm180) cc_final: 0.6319 (mtm110) REVERT: E 478 LYS cc_start: 0.6589 (tptp) cc_final: 0.6190 (mmtp) REVERT: E 507 GLU cc_start: 0.7084 (mp0) cc_final: 0.6701 (tm-30) REVERT: E 515 MET cc_start: 0.8361 (ttp) cc_final: 0.8078 (tpp) REVERT: E 567 LYS cc_start: 0.7786 (tptp) cc_final: 0.7544 (tptp) REVERT: E 741 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6336 (tt0) REVERT: E 750 ARG cc_start: 0.4836 (ttp80) cc_final: 0.3836 (tpt90) REVERT: E 777 MET cc_start: 0.6494 (tpp) cc_final: 0.5940 (ttp) REVERT: F 424 GLN cc_start: 0.7061 (tp40) cc_final: 0.6298 (tt0) REVERT: F 649 MET cc_start: 0.6119 (mmm) cc_final: 0.5889 (mmm) REVERT: F 740 MET cc_start: 0.7102 (ttp) cc_final: 0.6389 (tmm) REVERT: F 754 GLN cc_start: 0.6555 (mt0) cc_final: 0.6013 (pp30) REVERT: F 782 LYS cc_start: 0.6460 (ptpp) cc_final: 0.6199 (tttp) REVERT: F 786 GLU cc_start: 0.5986 (mp0) cc_final: 0.5025 (mt-10) REVERT: G 17 LEU cc_start: 0.8310 (mp) cc_final: 0.8010 (mp) outliers start: 60 outliers final: 19 residues processed: 429 average time/residue: 0.7736 time to fit residues: 373.7323 Evaluate side-chains 360 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 333 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE 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 506 LEU 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: 9.9990 chunk 62 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 557 ASN B 424 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 ASN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.169291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129170 restraints weight = 48835.873| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.87 r_work: 0.3122 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24279 Z= 0.156 Angle : 0.544 8.725 32873 Z= 0.272 Chirality : 0.043 0.207 3762 Planarity : 0.004 0.040 4214 Dihedral : 6.076 94.822 3376 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.60 % Rotamer: Outliers : 2.76 % Allowed : 11.71 % Favored : 85.53 % 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: 0.86 (0.16), residues: 3006 helix: 0.79 (0.13), residues: 1601 sheet: 0.31 (0.26), residues: 384 loop : 0.63 (0.22), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 375 TYR 0.011 0.001 TYR B 406 PHE 0.022 0.002 PHE E 527 TRP 0.011 0.001 TRP F 466 HIS 0.003 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (24279) covalent geometry : angle 0.54446 / 0.27 (32873) hydrogen bonds : bond 0.04312 / 2.92 ( 1172) hydrogen bonds : angle 4.37431 / 3.19 ( 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 414 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 344 time to evaluate : 1.004 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 204 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8414 (mp) REVERT: A 223 ARG cc_start: 0.6434 (tpm170) cc_final: 0.6170 (tpt170) REVERT: A 351 ARG cc_start: 0.7383 (mmp-170) cc_final: 0.6831 (tpp-160) REVERT: A 371 MET cc_start: 0.8937 (mtt) cc_final: 0.8590 (mtt) REVERT: A 560 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8946 (mttp) REVERT: A 735 ASP cc_start: 0.9035 (m-30) cc_final: 0.8674 (m-30) REVERT: A 796 LYS cc_start: 0.5976 (tmtp) cc_final: 0.5336 (mmpt) REVERT: B 320 SER cc_start: 0.8438 (t) cc_final: 0.8225 (m) REVERT: B 325 GLU cc_start: 0.8139 (tp30) cc_final: 0.7620 (tp30) REVERT: B 335 GLN cc_start: 0.8051 (mt0) cc_final: 0.7800 (mp10) REVERT: B 433 GLN cc_start: 0.7766 (tp40) cc_final: 0.7419 (tm-30) REVERT: B 477 ARG cc_start: 0.8225 (mtt90) cc_final: 0.7907 (mtt90) REVERT: B 515 MET cc_start: 0.9033 (tpt) cc_final: 0.8806 (tpp) REVERT: B 755 ARG cc_start: 0.6540 (ttp-170) cc_final: 0.6318 (ttp80) REVERT: B 777 MET cc_start: 0.8810 (tpt) cc_final: 0.8525 (tpt) REVERT: C 286 ASP cc_start: 0.8127 (m-30) cc_final: 0.7624 (m-30) REVERT: C 635 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8579 (ppt-90) REVERT: C 757 GLN cc_start: 0.6496 (tt0) cc_final: 0.6178 (mt0) REVERT: D 330 MET cc_start: 0.9103 (mtp) cc_final: 0.8825 (mtm) REVERT: D 421 GLU cc_start: 0.7805 (tp30) cc_final: 0.7198 (tp30) REVERT: D 533 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8098 (mptp) REVERT: D 781 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7373 (mp0) REVERT: E 223 ARG cc_start: 0.8086 (tpm170) cc_final: 0.7708 (mmt-90) REVERT: E 282 LYS cc_start: 0.7441 (tttt) cc_final: 0.7161 (tptt) REVERT: E 286 ASP cc_start: 0.7880 (m-30) cc_final: 0.7671 (m-30) REVERT: E 318 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6984 (ttt) REVERT: E 320 SER cc_start: 0.7586 (t) cc_final: 0.7265 (m) REVERT: E 371 MET cc_start: 0.8201 (mmt) cc_final: 0.7986 (mmt) REVERT: E 477 ARG cc_start: 0.6713 (mtm180) cc_final: 0.6221 (mtp-110) REVERT: E 478 LYS cc_start: 0.6501 (tptp) cc_final: 0.6059 (mmtm) REVERT: E 526 LEU cc_start: 0.8035 (tp) cc_final: 0.7832 (tp) REVERT: E 585 GLN cc_start: 0.8294 (tt0) cc_final: 0.8018 (mm-40) REVERT: E 602 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7553 (tt0) REVERT: E 646 ARG cc_start: 0.7820 (mtp180) cc_final: 0.7598 (mtp-110) REVERT: E 741 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6428 (tt0) REVERT: F 424 GLN cc_start: 0.7139 (tp40) cc_final: 0.6335 (tt0) REVERT: F 539 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6902 (tm) REVERT: F 603 MET cc_start: 0.5973 (OUTLIER) cc_final: 0.5603 (ttm) REVERT: F 740 MET cc_start: 0.7261 (ttp) cc_final: 0.6983 (tmm) REVERT: F 754 GLN cc_start: 0.6472 (mt0) cc_final: 0.5890 (pt0) REVERT: F 782 LYS cc_start: 0.6581 (ptpp) cc_final: 0.6101 (tttp) REVERT: G 17 LEU cc_start: 0.8388 (mp) cc_final: 0.8067 (mp) outliers start: 70 outliers final: 26 residues processed: 381 average time/residue: 0.7424 time to fit residues: 317.3270 Evaluate side-chains 352 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 318 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL 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 751 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 B residue 429 SER 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 361 ARG Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain E residue 318 MET 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 604 ASP 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 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: 3.9990 chunk 236 optimal weight: 2.9990 chunk 27 optimal weight: 0.0870 chunk 137 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 267 optimal weight: 7.9990 chunk 243 optimal weight: 0.0070 chunk 25 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 overall best weight: 2.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 GLN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN F 741 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.170358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130672 restraints weight = 51470.936| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 4.05 r_work: 0.3139 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24279 Z= 0.118 Angle : 0.513 8.187 32873 Z= 0.253 Chirality : 0.042 0.165 3762 Planarity : 0.004 0.042 4214 Dihedral : 5.921 92.055 3373 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.80 % Rotamer: Outliers : 2.21 % Allowed : 13.37 % Favored : 84.42 % 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: 1.07 (0.16), residues: 3006 helix: 1.00 (0.13), residues: 1616 sheet: 0.21 (0.26), residues: 380 loop : 0.73 (0.22), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 375 TYR 0.009 0.001 TYR A 752 PHE 0.021 0.001 PHE E 527 TRP 0.014 0.001 TRP F 466 HIS 0.003 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (24279) covalent geometry : angle 0.51252 / 0.25 (32873) hydrogen bonds : bond 0.03597 / 2.43 ( 1172) hydrogen bonds : angle 4.15754 / 3.03 ( 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 399 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 343 time to evaluate : 1.007 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 204 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8432 (mp) REVERT: A 321 ARG cc_start: 0.6845 (mtm110) cc_final: 0.6494 (ptm-80) REVERT: A 351 ARG cc_start: 0.7420 (mmp-170) cc_final: 0.6963 (tpp-160) REVERT: A 401 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8016 (tptt) REVERT: A 560 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8962 (mttp) REVERT: A 735 ASP cc_start: 0.9010 (m-30) cc_final: 0.8646 (m-30) REVERT: A 796 LYS cc_start: 0.6275 (tmtp) cc_final: 0.5542 (mmpt) REVERT: B 325 GLU cc_start: 0.8100 (tp30) cc_final: 0.7583 (tp30) REVERT: B 433 GLN cc_start: 0.7723 (tp40) cc_final: 0.7428 (tm-30) REVERT: B 477 ARG cc_start: 0.8203 (mtt90) cc_final: 0.7854 (mtt90) REVERT: B 755 ARG cc_start: 0.6528 (ttp-170) cc_final: 0.6302 (ttp80) REVERT: B 777 MET cc_start: 0.8800 (tpt) cc_final: 0.8472 (mmm) REVERT: C 231 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7518 (ptm) REVERT: C 286 ASP cc_start: 0.8161 (m-30) cc_final: 0.7835 (m-30) REVERT: C 435 ARG cc_start: 0.6882 (mtt90) cc_final: 0.6490 (mtt90) REVERT: C 635 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8284 (ppt170) REVERT: D 330 MET cc_start: 0.9074 (mtp) cc_final: 0.8801 (mtm) REVERT: D 421 GLU cc_start: 0.7742 (tp30) cc_final: 0.7164 (tp30) REVERT: D 533 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8078 (mptp) REVERT: D 778 GLU cc_start: 0.8308 (pt0) cc_final: 0.7549 (tp30) REVERT: E 223 ARG cc_start: 0.8135 (tpm170) cc_final: 0.7687 (mmt-90) REVERT: E 234 ARG cc_start: 0.7617 (mtt90) cc_final: 0.7366 (ttp-110) REVERT: E 282 LYS cc_start: 0.7431 (tttt) cc_final: 0.7064 (tptt) REVERT: E 286 ASP cc_start: 0.7919 (m-30) cc_final: 0.7629 (m-30) REVERT: E 318 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7001 (ttt) REVERT: E 320 SER cc_start: 0.7574 (t) cc_final: 0.7292 (m) REVERT: E 341 LYS cc_start: 0.8367 (mptt) cc_final: 0.7795 (mmmt) REVERT: E 371 MET cc_start: 0.8279 (mmt) cc_final: 0.7993 (mmt) REVERT: E 477 ARG cc_start: 0.6692 (mtm180) cc_final: 