Starting phenix.real_space_refine on Mon Sep 30 01:48:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swl_25474/09_2024/7swl_25474.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swl_25474/09_2024/7swl_25474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swl_25474/09_2024/7swl_25474.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swl_25474/09_2024/7swl_25474.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swl_25474/09_2024/7swl_25474.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swl_25474/09_2024/7swl_25474.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP: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: {'GLU:plan': 3, 'ASP:plan': 1} 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: 17.29, per 1000 atoms: 0.72 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: 5.62 Conformation dependent library (CDL) restraints added in 3.9 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: 3.08 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: 7.60 Time building geometry restraints manager: 6.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8024 1.34 - 1.46: 4124 1.46 - 1.58: 11891 1.58 - 1.69: 48 1.69 - 1.81: 192 Bond restraints: 24279 Sorted by residual: bond pdb=" O5' ATP E 902 " pdb=" PA ATP E 902 " ideal model delta sigma weight residual 1.579 1.610 -0.031 1.10e-02 8.26e+03 7.98e+00 bond pdb=" O5' ATP A 901 " pdb=" PA ATP A 901 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.43e+00 bond pdb=" O5' ATP A 902 " pdb=" PA ATP A 902 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.36e+00 bond pdb=" O5' ATP D 901 " pdb=" PA ATP D 901 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.33e+00 bond pdb=" O5' ATP B 901 " pdb=" PA ATP B 901 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.24e+00 ... (remaining 24274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 32534 2.09 - 4.18: 271 4.18 - 6.27: 49 6.27 - 8.36: 12 8.36 - 10.45: 7 Bond angle restraints: 32873 Sorted by residual: angle pdb=" PB ATP E 902 " pdb=" O3B ATP E 902 " pdb=" PG ATP E 902 " ideal model delta sigma weight residual 139.87 129.42 10.45 1.00e+00 1.00e+00 1.09e+02 angle pdb=" PB ATP B 901 " pdb=" O3B ATP B 901 " pdb=" PG ATP B 901 " ideal model delta sigma weight residual 139.87 129.59 10.28 1.00e+00 1.00e+00 1.06e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 129.89 9.98 1.00e+00 1.00e+00 9.95e+01 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 130.23 9.64 1.00e+00 1.00e+00 9.30e+01 angle pdb=" PB ATP D 902 " pdb=" O3B ATP D 902 " pdb=" PG ATP D 902 " ideal model delta sigma weight residual 139.87 130.92 8.95 1.00e+00 1.00e+00 8.01e+01 ... (remaining 32868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 14690 24.83 - 49.65: 329 49.65 - 74.48: 85 74.48 - 99.31: 9 99.31 - 124.13: 1 Dihedral angle restraints: 15114 sinusoidal: 6318 harmonic: 8796 Sorted by residual: dihedral pdb=" C5' ADP E 901 " pdb=" O5' ADP E 901 " pdb=" PA ADP E 901 " pdb=" O2A ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 175.87 124.13 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" O2A ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PA ADP E 901 " pdb=" PB ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 -134.83 74.83 1 2.00e+01 2.50e-03 1.77e+01 dihedral pdb=" CA ARG D 635 " pdb=" CB ARG D 635 " pdb=" CG ARG D 635 " pdb=" CD ARG D 635 " ideal model delta sinusoidal sigma weight residual 60.00 118.64 -58.64 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 15111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2259 0.029 - 0.058: 1036 0.058 - 0.087: 220 0.087 - 0.116: 211 0.116 - 0.144: 36 Chirality restraints: 3762 Sorted by residual: chirality pdb=" C3' ATP D 902 " pdb=" C2' ATP D 902 " pdb=" C4' ATP D 902 " pdb=" O3' ATP D 902 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" C3' ATP E 902 " pdb=" C2' ATP E 902 " pdb=" C4' ATP E 902 " pdb=" O3' ATP E 902 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" C3' ATP A 901 " pdb=" C2' ATP A 901 " pdb=" C4' ATP A 901 " pdb=" O3' ATP A 901 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 3759 not shown) Planarity restraints: 4214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 356 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 357 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 357 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 357 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 519 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.43e+00 pdb=" N PRO A 520 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 520 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 220 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO D 221 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " -0.016 5.00e-02 4.00e+02 ... (remaining 4211 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 172 2.54 - 3.13: 18071 3.13 - 3.72: 36542 3.72 - 4.31: 53475 4.31 - 4.90: 89334 Nonbonded interactions: 197594 Sorted by model distance: