Starting phenix.real_space_refine on Fri Jun 5 13:38:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6aei_9615/06_2026/6aei_9615.cif Found real_map, /net/cci-nas-00/data/ceres_data/6aei_9615/06_2026/6aei_9615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6aei_9615/06_2026/6aei_9615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6aei_9615/06_2026/6aei_9615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6aei_9615/06_2026/6aei_9615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6aei_9615/06_2026/6aei_9615.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 4 5.49 5 S 104 5.16 5 Na 5 4.78 5 C 13873 2.51 5 N 3404 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21142 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5207 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 23, 'TRANS': 618} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 5204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5204 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 618} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 5205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5205 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 618} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 5205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5205 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 618} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {' NA': 2, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' NA': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' NA': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' NA': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.74, per 1000 atoms: 0.27 Number of scatterers: 21142 At special positions: 0 Unit cell: (134.07, 135.3, 136.53, 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 104 16.00 P 4 15.00 Na 5 11.00 O 3752 8.00 N 3404 7.00 C 13873 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 1.0 seconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4928 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 0 sheets defined 75.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 30 through 40 Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.738A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 91 removed outlier: 3.574A pdb=" N MET A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 106 removed outlier: 3.593A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 117 removed outlier: 3.921A pdb=" N LEU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 189 through 204 removed outlier: 3.552A pdb=" N SER A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.606A pdb=" N GLU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.834A pdb=" N LEU A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 370 through 385 removed outlier: 3.833A pdb=" N SER A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 424 Proline residue: A 409 - end of helix removed outlier: 3.642A pdb=" N ASP A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.508A pdb=" N HIS A 432 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 428 through 433' Processing helix chain 'A' and resid 433 through 458 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 491 Processing helix chain 'A' and resid 492 through 498 removed outlier: 4.014A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 4.112A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.678A pdb=" N GLU A 549 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Proline residue: A 550 - end of helix removed outlier: 3.569A pdb=" N CYS A 553 " --> pdb=" O PRO A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.566A pdb=" N THR A 588 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 589 " --> pdb=" O TYR A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 614 Processing helix chain 'A' and resid 615 through 635 removed outlier: 3.599A pdb=" N LEU A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 removed outlier: 3.568A pdb=" N ALA A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 736 removed outlier: 3.895A pdb=" N ASN A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 761 Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 46 through 58 removed outlier: 3.738A pdb=" N GLU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 91 removed outlier: 3.574A pdb=" N MET B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 106 removed outlier: 3.593A pdb=" N ALA B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 117 removed outlier: 3.921A pdb=" N LEU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.551A pdb=" N SER B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.606A pdb=" N GLU B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 340 removed outlier: 3.835A pdb=" N LEU B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 346 Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 370 through 385 removed outlier: 3.834A pdb=" N SER B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 424 Proline residue: B 409 - end of helix removed outlier: 3.643A pdb=" N ASP B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.508A