0.6437 (mtm-85) REVERT: E 478 LYS cc_start: 0.6566 (tptp) cc_final: 0.6168 (mmtp) REVERT: E 526 LEU cc_start: 0.8105 (tp) cc_final: 0.7709 (tp) REVERT: E 550 LEU cc_start: 0.8204 (tp) cc_final: 0.7983 (tt) REVERT: E 567 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7550 (tptp) REVERT: E 585 GLN cc_start: 0.8321 (tt0) cc_final: 0.8040 (mm-40) REVERT: E 602 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7523 (tt0) REVERT: E 639 TYR cc_start: 0.8189 (m-80) cc_final: 0.7959 (m-80) REVERT: E 741 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.6752 (mm-40) REVERT: F 424 GLN cc_start: 0.7026 (tp40) cc_final: 0.6195 (tt0) REVERT: F 539 LEU cc_start: 0.7186 (tm) cc_final: 0.6944 (tm) REVERT: F 603 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.5582 (ttm) REVERT: F 754 GLN cc_start: 0.6569 (mt0) cc_final: 0.6070 (pt0) REVERT: F 782 LYS cc_start: 0.6799 (ptpp) cc_final: 0.6443 (tttp) REVERT: F 786 GLU cc_start: 0.6149 (mp0) cc_final: 0.5227 (mt-10) REVERT: G 17 LEU cc_start: 0.8348 (mp) cc_final: 0.8014 (mp) outliers start: 56 outliers final: 27 residues processed: 378 average time/residue: 0.7514 time to fit residues: 319.6025 Evaluate side-chains 356 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 345 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 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 C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 322 ILE 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 455 LEU Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 533 LYS 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 503 VAL Chi-restraints excluded: chain F residue 506 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 165 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 278 optimal weight: 40.0000 chunk 99 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN F 741 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.168606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.124805 restraints weight = 53625.936| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.15 r_work: 0.3169 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24279 Z= 0.146 Angle : 0.528 9.236 32873 Z= 0.260 Chirality : 0.043 0.158 3762 Planarity : 0.004 0.042 4214 Dihedral : 5.970 88.884 3373 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.54 % Rotamer: Outliers : 2.72 % Allowed : 13.60 % Favored : 83.68 % 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: 1.05 (0.13), residues: 1616 sheet: 0.20 (0.26), residues: 376 loop : 0.67 (0.22), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 375 TYR 0.010 0.001 TYR B 406 PHE 0.014 0.001 PHE E 527 TRP 0.010 0.001 TRP F 466 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (24279) covalent geometry : angle 0.52824 / 0.26 (32873) hydrogen bonds : bond 0.03601 / 2.44 ( 1172) hydrogen bonds : angle 4.12188 / 3.00 ( 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 398 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 329 time to evaluate : 0.977 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 318 MET cc_start: 0.5915 (mtt) cc_final: 0.5547 (mtt) REVERT: A 330 MET cc_start: 0.6385 (tpp) cc_final: 0.6173 (tpp) REVERT: A 351 ARG cc_start: 0.7474 (mmp-170) cc_final: 0.6983 (tpp-160) REVERT: A 560 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8900 (mttp) REVERT: A 735 ASP cc_start: 0.8996 (m-30) cc_final: 0.8622 (m-30) REVERT: A 796 LYS cc_start: 0.6328 (tmtp) cc_final: 0.5573 (mmpt) REVERT: B 325 GLU cc_start: 0.8022 (tp30) cc_final: 0.7480 (tp30) REVERT: B 433 GLN cc_start: 0.7616 (tp40) cc_final: 0.7360 (tm-30) REVERT: B 477 ARG cc_start: 0.8146 (mtt90) cc_final: 0.7794 (mtt90) REVERT: B 755 ARG cc_start: 0.6563 (ttp-170) cc_final: 0.6323 (ttp80) REVERT: B 777 MET cc_start: 0.8775 (tpt) cc_final: 0.8458 (mmm) REVERT: C 231 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7636 (ptm) REVERT: C 286 ASP cc_start: 0.7990 (m-30) cc_final: 0.7666 (m-30) REVERT: C 435 ARG cc_start: 0.6815 (mtt90) cc_final: 0.6429 (mtt90) REVERT: C 635 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8503 (ppt-90) REVERT: D 330 MET cc_start: 0.9022 (mtp) cc_final: 0.8737 (mtm) REVERT: D 421 GLU cc_start: 0.7589 (tp30) cc_final: 0.7051 (tp30) REVERT: D 423 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: E 223 ARG cc_start: 0.7986 (tpm170) cc_final: 0.7580 (mmt-90) REVERT: E 234 ARG cc_start: 0.7566 (mtt90) cc_final: 0.7161 (ttp-110) REVERT: E 282 LYS cc_start: 0.7365 (tttt) cc_final: 0.7021 (tptt) REVERT: E 286 ASP cc_start: 0.7786 (m-30) cc_final: 0.7489 (m-30) REVERT: E 318 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6940 (ttt) REVERT: E 320 SER cc_start: 0.7598 (t) cc_final: 0.7303 (m) REVERT: E 371 MET cc_start: 0.8285 (mmt) cc_final: 0.8023 (mmt) REVERT: E 477 ARG cc_start: 0.6581 (mtm180) cc_final: 0.6251 (mtm-85) REVERT: E 478 LYS cc_start: 0.6565 (tptp) cc_final: 0.6144 (mmtm) REVERT: E 550 LEU cc_start: 0.8162 (tp) cc_final: 0.7937 (tt) REVERT: E 567 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7532 (tptp) REVERT: E 585 GLN cc_start: 0.8220 (tt0) cc_final: 0.7975 (mm-40) REVERT: E 602 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7552 (tt0) REVERT: E 639 TYR cc_start: 0.8172 (m-80) cc_final: 0.7916 (m-80) REVERT: F 424 GLN cc_start: 0.7076 (tp40) cc_final: 0.6222 (tt0) REVERT: F 539 LEU cc_start: 0.7203 (tm) cc_final: 0.6958 (tm) REVERT: F 603 MET cc_start: 0.6004 (ttm) cc_final: 0.5568 (ttm) REVERT: F 754 GLN cc_start: 0.6503 (mt0) cc_final: 0.6048 (pt0) REVERT: F 782 LYS cc_start: 0.6707 (ptpp) cc_final: 0.6237 (tttp) REVERT: G 17 LEU cc_start: 0.8332 (mp) cc_final: 0.7994 (mp) outliers start: 69 outliers final: 37 residues processed: 370 average time/residue: 0.7569 time to fit residues: 314.8741 Evaluate side-chains 354 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 311 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 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 359 ILE 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 C residue 207 VAL Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 322 ILE 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 423 PHE 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 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 557 ASN Chi-restraints excluded: chain F residue 604 ASP 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 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: 9.9990 chunk 171 optimal weight: 4.9990 chunk 293 optimal weight: 50.0000 chunk 117 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 160 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN F 741 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.166632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125737 restraints weight = 53340.679| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 4.02 r_work: 0.3084 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24279 Z= 0.209 Angle : 0.577 10.934 32873 Z= 0.283 Chirality : 0.045 0.215 3762 Planarity : 0.004 0.043 4214 Dihedral : 6.136 84.035 3371 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.53 % Favored : 96.40 % Rotamer: Outliers : 2.41 % Allowed : 14.20 % Favored : 83.40 % 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: 1.00 (0.13), residues: 1603 sheet: 0.08 (0.26), residues: 375 loop : 0.54 (0.21), residues: 1028 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 C 354 TRP 0.010 0.001 TRP E 500 HIS 0.004 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (24279) covalent geometry : angle 0.57687 / 0.28 (32873) hydrogen bonds : bond 0.03927 / 2.66 ( 1172) hydrogen bonds : angle 4.17933 / 3.05 ( 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 381 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 320 time to evaluate : 0.873 Fit side-chains revert: symmetry clash 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 330 MET cc_start: 0.6350 (tpp) cc_final: 0.6130 (tpp) REVERT: A 351 ARG cc_start: 0.7495 (mmp-170) cc_final: 0.6935 (tpp-160) REVERT: A 560 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8921 (mttp) REVERT: A 735 ASP cc_start: 0.9075 (m-30) cc_final: 0.8706 (m-30) REVERT: A 796 LYS cc_start: 0.6254 (tmtp) cc_final: 0.5470 (mmpt) REVERT: B 325 GLU cc_start: 0.8154 (tp30) cc_final: 0.7592 (tp30) REVERT: B 433 GLN cc_start: 0.7671 (tp40) cc_final: 0.7381 (tm-30) REVERT: B 755 ARG cc_start: 0.6609 (ttp-170) cc_final: 0.6330 (ttp80) REVERT: B 777 MET cc_start: 0.8793 (tpt) cc_final: 0.8473 (mmm) REVERT: C 231 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7599 (ptm) REVERT: C 286 ASP cc_start: 0.8074 (m-30) cc_final: 0.7662 (m-30) REVERT: C 435 ARG cc_start: 0.6856 (mtt90) cc_final: 0.6479 (mtt90) REVERT: D 330 MET cc_start: 0.9057 (mtp) cc_final: 0.8850 (mtm) REVERT: D 421 GLU cc_start: 0.7748 (tp30) cc_final: 0.7155 (tp30) REVERT: E 212 GLN cc_start: 0.8135 (tt0) cc_final: 0.7825 (mt0) REVERT: E 234 ARG cc_start: 0.7588 (mtt90) cc_final: 0.7126 (ttp-110) REVERT: E 282 LYS cc_start: 0.7360 (tttt) cc_final: 0.6971 (tptt) REVERT: E 286 ASP cc_start: 0.7846 (m-30) cc_final: 0.7513 (m-30) REVERT: E 318 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6863 (ttt) REVERT: E 320 SER cc_start: 0.7664 (t) cc_final: 0.7350 (m) REVERT: E 550 LEU cc_start: 0.8188 (tp) cc_final: 0.7950 (tt) REVERT: E 567 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7536 (tptp) REVERT: E 585 GLN cc_start: 0.8310 (tt0) cc_final: 0.8016 (mm-40) REVERT: E 639 TYR cc_start: 0.8336 (m-80) cc_final: 0.7990 (m-80) REVERT: F 424 GLN cc_start: 0.7030 (tp40) cc_final: 0.6197 (tt0) REVERT: F 539 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6832 (tm) REVERT: F 603 MET cc_start: 0.6208 (OUTLIER) cc_final: 0.5744 (ttm) REVERT: F 754 GLN cc_start: 0.6526 (mt0) cc_final: 0.6082 (pt0) REVERT: F 782 LYS cc_start: 0.6739 (ptpp) cc_final: 0.6387 (tttp) REVERT: F 786 GLU cc_start: 0.6552 (mp0) cc_final: 0.5592 (mt-10) outliers start: 61 outliers