nonbonded pdb=" O1B ATP B 901 " pdb="MG MG B 903 " model vdw 1.953 2.170 nonbonded pdb=" O1B ATP C 902 " pdb="MG MG C 904 " model vdw 1.970 2.170 nonbonded pdb=" O1B ATP D 902 " pdb="MG MG D 904 " model vdw 1.993 2.170 nonbonded pdb=" O2G ATP D 901 " pdb="MG MG D 903 " model vdw 1.994 2.170 nonbonded pdb=" O2G ATP C 902 " pdb="MG MG C 904 " model vdw 1.995 2.170 ... (remaining 197589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 200 through 302 or resid 304 through 388 or resid 394 thro \ ugh 425 or resid 470 through 483 or (resid 484 and (name N or name CA or name C \ or name O or name CB )) or resid 485 through 487 or resid 494 through 588 or res \ id 590 through 634 or (resid 635 and (name N or name CA or name C or name O or n \ ame CB )) or resid 636 through 654 or resid 656 through 726 or resid 732 through \ 751 or resid 775 through 788 or resid 904)) selection = (chain 'B' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 388 or resid 394 through 425 or resid 470 through 483 or (resid 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 through 487 or res \ id 494 through 588 or resid 590 through 634 or (resid 635 and (name N or name CA \ or name C or name O or name CB )) or resid 636 through 654 or resid 656 through \ 726 or resid 732 through 751 or resid 775 through 788 or resid 904)) selection = (chain 'C' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 388 or resid 394 through 425 or resid 470 through 483 or (resid 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 through 487 or res \ id 494 through 588 or resid 590 through 634 or (resid 635 and (name N or name CA \ or name C or name O or name CB )) or resid 636 through 654 or resid 656 through \ 726 or resid 732 through 751 or resid 775 through 788 or resid 904)) selection = (chain 'D' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 388 or resid 394 through 425 or resid 470 through 483 or (resid 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 through 487 or res \ id 494 through 588 or resid 590 through 634 or (resid 635 and (name N or name CA \ or name C or name O or name CB )) or resid 636 through 654 or resid 656 through \ 726 or resid 732 through 751 or resid 775 through 788 or resid 904)) selection = (chain 'E' and (resid 200 through 302 or resid 304 through 309 or resid 317 thro \ ugh 588 or resid 590 through 654 or resid 656 through 788 or resid 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 55.730 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24279 Z= 0.220 Angle : 0.509 10.455 32873 Z= 0.305 Chirality : 0.040 0.144 3762 Planarity : 0.003 0.035 4214 Dihedral : 11.234 124.134 9416 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (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 TRP 0.005 0.001 TRP E 541 HIS 0.003 0.001 HIS C 242 PHE 0.008 0.001 PHE C 264 TYR 0.009 0.001 TYR B 406 ARG 0.003 0.000 ARG C 377 *********************** 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 fitting. rotamer outliers: 24 poor density : 541 time to evaluate : 2.866 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: 1.6326 time to fit residues: 1022.8517 Evaluate side-chains 339 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 328 time to evaluate : 2.760 ------------------------------------------------------------------------------- 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 256 optimal weight: 5.9990 chunk 230 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 123 optimal weight: 50.0000 chunk 238 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 144 optimal weight: 0.4980 chunk 177 optimal weight: 7.9990 chunk 276 optimal weight: 50.0000 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN C 424 GLN C 438 HIS C 459 HIS C 562 ASN C 585 GLN D 433 GLN D 741 GLN E 335 GLN E 523 ASN E 602 GLN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 745 GLN F 433 GLN F 484 GLN F 785 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24279 Z= 0.239 Angle : 0.576 8.635 32873 Z= 0.296 Chirality : 0.044 0.267 3762 Planarity : 0.004 0.053 4214 Dihedral : 11.533 102.602 3662 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 2.56 % Allowed : 10.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 3006 helix: 0.48 (0.13), residues: 1613 sheet: 0.46 (0.27), residues: 382 loop : 0.71 (0.22), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 219 HIS 0.003 0.001 HIS C 242 PHE 0.022 0.002 PHE E 527 TYR 0.013 0.001 TYR A 752 ARG 0.007 0.001 ARG B 609 *********************** 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 448 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 383 time to evaluate : 2.657 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 355 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7293 (mp) REVERT: A 560 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8721 (mttp) REVERT: A 716 ASP cc_start: 0.7674 (t0) cc_final: 0.6977 (m-30) REVERT: A 735 ASP cc_start: 0.8577 (m-30) cc_final: 0.8210 (m-30) REVERT: A 795 GLU cc_start: 0.7128 (pp20) cc_final: 0.6865 (pp20) REVERT: A 796 LYS cc_start: 0.5285 (tmtp) cc_final: 0.4794 (mmpt) REVERT: B 320 SER cc_start: 0.8618 (t) cc_final: 0.8341 (m) REVERT: B 325 GLU cc_start: 0.7368 (tp30) cc_final: 0.7089 (tp30) REVERT: B 433 GLN cc_start: 0.7476 (tp40) cc_final: 0.7240 (tm-30) REVERT: B 777 MET cc_start: 0.8362 (tpt) cc_final: 0.8089 (tpt) REVERT: C 286 ASP cc_start: 0.7790 (m-30) cc_final: 0.7399 (m-30) REVERT: C 635 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8450 (ppt-90) REVERT: C 757 GLN cc_start: 0.6951 (tt0) cc_final: 0.6619 (mt0) REVERT: D 490 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7227 (mt-10) REVERT: D 533 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7698 (mptp) REVERT: D 778 GLU cc_start: 0.8046 (pt0) cc_final: 0.7461 (tp30) REVERT: D 781 GLU cc_start: 0.7259 (mp0) cc_final: 0.6937 (mp0) REVERT: E 318 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.7050 (ttt) REVERT: E 320 SER cc_start: 0.7667 (t) cc_final: 0.7348 (m) REVERT: E 416 LYS cc_start: 0.7570 (mttt) cc_final: 0.7194 (mmtm) REVERT: E 472 THR cc_start: 0.7222 (OUTLIER) cc_final: 0.6977 (t) REVERT: E 475 GLN cc_start: 0.5796 (mt0) cc_final: 0.5358 (mm-40) REVERT: E 567 LYS cc_start: 0.7842 (tptp) cc_final: 0.7628 (tptp) REVERT: E 741 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.6590 (tt0) REVERT: F 424 GLN cc_start: 0.7423 (tp40) cc_final: 0.6680 (tt0) REVERT: F 601 ASP cc_start: 0.6748 (p0) cc_final: 0.6438 (t0) REVERT: F 604 ASP cc_start: 0.7644 (p0) cc_final: 0.6836 (p0) REVERT: F 754 GLN cc_start: 0.6813 (mt0) cc_final: 0.6240 (pp30) REVERT: F 786 GLU cc_start: 0.5448 (mp0) cc_final: 0.4815 (mt-10) REVERT: G 17 LEU cc_start: 0.8099 (mp) cc_final: 0.7871 (mp) outliers start: 65 outliers final: 22 residues processed: 419 average time/residue: 1.5532 time to fit residues: 731.2984 Evaluate side-chains 354 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 325 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 560 LYS 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 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 407 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 508 ASP 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 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 276 optimal weight: 0.0870 chunk 298 optimal weight: 5.9990 chunk 246 optimal weight: 7.9990 chunk 274 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN B 424 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS D 350 ASN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24279 Z= 0.223 Angle : 0.539 8.196 32873 Z= 0.271 Chirality : 0.043 0.187 3762 Planarity : 0.004 0.042 4214 Dihedral : 11.391 94.619 3654 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.74 % Rotamer: Outliers : 2.60 % Allowed : 12.03 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 3006 helix: 0.74 (0.13), residues: 1607 sheet: 0.29 (0.26), residues: 382 loop : 0.59 (0.22), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 466 HIS 0.003 0.001 HIS B 242 PHE 0.020 0.001 PHE E 527 TYR 0.010 0.001 TYR A 752 ARG 0.008 0.001 ARG B 609 *********************** 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 419 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 353 time to evaluate : 2.491 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.8845 (mtt) cc_final: 0.8446 (mtt) REVERT: A 474 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7102 (mm-30) REVERT: A 560 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8784 (mttp) REVERT: A 735 ASP cc_start: 0.8567 (m-30) cc_final: 0.8180 (m-30) REVERT: A 796 LYS cc_start: 0.5741 (tmtp) cc_final: 0.5312 (mmpt) REVERT: B 320 SER cc_start: 0.8497 (t) cc_final: 0.8278 (m) REVERT: B 325 GLU cc_start: 0.7381 (tp30) cc_final: 0.7028 (tp30) REVERT: B 777 MET cc_start: 0.8379 (tpt) cc_final: 0.8064 (tpt) REVERT: C 286 ASP cc_start: 0.7653 (m-30) cc_final: 0.7241 (m-30) REVERT: C 635 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8407 (ppt-90) REVERT: C 757 GLN cc_start: 0.6667 (tt0) cc_final: 0.6405 (mt0) REVERT: D 330 MET cc_start: 0.8897 (mtp) cc_final: 0.8684 (mtm) REVERT: D 533 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7683 (mptp) REVERT: E 318 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6926 (ttt) REVERT: E 320 SER cc_start: 0.7784 (t) cc_final: 0.7479 (m) REVERT: E 741 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6589 (tt0) REVERT: F 424 GLN cc_start: 0.7540 (tp40) cc_final: 0.6755 (tt0) REVERT: F 539 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7577 (tm) REVERT: F 601 ASP cc_start: 0.6750 (p0) cc_final: 0.6424 (t0) REVERT: F 603 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6509 (ptm) REVERT: F 754 GLN cc_start: 0.6754 (mt0) cc_final: 0.6121 (pt0) REVERT: G 17 LEU cc_start: 0.8098 (mp) cc_final: 0.7841 (mp) outliers start: 66 outliers final: 26 residues processed: 391 average time/residue: 1.4783 time to fit residues: 650.1181 Evaluate side-chains 351 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 317 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 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 A residue 781 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 533 LYS Chi-restraints excluded: chain 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 622 VAL 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 273 optimal weight: 20.0000 chunk 207 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 277 optimal weight: 5.9990 chunk 293 optimal weight: 0.8980 chunk 145 optimal weight: 10.0000 chunk 263 optimal weight: 30.0000 chunk 79 optimal weight: 5.