pdb=" N HIS B 432 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 428 through 433' Processing helix chain 'B' and resid 433 through 458 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 491 Processing helix chain 'B' and resid 492 through 498 removed outlier: 4.014A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 4.111A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE B 520 " --> pdb=" O ASP B 516 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 545 through 553 removed outlier: 3.678A pdb=" N GLU B 549 " --> pdb=" O ALA B 546 " (cutoff:3.500A) Proline residue: B 550 - end of helix removed outlier: 3.569A pdb=" N CYS B 553 " --> pdb=" O PRO B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.566A pdb=" N THR B 588 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN B 589 " --> pdb=" O TYR B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 614 Processing helix chain 'B' and resid 615 through 635 removed outlier: 3.598A pdb=" N LEU B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 649 removed outlier: 3.568A pdb=" N ALA B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 736 removed outlier: 3.895A pdb=" N ASN B 719 " --> pdb=" O GLU B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 761 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 46 through 58 removed outlier: 3.737A pdb=" N GLU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 91 removed outlier: 3.574A pdb=" N MET C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 106 removed outlier: 3.593A pdb=" N ALA C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 106 " --> pdb=" O TYR C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 117 removed outlier: 3.921A pdb=" N LEU C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 189 through 204 removed outlier: 3.552A pdb=" N SER C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.607A pdb=" N GLU C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 removed outlier: 3.833A pdb=" N LEU C 340 " --> pdb=" O THR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 346 Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 370 through 385 removed outlier: 3.834A pdb=" N SER C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 424 Proline residue: C 409 - end of helix removed outlier: 3.642A pdb=" N ASP C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 433 removed outlier: 3.508A pdb=" N HIS C 432 " --> pdb=" O THR C 428 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 428 through 433' Processing helix chain 'C' and resid 433 through 458 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 491 Processing helix chain 'C' and resid 492 through 498 removed outlier: 4.015A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 4.110A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE C 520 " --> pdb=" O ASP C 516 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 545 through 553 removed outlier: 3.679A pdb=" N GLU C 549 " --> pdb=" O ALA C 546 " (cutoff:3.500A) Proline residue: C 550 - end of helix removed outlier: 3.569A pdb=" N CYS C 553 " --> pdb=" O PRO C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.567A pdb=" N THR C 588 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 589 " --> pdb=" O TYR C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 614 Processing helix chain 'C' and resid 615 through 635 removed outlier: 3.598A pdb=" N LEU C 630 " --> pdb=" O ASN C 626 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 649 removed outlier: 3.568A pdb=" N ALA C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 736 removed outlier: 3.896A pdb=" N ASN C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 761 Processing helix chain 'D' and resid 30 through 40 Processing helix chain 'D' and resid 46 through 58 removed outlier: 3.738A pdb=" N GLU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 91 removed outlier: 3.573A pdb=" N MET D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 106 removed outlier: 3.594A pdb=" N ALA D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 117 removed outlier: 3.920A pdb=" N LEU D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 189 through 204 removed outlier: 3.552A pdb=" N SER D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.607A pdb=" N GLU D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 326 through 340 removed outlier: 3.834A pdb=" N LEU D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 363 through 368 Processing helix chain 'D' and resid 370 through 385 removed outlier: 3.834A pdb=" N SER D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 424 Proline residue: D 409 - end of helix removed outlier: 3.643A pdb=" N ASP D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 removed outlier: 3.509A pdb=" N HIS D 432 " --> pdb=" O THR D 428 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 428 through 433' Processing helix chain 'D' and resid 433 through 458 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 491 Processing helix chain 'D' and resid 492 through 498 removed outlier: 