final: 33 residues processed: 357 average time/residue: 0.7487 time to fit residues: 301.5623 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 : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 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 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 C residue 207 VAL Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 322 ILE 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 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 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 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 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: 40.0000 chunk 74 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 289 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN C 459 HIS E 412 GLN E 502 HIS E 602 GLN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 645 ASN E 741 GLN F 433 GLN F 741 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.169709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128205 restraints weight = 40395.747| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.94 r_work: 0.3193 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24279 Z= 0.105 Angle : 0.514 10.883 32873 Z= 0.251 Chirality : 0.041 0.159 3762 Planarity : 0.004 0.043 4214 Dihedral : 5.910 85.374 3371 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 2.13 % Allowed : 14.87 % Favored : 83.00 % 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: 1.23 (0.16), residues: 3006 helix: 1.22 (0.13), residues: 1618 sheet: 0.09 (0.26), residues: 375 loop : 0.70 (0.22), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 609 TYR 0.010 0.001 TYR A 752 PHE 0.013 0.001 PHE E 527 TRP 0.009 0.001 TRP F 466 HIS 0.003 0.001 HIS C 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (24279) covalent geometry : angle 0.51436 / 0.25 (32873) hydrogen bonds : bond 0.03184 / 2.16 ( 1172) hydrogen bonds : angle 4.00654 / 2.92 ( 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 385 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 331 time to evaluate : 0.910 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 330 MET cc_start: 0.6364 (tpp) cc_final: 0.6142 (tpp) REVERT: A 351 ARG cc_start: 0.7429 (mmp-170) cc_final: 0.7010 (tpp-160) REVERT: A 735 ASP cc_start: 0.8974 (m-30) cc_final: 0.8591 (m-30) REVERT: A 796 LYS cc_start: 0.6369 (tmtp) cc_final: 0.5589 (mmpt) REVERT: B 325 GLU cc_start: 0.7994 (tp30) cc_final: 0.7469 (tp30) REVERT: B 433 GLN cc_start: 0.7480 (tp40) cc_final: 0.7280 (tm-30) REVERT: B 755 ARG cc_start: 0.6661 (ttp-170) cc_final: 0.6380 (ttp80) REVERT: B 777 MET cc_start: 0.8739 (tpt) cc_final: 0.8380 (mmm) REVERT: C 231 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7484 (ptm) REVERT: C 333 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7711 (pt) REVERT: C 635 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8280 (ppt170) REVERT: C 726 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8301 (mm) REVERT: D 330 MET cc_start: 0.9011 (mtp) cc_final: 0.8805 (mtm) REVERT: D 421 GLU cc_start: 0.7547 (tp30) cc_final: 0.7038 (tp30) REVERT: E 212 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: E 223 ARG cc_start: 0.7947 (tpm170) cc_final: 0.7592 (mmt-90) REVERT: E 234 ARG cc_start: 0.7583 (mtt90) cc_final: 0.7196 (ttp-110) REVERT: E 318 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6925 (ttt) REVERT: E 320 SER cc_start: 0.7526 (t) cc_final: 0.7260 (m) REVERT: E 371 MET cc_start: 0.8269 (mmt) cc_final: 0.7925 (mmm) REVERT: E 477 ARG cc_start: 0.6434 (mtm-85) cc_final: 0.6002 (mtm180) REVERT: E 550 LEU cc_start: 0.8134 (tp) cc_final: 0.7911 (tt) REVERT: E 585 GLN cc_start: 0.8206 (tt0) cc_final: 0.7979 (mm-40) REVERT: E 639 TYR cc_start: 0.8261 (m-80) cc_final: 0.7945 (m-80) REVERT: F 424 GLN cc_start: 0.7073 (tp40) cc_final: 0.6223 (tt0) REVERT: F 539 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6809 (tm) REVERT: F 603 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5712 (ttm) REVERT: F 754 GLN cc_start: 0.6499 (mt0) cc_final: 0.6111 (pt0) REVERT: F 782 LYS cc_start: 0.6744 (ptpp) cc_final: 0.6228 (tttp) REVERT: G 17 LEU cc_start: 0.8274 (mp) cc_final: 0.7976 (mp) REVERT: G 25 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8719 (tt) outliers start: 54 outliers final: 25 residues processed: 364 average time/residue: 0.7665 time to fit residues: 314.0100 Evaluate side-chains 338 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 304 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 318 MET Chi-restraints excluded: chain E residue 407 VAL 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 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 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 59 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 197 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 30.