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS E 602 GLN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24279 Z= 0.180 Angle : 0.525 8.030 32873 Z= 0.261 Chirality : 0.042 0.164 3762 Planarity : 0.004 0.040 4214 Dihedral : 11.194 92.254 3651 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.80 % Rotamer: Outliers : 2.37 % Allowed : 14.12 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.16), residues: 3006 helix: 0.96 (0.13), residues: 1623 sheet: 0.18 (0.26), residues: 381 loop : 0.67 (0.22), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 466 HIS 0.003 0.001 HIS B 242 PHE 0.015 0.001 PHE E 527 TYR 0.009 0.001 TYR A 752 ARG 0.011 0.001 ARG E 213 *********************** 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 408 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 348 time to evaluate : 2.576 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.8864 (mtt) cc_final: 0.8454 (mtt) REVERT: A 474 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7136 (mm-30) REVERT: A 560 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8788 (mttp) REVERT: A 735 ASP cc_start: 0.8537 (m-30) cc_final: 0.8137 (m-30) REVERT: A 795 GLU cc_start: 0.7300 (pp20) cc_final: 0.7072 (pp20) REVERT: A 796 LYS cc_start: 0.5940 (tmtp) cc_final: 0.5360 (mmpt) REVERT: B 320 SER cc_start: 0.8449 (t) cc_final: 0.8247 (m) REVERT: B 325 GLU cc_start: 0.7360 (tp30) cc_final: 0.7059 (tp30) REVERT: B 777 MET cc_start: 0.8412 (tpt) cc_final: 0.8109 (mmm) REVERT: C 231 MET cc_start: 0.7520 (mtp) cc_final: 0.7251 (ptm) REVERT: C 435 ARG cc_start: 0.6725 (mtt90) cc_final: 0.6385 (mtt90) REVERT: C 635 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8397 (ppt-90) REVERT: C 757 GLN cc_start: 0.6658 (tt0) cc_final: 0.6324 (mt0) REVERT: D 533 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7666 (mptp) REVERT: E 318 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6890 (ttt) REVERT: E 320 SER cc_start: 0.7739 (t) cc_final: 0.7455 (m) REVERT: E 477 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6880 (mtm-85) REVERT: E 550 LEU cc_start: 0.8295 (tp) cc_final: 0.8092 (tt) REVERT: E 567 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7545 (tptp) REVERT: E 741 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7130 (mm-40) REVERT: F 424 GLN cc_start: 0.7408 (tp40) cc_final: 0.6612 (tt0) REVERT: F 539 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7537 (tm) REVERT: F 603 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.6631 (ptp) REVERT: F 740 MET cc_start: 0.6831 (ttp) cc_final: 0.6476 (tmm) REVERT: F 741 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6748 (tp40) REVERT: F 754 GLN cc_start: 0.6708 (mt0) cc_final: 0.6163 (pt0) REVERT: G 17 LEU cc_start: 0.8050 (mp) cc_final: 0.7771 (mp) outliers start: 60 outliers final: 26 residues processed: 383 average time/residue: 1.5776 time to fit residues: 683.8734 Evaluate side-chains 352 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 315 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 778 GLU 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 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 477 ARG 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 218 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 chunk 263 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2732 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= 0.320 Angle : 0.574 7.892 32873 Z= 0.287 Chirality : 0.045 0.160 3762 Planarity : 0.004 0.052 4214 Dihedral : 11.439 88.724 3651 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 3.15 % Allowed : 14.12 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.16), residues: 3006 helix: 0.89 (0.13), residues: 1606 sheet: 0.04 (0.26), residues: 378 loop : 0.54 (0.21), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 466 HIS 0.004 0.001 HIS D 254 PHE 0.015 0.002 PHE E 527 TYR 0.012 0.001 TYR B 406 ARG 0.010 0.001 ARG B 609 *********************** 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 404 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 324 time to evaluate : 2.959 Fit side-chains TARDY: cannot create tardy model for: "MET B 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 199 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 199 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.8890 (mtt) cc_final: 0.8455 (mtt) REVERT: A 560 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8779 (mttp) REVERT: A 735 ASP cc_start: 0.8590 (m-30) cc_final: 0.8193 (m-30) REVERT: A 795 GLU cc_start: 0.7212 (pp20) cc_final: 0.6940 (pp20) REVERT: A 796 LYS cc_start: 0.5982 (tmtp) cc_final: 0.5365 (mmpt) REVERT: B 320 SER cc_start: 0.8495 (t) cc_final: 0.8284 (m) REVERT: B 325 GLU cc_start: 0.7403 (tp30) cc_final: 0.7017 (tp30) REVERT: B 777 MET cc_start: 0.8350 (tpt) cc_final: 0.8097 (tpt) REVERT: C 231 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7386 (ptm) REVERT: C 435 ARG cc_start: 0.6716 (mtt90) cc_final: 0.6391 (mtt90) REVERT: C 635 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8383 (ppt-90) REVERT: D 423 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: D 533 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7679 (mptp) REVERT: E 212 GLN cc_start: 0.8248 (tt0) cc_final: 0.7857 (mt0) REVERT: E 318 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6907 (ttt) REVERT: E 320 SER cc_start: 0.7892 (t) cc_final: 0.7591 (m) REVERT: E 477 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6630 (mtm-85) REVERT: E 526 LEU cc_start: 0.8284 (tp) cc_final: 0.7969 (tp) REVERT: E 639 TYR cc_start: 0.7818 (m-80) cc_final: 0.7578 (m-80) REVERT: E 741 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7217 (mm-40) REVERT: F 424 GLN cc_start: 0.7445 (tp40) cc_final: 0.6628 (tt0) REVERT: F 539 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7548 (tm) REVERT: F 603 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6550 (ptp) REVERT: F 740 MET cc_start: 0.6720 (ttp) cc_final: 0.6441 (tmm) REVERT: F 741 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6717 (tp40) REVERT: F 754 GLN cc_start: 0.6761 (mt0) cc_final: 0.6205 (pt0) REVERT: F 782 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7597 (tttp) REVERT: F 786 GLU cc_start: 0.5865 (mp0) cc_final: 0.5024 (mt-10) outliers start: 80 outliers final: 41 residues processed: 371 average time/residue: 1.6024 time to fit residues: 669.5459 Evaluate side-chains 357 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 304 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 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 B residue 592 SER Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 778 GLU 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 423 PHE 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 473 MET Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 741 GLN Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 474 GLU 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 604 ASP Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 629 LEU 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 F residue 779 ASP Chi-restraints excluded: chain F residue 782 LYS 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 98 optimal weight: 7.9990 chunk 264 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 chunk 172 optimal weight: 0.0470 chunk 72 optimal weight: 0.6980 chunk 294 optimal weight: 30.0000 chunk 244 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN C 459 HIS E 602 GLN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24279 Z= 0.201 Angle : 0.534 9.291 32873 Z= 0.265 Chirality : 0.042 0.158 3762 Planarity : 0.004 0.043 4214 Dihedral : 11.249 88.708 3651 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Rotamer: Outliers : 2.52 % Allowed : 15.22 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.16), residues: 3006 helix: 1.10 (0.13), residues: 1610 sheet: 0.04 (0.26), residues: 375 loop : 0.61 (0.21), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 466 HIS 0.003 0.001 HIS B 242 PHE 0.012 0.001 PHE E 527 TYR 0.008 0.001 TYR B 406 ARG 0.010 0.001 ARG B 755 *********************** 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 389 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 325 time to evaluate : 2.718 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: symmetry clash REVERT: A 371 MET cc_start: 0.8845 (mtt) cc_final: 0.8382 (mtt) REVERT: A 560 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8797 (mttp) REVERT: A 735 ASP cc_start: 0.8570 (m-30) cc_final: 0.8167 (m-30) REVERT: A 796 LYS cc_start: 0.5884 (tmtp) cc_final: 0.5279 (mmpt) REVERT: B 325 GLU cc_start: 0.7387 (tp30) cc_final: 0.7022 (tp30) REVERT: B 777 MET cc_start: 0.8376 (tpt) cc_final: 0.8084 (mmm) REVERT: C 231 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7304 (ptm) REVERT: C 435 ARG cc_start: 0.6627 (mtt90) cc_final: 0.6315 (mtt90) REVERT: E 212 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: E 318 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6920 (ttt) REVERT: E 320 SER cc_start: 0.7798 (t) cc_final: 0.7530 (m) REVERT: E 341 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8215 (mtmt) REVERT: E 526 LEU cc_start: 0.8204 (tp) cc_final: 0.7928 (tp) REVERT: E 567 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7552 (tptp) REVERT: E 639 TYR cc_start: 0.7807 (m-80) cc_final: 0.7531 (m-80) REVERT: F 424 GLN cc_start: 0.7473 (tp40) cc_final: 0.6522 (tt0) REVERT: F 539 LEU cc_start: 0.7711 (tm) cc_final: 0.7493 (tm) REVERT: F 741 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6394 (tp40) REVERT: F 754 GLN cc_start: 0.6597 (mt0) cc_final: 0.6200 (pt0) REVERT: F 786 GLU cc_start: 0.5728 (mp0) cc_final: 0.5045 (mt-10) REVERT: G 17 LEU cc_start: 0.8039 (mp) cc_final: 0.7817 (mp) outliers start: 64 outliers final: 37 residues processed: 366 average time/residue: 1.5938 time to fit residues: 657.2789 Evaluate side-chains 348 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 304 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 778 GLU 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 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 455 LEU 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 341 LYS Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 557 ASN Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 673 ASP Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 741 GLN Chi-restraints excluded: chain F residue 774 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 30.0000 chunk 33 optimal weight: 0.0470 chunk 167 optimal weight: 0.6980 chunk 214 optimal weight: 8.9990 chunk 166 optimal weight: 0.9980 chunk 247 optimal weight: 20.0000 chunk 164 optimal weight: 4.9990 chunk 293 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN F 741 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24279 Z= 0.141 Angle : 0.516 12.030 32873 Z= 0.254 Chirality : 0.041 0.293 3762 Planarity : 0.004 0.044 4214 Dihedral : 10.952 89.250 3651 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 2.33 % Allowed : 15.58 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.16), residues: 3006 helix: 1.30 (0.13), residues: 1613 sheet: 0.06 (0.26), residues: 376 loop : 0.73 (0.22), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 466 HIS 0.003 0.001 HIS C 459 PHE 0.010 0.001 PHE E 527 TYR 0.007 0.001 TYR A 752 ARG 0.011 0.000 ARG B 755 *********************** 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 395 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 336 time to evaluate : 2.488 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 735 ASP cc_start: 0.8546 (m-30) cc_final: 0.8096 (m-30) REVERT: A 795 GLU cc_start: 0.7355 (pp20) cc_final: 0.7129 (pp20) REVERT: A 796 LYS cc_start: 0.6077 (tmtp) cc_final: 0.5475 (mmpt) REVERT: B 325 GLU cc_start: 0.7289 (tp30) cc_final: 0.6973 (tp30) REVERT: B 777 MET cc_start: 0.8389 (tpt) cc_final: 0.8087 (mmm) REVERT: C 333 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7707 (pt) REVERT: C 635 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8195 (ppt170) REVERT: C 755 ARG cc_start: 0.7604 (ttp80) cc_final: 0.6947 (ttm170) REVERT: E 212 GLN cc_start: 0.8150 (tt0) cc_final: 0.7776 (mm-40) REVERT: E 286 ASP cc_start: 0.7496 (m-30) cc_final: 0.7261 (m-30) REVERT: E 318 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6919 (ttt) REVERT: E 320 SER cc_start: 0.7655 (t) cc_final: 0.7422 (m) REVERT: E 375 ARG cc_start: 0.8096 (tpp80) cc_final: 0.7840 (tpt-90) REVERT: E 567 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7542 (tptp) REVERT: E 639 TYR cc_start: 0.7778 (m-80) cc_final: 0.7547 (m-80) REVERT: E 648 ASP cc_start: 0.7882 (m-30) cc_final: 0.7664 (t0) REVERT: F 424 GLN cc_start: 0.7425 (tp40) cc_final: 0.6608 (tt0) REVERT: F 539 LEU cc_start: 0.7668 (tm) cc_final: 0.7442 (tm) REVERT: F 749 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6838 (tt0) REVERT: F 754 GLN cc_start: 0.6519 (mt0) cc_final: 0.6168 (pt0) REVERT: G 11 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6787 (mt) outliers start: 59 outliers final: 24 residues processed: 373 average time/residue: 1.5625 time to fit residues: 657.8272 Evaluate side-chains 332 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 302 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 796 LYS 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 D residue 361 ARG 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 473 MET Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 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 11 LEU Chi-restraints excluded: chain G residue 18 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 230 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS D 350 ASN E 502 HIS ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 741 GLN F 433 GLN F 741 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24279 Z= 0.189 Angle : 0.532 10.828 32873 Z= 0.262 Chirality : 0.042 0.157 3762 Planarity : 0.004 0.044 4214 Dihedral : 10.945 88.957 3650 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 1.97 % Allowed : 16.44 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.16), residues: 3006 helix: 1.30 (0.13), residues: 1620 sheet: 0.05 (0.26), residues: 377 loop : 0.73 (0.22), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 