4.015A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 4.110A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 519 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE D 520 " --> pdb=" O ASP D 516 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 545 through 553 removed outlier: 3.678A pdb=" N GLU D 549 " --> pdb=" O ALA D 546 " (cutoff:3.500A) Proline residue: D 550 - end of helix removed outlier: 3.570A pdb=" N CYS D 553 " --> pdb=" O PRO D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.567A pdb=" N THR D 588 " --> pdb=" O LEU D 585 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN D 589 " --> pdb=" O TYR D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 614 Processing helix chain 'D' and resid 615 through 635 removed outlier: 3.597A pdb=" N LEU D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 649 removed outlier: 3.567A pdb=" N ALA D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 736 removed outlier: 3.896A pdb=" N ASN D 719 " --> pdb=" O GLU D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 761 1246 hydrogen bonds defined for protein. 3648 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: 3.44 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3678 1.32 - 1.45: 5675 1.45 - 1.58: 12102 1.58 - 1.70: 8 1.70 - 1.83: 176 Bond restraints: 21639 Sorted by residual: bond pdb=" O5 LPP B 803 " pdb=" P1 LPP B 803 " ideal model delta sigma weight residual 2.278 1.595 0.683 2.00e-02 2.50e+03 1.17e+03 bond pdb=" O5 LPP D 803 " pdb=" P1 LPP D 803 " ideal model delta sigma weight residual 2.278 1.595 0.683 2.00e-02 2.50e+03 1.17e+03 bond pdb=" O5 LPP C 803 " pdb=" P1 LPP C 803 " ideal model delta sigma weight residual 2.278 1.595 0.683 2.00e-02 2.50e+03 1.17e+03 bond pdb=" O5 LPP A 804 " pdb=" P1 LPP A 804 " ideal model delta sigma weight residual 2.278 1.596 0.682 2.00e-02 2.50e+03 1.16e+03 bond pdb=" O4 LPP A 804 " pdb=" P1 LPP A 804 " ideal model delta sigma weight residual 1.764 1.511 0.253 2.00e-02 2.50e+03 1.60e+02 ... (remaining 21634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.63: 29263 8.63 - 17.25: 35 17.25 - 25.88: 8 25.88 - 34.50: 4 34.50 - 43.13: 8 Bond angle restraints: 29318 Sorted by residual: angle pdb=" O4 LPP A 804 " pdb=" P1 LPP A 804 " pdb=" O5 LPP A 804 " ideal model delta sigma weight residual 62.99 106.12 -43.13 3.00e+00 1.11e-01 2.07e+02 angle pdb=" O4 LPP B 803 " pdb=" P1 LPP B 803 " pdb=" O5 LPP B 803 " ideal model delta sigma weight residual 62.99 106.12 -43.13 3.00e+00 1.11e-01 2.07e+02 angle pdb=" O4 LPP C 803 " pdb=" P1 LPP C 803 " pdb=" O5 LPP C 803 " ideal model delta sigma weight residual 62.99 106.10 -43.11 3.00e+00 1.11e-01 2.07e+02 angle pdb=" O4 LPP D 803 " pdb=" P1 LPP D 803 " pdb=" O5 LPP D 803 " ideal model delta sigma weight residual 62.99 106.10 -43.11 3.00e+00 1.11e-01 2.06e+02 angle pdb=" C6 LPP C 803 " pdb=" O5 LPP C 803 " pdb=" P1 LPP C 803 " ideal model delta sigma weight residual 82.33 118.24 -35.91 3.00e+00 1.11e-01 1.43e+02 ... (remaining 29313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 12303 17.24 - 34.47: 589 34.47 - 51.71: 150 51.71 - 68.94: 54 68.94 - 86.18: 20 Dihedral angle restraints: 13116 sinusoidal: 5536 harmonic: 7580 Sorted by residual: dihedral pdb=" CA CYS C 369 " pdb=" C CYS C 369 " pdb=" N HIS C 370 " pdb=" CA HIS C 370 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA CYS D 369 " pdb=" C CYS D 369 " pdb=" N HIS D 370 " pdb=" CA HIS D 370 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA CYS B 369 " pdb=" C CYS B 369 " pdb=" N HIS B 370 " pdb=" CA HIS B 370 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 13113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3042 0.099 - 0.198: 224 0.198 - 0.297: 20 0.297 - 0.397: 8 0.397 - 0.496: 9 Chirality restraints: 3303 Sorted by residual: chirality pdb=" CBH Y01 C 802 " pdb=" CAT Y01 C 802 " pdb=" CAZ Y01 C 802 " pdb=" CBF Y01 C 802 " both_signs ideal model delta sigma weight residual False -2.85 -2.36 -0.50 2.00e-01 2.50e+01 6.14e+00 chirality pdb=" CBH Y01 A 803 " pdb=" CAT Y01 A 803 " pdb=" CAZ Y01 A 803 " pdb=" CBF Y01 A 803 " both_signs ideal model delta sigma weight residual False -2.85 -2.36 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CBH Y01 D 802 " pdb=" CAT Y01 D 802 " pdb=" CAZ Y01 D 802 " pdb=" CBF Y01 D 802 " both_signs ideal model delta sigma weight residual False -2.85 -2.36 -0.49 2.00e-01 2.50e+01 6.11e+00 ... (remaining 3300 not shown) Planarity restraints: 3610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 657 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO A 658 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 658 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 658 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 67 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO D 68 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 68 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 68 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 67 " -0.039 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO C 68 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 