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS E 335 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.169893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.128823 restraints weight = 45560.496| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.30 r_work: 0.3174 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24279 Z= 0.109 Angle : 0.517 11.078 32873 Z= 0.253 Chirality : 0.042 0.160 3762 Planarity : 0.004 0.046 4214 Dihedral : 5.862 85.957 3371 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.80 % Rotamer: Outliers : 2.09 % Allowed : 15.54 % Favored : 82.37 % 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: 1.31 (0.16), residues: 3006 helix: 1.31 (0.13), residues: 1616 sheet: 0.12 (0.26), residues: 375 loop : 0.68 (0.22), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 609 TYR 0.010 0.001 TYR A 752 PHE 0.014 0.001 PHE E 527 TRP 0.011 0.001 TRP B 219 HIS 0.003 0.001 HIS C 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (24279) covalent geometry : angle 0.51672 / 0.25 (32873) hydrogen bonds : bond 0.03112 / 2.10 ( 1172) hydrogen bonds : angle 3.94963 / 2.88 ( 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 362 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 309 time to evaluate : 0.950 Fit side-chains revert: symmetry clash 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 330 MET cc_start: 0.6349 (tpp) cc_final: 0.6140 (tpp) REVERT: A 351 ARG cc_start: 0.7412 (mmp-170) cc_final: 0.6972 (tpp-160) REVERT: A 673 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: A 735 ASP cc_start: 0.8992 (m-30) cc_final: 0.8579 (m-30) REVERT: A 795 GLU cc_start: 0.7483 (pp20) cc_final: 0.7266 (pp20) REVERT: A 796 LYS cc_start: 0.6355 (tmtp) cc_final: 0.5584 (mmpt) REVERT: B 325 GLU cc_start: 0.8022 (tp30) cc_final: 0.7488 (tp30) REVERT: B 335 GLN cc_start: 0.7866 (mt0) cc_final: 0.7633 (tt0) REVERT: B 618 SER cc_start: 0.8158 (OUTLIER) cc_final: 0.7926 (m) REVERT: B 755 ARG cc_start: 0.6619 (ttp-170) cc_final: 0.6335 (ttp80) REVERT: B 777 MET cc_start: 0.8776 (tpt) cc_final: 0.8445 (mmm) REVERT: C 231 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7506 (ptm) REVERT: C 286 ASP cc_start: 0.8084 (m-30) cc_final: 0.7793 (m-30) REVERT: C 333 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7737 (pt) REVERT: C 635 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8303 (ppt170) REVERT: C 726 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8332 (mm) REVERT: C 755 ARG cc_start: 0.7491 (ttp80) cc_final: 0.6864 (ttm170) REVERT: D 330 MET cc_start: 0.9035 (mtp) cc_final: 0.8776 (mtm) REVERT: D 421 GLU cc_start: 0.7692 (tp30) cc_final: 0.7307 (tp30) REVERT: E 212 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7795 (mm-40) REVERT: E 223 ARG cc_start: 0.7997 (tpm170) cc_final: 0.7575 (mmt-90) REVERT: E 233 TYR cc_start: 0.7807 (t80) cc_final: 0.7599 (t80) REVERT: E 234 ARG cc_start: 0.7587 (mtt90) cc_final: 0.7223 (ttp-110) REVERT: E 279 GLU cc_start: 0.7276 (tt0) cc_final: 0.6892 (tt0) REVERT: E 286 ASP cc_start: 0.7616 (m-30) cc_final: 0.7179 (m-30) REVERT: E 318 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6945 (ttt) REVERT: E 320 SER cc_start: 0.7559 (t) cc_final: 0.7302 (m) REVERT: E 382 ARG cc_start: 0.7630 (mtt180) cc_final: 0.7414 (mpt-90) REVERT: E 550 LEU cc_start: 0.8141 (tp) cc_final: 0.7928 (tt) REVERT: E 585 GLN cc_start: 0.8256 (tt0) cc_final: 0.8003 (mm-40) REVERT: E 639 TYR cc_start: 0.8306 (m-80) cc_final: 0.7997 (m-80) REVERT: E 777 MET cc_start: 0.6344 (tpt) cc_final: 0.5962 (tpt) REVERT: F 424 GLN cc_start: 0.7083 (tp40) cc_final: 0.6232 (tt0) REVERT: F 539 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6848 (tm) REVERT: F 603 MET cc_start: 0.6253 (OUTLIER) cc_final: 0.5764 (ttm) REVERT: F 754 GLN cc_start: 0.6439 (mt0) cc_final: 0.6142 (pt0) REVERT: F 782 LYS cc_start: 0.6767 (ptpp) cc_final: 0.6380 (tttp) REVERT: F 786 GLU cc_start: 0.6321 (mp0) cc_final: 0.5282 (mt-10) REVERT: G 25 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8724 (tt) outliers start: 53 outliers final: 27 residues processed: 343 average time/residue: 0.7121 time to fit residues: 275.0078 Evaluate side-chains 338 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 300 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 204 ILE 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 618 SER 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 C residue 740 MET Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 508 ASP 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 217 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 61 optimal weight: 0.1980 chunk 71 optimal weight: 10.0000 chunk 302 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 E 502 HIS ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.167114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126235 restraints weight = 54202.363| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 4.11 r_work: 0.3093 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24279 Z= 0.183 Angle : 0.574 13.167 32873 Z= 0.282 