780 HIS 0.003 0.001 HIS C 459 PHE 0.012 0.001 PHE C 354 TYR 0.008 0.001 TYR B 406 ARG 0.012 0.001 ARG B 755 *********************** 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 370 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 320 time to evaluate : 2.676 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 359 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7559 (mm) REVERT: A 735 ASP cc_start: 0.8554 (m-30) cc_final: 0.8100 (m-30) REVERT: A 796 LYS cc_start: 0.6049 (tmtp) cc_final: 0.5420 (mmpt) REVERT: B 325 GLU cc_start: 0.7363 (tp30) cc_final: 0.7016 (tp30) REVERT: B 333 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7986 (pt) REVERT: C 333 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7730 (pt) REVERT: C 635 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8009 (ppt170) REVERT: E 212 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7808 (mm-40) REVERT: E 318 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6953 (ttt) REVERT: E 320 SER cc_start: 0.7747 (t) cc_final: 0.7514 (m) REVERT: E 567 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7566 (tptp) REVERT: E 639 TYR cc_start: 0.7818 (m-80) cc_final: 0.7585 (m-80) REVERT: F 424 GLN cc_start: 0.7429 (tp40) cc_final: 0.6621 (tt0) REVERT: F 539 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7495 (tm) REVERT: F 754 GLN cc_start: 0.6546 (mt0) cc_final: 0.6276 (pt0) REVERT: F 786 GLU cc_start: 0.5686 (mp0) cc_final: 0.4774 (mt-10) outliers start: 50 outliers final: 23 residues processed: 349 average time/residue: 1.5573 time to fit residues: 612.0519 Evaluate side-chains 344 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 313 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 359 ILE 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 333 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 796 LYS 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 D residue 346 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 539 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 0.4980 chunk 280 optimal weight: 50.0000 chunk 256 optimal weight: 4.9990 chunk 273 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 246 optimal weight: 7.9990 chunk 258 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS D 350 ASN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24279 Z= 0.281 Angle : 0.578 10.789 32873 Z= 0.285 Chirality : 0.044 0.157 3762 Planarity : 0.004 0.057 4214 Dihedral : 11.188 88.186 3650 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.27 % Rotamer: Outliers : 2.13 % Allowed : 16.36 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.16), residues: 3006 helix: 1.19 (0.13), residues: 1609 sheet: 0.06 (0.26), residues: 372 loop : 0.62 (0.21), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 219 HIS 0.003 0.001 HIS C 242 PHE 0.015 0.002 PHE C 354 TYR 0.012 0.001 TYR B 406 ARG 0.013 0.001 ARG B 755 *********************** 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 371 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 317 time to evaluate : 2.632 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 371 MET cc_start: 0.8835 (mtt) cc_final: 0.8301 (mtt) REVERT: A 673 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: A 682 TYR cc_start: 0.8806 (t80) cc_final: 0.8544 (t80) REVERT: A 735 ASP cc_start: 0.8601 (m-30) cc_final: 0.8155 (m-30) REVERT: A 795 GLU cc_start: 0.7431 (pp20) cc_final: 0.7147 (pp20) REVERT: A 796 LYS cc_start: 0.5918 (tmtp) cc_final: 0.5291 (mmpt) REVERT: B 325 GLU cc_start: 0.7410 (tp30) cc_final: 0.7054 (tp30) REVERT: B 333 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8033 (pt) REVERT: B 335 GLN cc_start: 0.7500 (mt0) cc_final: 0.7296 (tt0) REVERT: B 618 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7871 (m) REVERT: C 333 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7778 (pt) REVERT: C 435 ARG cc_start: 0.6801 (mtt90) cc_final: 0.6428 (mpt90) REVERT: C 755 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7072 (ttm170) REVERT: E 203 ASP cc_start: 0.7066 (m-30) cc_final: 0.6465 (t0) REVERT: E 212 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7846 (mm-40) REVERT: E 234 ARG cc_start: 0.7909 (ttp-110) cc_final: 0.7680 (ttp-110) REVERT: E 318 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6963 (ttt) REVERT: E 320 SER cc_start: 0.7829 (t) cc_final: 0.7571 (m) REVERT: E 639 TYR cc_start: 0.7943 (m-80) cc_final: 0.7646 (m-80) REVERT: F 424 GLN cc_start: 0.7447 (tp40) cc_final: 0.6632 (tt0) REVERT: F 754 GLN cc_start: 0.6556 (mt0) cc_final: 0.6264 (pt0) REVERT: F 786 GLU cc_start: 0.5634 (mp0) cc_final: 0.4799 (mt-10) outliers start: 54 outliers final: 31 residues processed: 347 average time/residue: 1.5802 time to fit residues: 619.3021 Evaluate side-chains 342 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 305 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 THR 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 B residue 796 LYS 