Chirality : 0.044 0.160 3762 Planarity : 0.004 0.055 4214 Dihedral : 6.061 84.008 3370 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.70 % Favored : 96.24 % Rotamer: Outliers : 1.97 % Allowed : 15.69 % 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: 1.11 (0.16), residues: 3006 helix: 1.15 (0.13), residues: 1610 sheet: -0.01 (0.26), residues: 376 loop : 0.60 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 609 TYR 0.012 0.001 TYR A 752 PHE 0.015 0.002 PHE D 220 TRP 0.035 0.001 TRP F 466 HIS 0.003 0.001 HIS D 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.18 (24279) covalent geometry : angle 0.57421 / 0.28 (32873) hydrogen bonds : bond 0.03654 / 2.47 ( 1172) hydrogen bonds : angle 4.08206 / 2.98 ( 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 362 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 312 time to evaluate : 1.027 Fit side-chains revert: symmetry clash 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: 0.7483 (mmp-170) cc_final: 0.6980 (tpp-160) REVERT: A 673 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7961 (m-30) REVERT: A 735 ASP cc_start: 0.9081 (m-30) cc_final: 0.8716 (m-30) REVERT: A 795 GLU cc_start: 0.7436 (pp20) cc_final: 0.7185 (pp20) REVERT: A 796 LYS cc_start: 0.6262 (tmtp) cc_final: 0.5478 (mmpt) REVERT: B 325 GLU cc_start: 0.8162 (tp30) cc_final: 0.7633 (tp30) REVERT: B 333 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8074 (pt) REVERT: B 335 GLN cc_start: 0.7948 (mt0) cc_final: 0.7709 (tt0) REVERT: B 618 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.7967 (m) REVERT: B 755 ARG cc_start: 0.6641 (ttp-170) cc_final: 0.6340 (ttp80) REVERT: B 777 MET cc_start: 0.8851 (tpt) cc_final: 0.8562 (mmm) REVERT: C 231 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7528 (ptp) REVERT: C 286 ASP cc_start: 0.8162 (m-30) cc_final: 0.7854 (m-30) REVERT: C 333 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7785 (pt) REVERT: C 726 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8387 (mm) REVERT: C 755 ARG cc_start: 0.7538 (ttp80) cc_final: 0.6874 (ttm170) REVERT: D 330 MET cc_start: 0.9058 (mtp) cc_final: 0.8851 (mtm) REVERT: D 421 GLU cc_start: 0.7713 (tp30) cc_final: 0.7226 (tp30) REVERT: E 212 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7845 (mm-40) REVERT: E 223 ARG cc_start: 0.7986 (tpm170) cc_final: 0.7547 (mmt-90) REVERT: E 234 ARG cc_start: 0.7621 (mtt90) cc_final: 0.7163 (ttp-110) REVERT: E 318 MET cc_start: 0.7261 (ttp) cc_final: 0.6951 (ttt) REVERT: E 320 SER cc_start: 0.7680 (t) cc_final: 0.7387 (m) REVERT: E 371 MET cc_start: 0.8217 (mmt) cc_final: 0.7962 (mmt) REVERT: E 382 ARG cc_start: 0.7627 (mtt180) cc_final: 0.7354 (mpt-90) REVERT: E 550 LEU cc_start: 0.8164 (tp) cc_final: 0.7949 (tt) REVERT: E 585 GLN cc_start: 0.8375 (tt0) cc_final: 0.8080 (mm-40) REVERT: E 639 TYR cc_start: 0.8382 (m-80) cc_final: 0.8055 (m-80) REVERT: E 777 MET cc_start: 0.6343 (tpt) cc_final: 0.5958 (tpt) REVERT: F 424 GLN cc_start: 0.7069 (tp40) cc_final: 0.6195 (tt0) REVERT: F 539 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6795 (tm) REVERT: F 603 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.5878 (ttm) REVERT: F 754 GLN cc_start: 0.6474 (mt0) cc_final: 0.6150 (pt0) REVERT: F 782 LYS cc_start: 0.6852 (ptpp) cc_final: 0.6439 (tttm) REVERT: F 786 GLU cc_start: 0.6360 (mp0) cc_final: 0.5375 (mt-10) outliers start: 50 outliers final: 29 residues processed: 337 average time/residue: 0.7579 time to fit residues: 287.2109 Evaluate side-chains 343 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 305 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 618 SER 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 C residue 740 MET 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 581 ARG Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 407 VAL 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 603 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 281 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 24 optimal weight: 0.0010 chunk 242 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 233 optimal weight: 7.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3992 r_free = 0.3992 target = 0.168757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128208 restraints weight = 48801.404| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.75 r_work: 0.3130 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24279 Z= 0.133 Angle : 0.548 11.731 32873 Z= 0.266 Chirality : 0.042 0.160 3762 Planarity : 0.004 0.045 4214 Dihedral : 5.961 84.688 3370 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 1.66 % Allowed : 16.29 % Favored : 82.06 % 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: 1.23 (0.16), residues: 3006 helix: 1.27 (0.13), residues: 1610 sheet: 0.01 (0.26), residues: 377 loop : 0.64 (0.22), residues: 1019 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 0.015 0.001 PHE A 220 TRP 0.047 0.001 TRP F 466 HIS 0.003 0.001 HIS C 