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 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 D residue 726 LEU Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 476 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 557 ASN Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 722 VAL Chi-restraints excluded: chain F residue 741 GLN Chi-restraints excluded: chain F residue 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 179 optimal weight: 5.9990 chunk 288 optimal weight: 20.0000 chunk 176 optimal weight: 0.8980 chunk 136 optimal weight: 20.0000 chunk 200 optimal weight: 2.9990 chunk 302 optimal weight: 0.0570 chunk 278 optimal weight: 0.3980 chunk 241 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 684 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** 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** E 741 GLN F 433 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24279 Z= 0.150 Angle : 0.539 11.855 32873 Z= 0.262 Chirality : 0.041 0.159 3762 Planarity : 0.004 0.049 4214 Dihedral : 10.763 88.914 3650 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.07 % Rotamer: Outliers : 1.34 % Allowed : 17.47 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.16), residues: 3006 helix: 1.35 (0.13), residues: 1624 sheet: 0.08 (0.26), residues: 375 loop : 0.73 (0.22), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 780 HIS 0.003 0.001 HIS C 459 PHE 0.014 0.001 PHE B 423 TYR 0.008 0.001 TYR D 235 ARG 0.012 0.000 ARG B 755 ********************** 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 366 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 332 time to evaluate : 2.515 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 682 TYR cc_start: 0.8692 (t80) cc_final: 0.8458 (t80) REVERT: A 735 ASP cc_start: 0.8534 (m-30) cc_final: 0.8084 (m-30) REVERT: A 796 LYS cc_start: 0.6107 (tmtp) cc_final: 0.5478 (mmpt) REVERT: B 325 GLU cc_start: 0.7296 (tp30) cc_final: 0.6962 (tp30) REVERT: B 333 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8138 (pt) REVERT: C 333 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7697 (pt) REVERT: C 515 MET cc_start: 0.8673 (tpp) cc_final: 0.8439 (tpt) REVERT: C 581 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7880 (ttm-80) REVERT: C 635 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8115 (ppt-90) REVERT: C 755 ARG cc_start: 0.7623 (ttp80) cc_final: 0.7010 (ttm170) REVERT: D 778 GLU cc_start: 0.7902 (pt0) cc_final: 0.7373 (tp30) REVERT: E 203 ASP cc_start: 0.6988 (m-30) cc_final: 0.6414 (t0) REVERT: E 212 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7809 (mm-40) REVERT: E 318 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.7006 (ttt) REVERT: E 320 SER cc_start: 0.7647 (t) cc_final: 0.7428 (m) REVERT: E 639 TYR cc_start: 0.7820 (m-80) cc_final: 0.7556 (m-80) REVERT: F 424 GLN cc_start: 0.7452 (tp40) cc_final: 0.6634 (tt0) REVERT: F 754 GLN cc_start: 0.6605 (mt0) cc_final: 0.6301 (pt0) REVERT: F 786 GLU cc_start: 0.5703 (mp0) cc_final: 0.4917 (mt-10) outliers start: 34 outliers final: 17 residues processed: 350 average time/residue: 1.5709 time to fit residues: 618.7998 Evaluate side-chains 333 residues out of total 2554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 311 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 345 VAL 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 333 ILE Chi-restraints excluded: chain B residue 796 LYS Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 635 ARG Chi-restraints excluded: chain D residue 361 ARG Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 473 MET 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 622 VAL Chi-restraints excluded: chain F residue 722 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 8.9990 chunk 256 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 241 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS E 502 HIS ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 741 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.168555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.121986 restraints weight = 53992.638| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.61 r_work: 0.3223 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24279 Z= 0.224 Angle : 0.573 11.931 32873 Z= 0.282 Chirality : 0.043 0.165 3762 Planarity : 0.004 0.062 4214 Dihedral : 10.826 88.429 3647 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 1.26 % Allowed : 18.10 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.16), residues: 3006 helix: 1.31 (0.13), residues: 1621 sheet: 0.06 (0.26), residues: 375 loop : 0.66 (0.22), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP F 466 HIS 0.003 0.001 HIS C 459 PHE 0.017 0.002 PHE A 288 TYR 0.008 0.001 TYR B 406 ARG 0.013 0.001 ARG B 375 =============================================================================== Job complete usr+sys time: 10320.21 seconds wall clock time: 181 minutes 4.02 seconds (10864.02 seconds total)