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (24279) covalent geometry : angle 0.54777 / 0.27 (32873) hydrogen bonds : bond 0.03283 / 2.21 ( 1172) hydrogen bonds : angle 4.00288 / 2.92 ( 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: 42 poor density : 312 time to evaluate : 0.950 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 202 LEU cc_start: 0.8190 (mt) cc_final: 0.7973 (mm) REVERT: A 351 ARG cc_start: 0.7464 (mmp-170) cc_final: 0.6987 (tpp-160) REVERT: A 673 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7925 (m-30) REVERT: A 735 ASP cc_start: 0.9052 (m-30) cc_final: 0.8678 (m-30) REVERT: A 796 LYS cc_start: 0.6164 (tmtp) cc_final: 0.5409 (mmpt) REVERT: B 325 GLU cc_start: 0.8066 (tp30) cc_final: 0.7558 (tp30) REVERT: B 333 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8076 (pt) REVERT: B 618 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.7952 (m) REVERT: B 755 ARG cc_start: 0.6613 (ttp-170) cc_final: 0.6326 (ttp80) REVERT: B 777 MET cc_start: 0.8790 (tpt) cc_final: 0.8450 (mmm) REVERT: C 231 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7549 (ptm) REVERT: C 286 ASP cc_start: 0.8143 (m-30) cc_final: 0.7853 (m-30) REVERT: C 333 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7822 (pt) REVERT: C 635 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8248 (ppt170) REVERT: C 726 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8403 (mm) REVERT: C 755 ARG cc_start: 0.7540 (ttp80) cc_final: 0.6896 (ttm170) REVERT: D 330 MET cc_start: 0.9039 (mtp) cc_final: 0.8748 (mtm) REVERT: D 369 MET cc_start: 0.8638 (mtp) cc_final: 0.8300 (mtp) REVERT: D 421 GLU cc_start: 0.7762 (tp30) cc_final: 0.7353 (tp30) REVERT: E 212 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7796 (mm-40) REVERT: E 223 ARG cc_start: 0.8005 (tpm170) cc_final: 0.7565 (mmt-90) REVERT: E 234 ARG cc_start: 0.7610 (mtt90) cc_final: 0.7203 (ttp-110) REVERT: E 318 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6970 (ttt) REVERT: E 320 SER cc_start: 0.7591 (t) cc_final: 0.7326 (m) REVERT: E 371 MET cc_start: 0.8157 (mmt) cc_final: 0.7906 (mmt) REVERT: E 550 LEU cc_start: 0.8129 (tp) cc_final: 0.7913 (tt) REVERT: E 567 LYS cc_start: 0.8160 (tppp) cc_final: 0.7806 (tppp) REVERT: E 585 GLN cc_start: 0.8313 (tt0) cc_final: 0.8038 (mm-40) REVERT: E 639 TYR cc_start: 0.8336 (m-80) cc_final: 0.7969 (m-80) REVERT: E 777 MET cc_start: 0.6366 (tpt) cc_final: 0.6015 (tpt) REVERT: F 421 GLU cc_start: 0.7474 (tt0) cc_final: 0.7033 (tp30) REVERT: F 424 GLN cc_start: 0.7049 (tp40) cc_final: 0.5916 (tt0) REVERT: F 539 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6752 (tm) REVERT: F 603 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.5826 (ttm) REVERT: F 754 GLN cc_start: 0.6463 (mt0) cc_final: 0.6141 (pt0) REVERT: F 782 LYS cc_start: 0.6733 (ptpp) cc_final: 0.6349 (tttm) REVERT: F 786 GLU cc_start: 0.6424 (mp0) cc_final: 0.5557 (mt-10) outliers start: 42 outliers final: 27 residues processed: 336 average time/residue: 0.7679 time to fit residues: 290.1010 Evaluate side-chains 342 residues out of total 2554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 304 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 618 SER 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 C residue 740 MET 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 E residue 212 GLN Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL 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 603 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 35 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 270 optimal weight: 0.2980 chunk 157 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 274 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 ASN ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.169864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128729 restraints weight = 38111.071| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.60 r_work: 0.3212 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24279 Z= 0.113 Angle : 0.550 13.231 32873 Z= 0.266 Chirality : 0.042 0.160 3762 Planarity : 0.004 0.047 4214 Dihedral : 5.858 85.436 3370 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.67 % Rotamer: Outliers : 1.58 % Allowed : 16.68 % 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: 1.34 (0.16), residues: 3006 helix: 1.36 (0.13), residues: 1618 sheet: 0.04 (0.26), residues: 375 loop : 0.70 (0.22), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 609 TYR 0.011 0.001 TYR A 752 PHE 0.018 0.001 PHE E 527 TRP 0.049 0.001 TRP F 466 HIS 0.003 0.001 HIS C 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (24279) covalent geometry : angle 0.54999 / 0.27 (32873) hydrogen bonds : bond 0.03086 / 2.08 ( 1172) hydrogen bonds : angle 3.94568 / 2.87 ( 3272) =============================================================================== Job complete usr+sys time: 9187.05 seconds wall clock time: 156 minutes 53.51 seconds (9413.51 seconds total)