68 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 68 " -0.033 5.00e-02 4.00e+02 ... (remaining 3607 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1761 2.74 - 3.28: 21052 3.28 - 3.82: 33918 3.82 - 4.36: 43192 4.36 - 4.90: 71923 Nonbonded interactions: 171846 Sorted by model distance: nonbonded pdb=" OD1 ASN A 436 " pdb="NA NA A 802 " model vdw 2.198 2.470 nonbonded pdb=" OD1 ASN C 436 " pdb="NA NA C 801 " model vdw 2.204 2.470 nonbonded pdb=" CD1 LEU A 529 " pdb=" CAA Y01 B 802 " model vdw 2.208 3.880 nonbonded pdb=" OH TYR C 316 " pdb=" OAF Y01 C 802 " model vdw 2.211 3.040 nonbonded pdb=" O LEU C 657 " pdb=" CB ASN C 662 " model vdw 2.215 3.440 ... (remaining 171841 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 29 through 656 or (resid 657 and (name N or name CA or nam \ e C or name O or name CB )) or resid 658 or (resid 659 through 660 and (name N o \ r name CA or name C or name O or name CB )) or resid 661 through 801)) selection = (chain 'B' and (resid 29 through 658 or (resid 659 through 660 and (name N or na \ me CA or name C or name O or name CB )) or resid 661 through 801)) selection = (chain 'C' and (resid 29 through 656 or (resid 657 and (name N or name CA or nam \ e C or name O or name CB )) or resid 658 through 801)) selection = (chain 'D' and (resid 29 through 656 or (resid 657 and (name N or name CA or nam \ e C or name O or name CB )) or resid 658 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.470 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 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 : 0.013 0.683 21643 Z= 0.618 Angle : 1.341 43.127 29326 Z= 0.638 Chirality : 0.064 0.496 3303 Planarity : 0.007 0.102 3610 Dihedral : 12.472 86.176 8176 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.26 % Favored : 97.58 % Rotamer: Outliers : 0.75 % Allowed : 3.64 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.46 (0.12), residues: 2520 helix: -2.99 (0.08), residues: 1812 sheet: None (None), residues: 0 loop : -2.16 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 723 TYR 0.020 0.003 TYR D 241 PHE 0.033 0.004 PHE B 753 TRP 0.032 0.003 TRP C 410 HIS 0.012 0.002 HIS A 473 Details of bonding type rmsd/Z covalent geometry : bond 0.01251 / 0.62 (21639) covalent geometry : angle 1.34106 / 0.64 (29318) SS BOND : bond 0.00115 / 0.06 ( 4) SS BOND : angle 1.80706 / 0.75 ( 8) hydrogen bonds : bond 0.14549 / 9.68 ( 1246) hydrogen bonds : angle 8.01510 / 5.64 ( 3648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 649 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 243 GLU cc_start: 0.7197 (tt0) cc_final: 0.6723 (tm-30) REVERT: A 249 LYS cc_start: 0.8108 (mttt) cc_final: 0.7889 (mttp) REVERT: A 254 ASP cc_start: 0.7206 (m-30) cc_final: 0.6927 (m-30) REVERT: A 266 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6697 (mm-30) REVERT: A 416 TRP cc_start: 0.7661 (t-100) cc_final: 0.7141 (t-100) REVERT: A 467 GLU cc_start: 0.7856 (pm20) cc_final: 0.7629 (pm20) REVERT: A 516 ASP cc_start: 0.7394 (m-30) cc_final: 0.6977 (m-30) REVERT: A 630 LEU cc_start: 0.8370 (mt) cc_final: 0.7744 (mt) REVERT: A 638 GLU cc_start: 0.7463 (tp30) cc_final: 0.7216 (tp30) REVERT: A 652 ASP cc_start: 0.7407 (m-30) cc_final: 0.7138 (m-30) REVERT: B 81 GLU cc_start: 0.5536 (mt-10) cc_final: 0.5223 (mt-10) REVERT: B 243 GLU cc_start: 0.7156 (tt0) cc_final: 0.6580 (tp30) REVERT: B 247 GLN cc_start: 0.8495 (tt0) cc_final: 0.8180 (tt0) REVERT: B 266 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6619 (mt-10) REVERT: B 286 ASP cc_start: 0.6962 (m-30) cc_final: 0.6570 (m-30) REVERT: B 406 MET cc_start: 0.6712 (mtp) cc_final: 0.6436 (mtm) REVERT: B 548 ASP cc_start: 0.6132 (m-30) cc_final: 0.5749 (m-30) REVERT: B 623 MET cc_start: 0.7291 (ttm) cc_final: 0.6998 (ttm) REVERT: B 633 ASP cc_start: 0.6616 (m-30) cc_final: 0.6312 (m-30) REVERT: B 637 ILE cc_start: 0.7649 (pp) cc_final: 0.7408 (mp) REVERT: B 711 GLN cc_start: 0.7793 (mt0) cc_final: 0.7522 (mt0) REVERT: B 745 GLU cc_start: 0.6737 (mt-10) cc_final: 0.5993 (mt-10) REVERT: B 751 SER cc_start: 0.8314 (t) cc_final: 0.8059 (p) REVERT: B 754 ARG cc_start: 0.6842 (ttt-90) cc_final: 0.6593 (ttt90) REVERT: C 75 LEU cc_start: 0.8493 (mt) cc_final: 0.8210 (mm) REVERT: C 226 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6774 (tt0) REVERT: C 243 GLU cc_start: 0.7107 (tt0) cc_final: 0.6812 (tm-30) REVERT: C 314 LEU cc_start: 0.7998 (mt) cc_final: 0.7762 (mt) REVERT: C 528 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7439 (tt) REVERT: C 711 GLN cc_start: 0.7670 (mt0) cc_final: 0.7394 (mt0) REVERT: D 107 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7024 (mt-10) REVERT: D 160 LEU cc_start: 0.7965 (mt) cc_final: 0.7653 (mp) REVERT: D 243 GLU cc_start: 0.6996 (tt0) cc_final: 0.6703 (tt0) REVERT: D 439 ASP cc_start: 0.7604 (m-30) cc_final: 0.7177 (m-30) REVERT: D 468 GLU cc_start: 0.5597 (tt0) cc_final: 0.5388 (tm-30) REVERT: D 528 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8117 (tt) REVERT: D 745 GLU cc_start: 0.6928 (mt-10) cc_final: 0.5951 (mt-10) REVERT: D 749 ASP cc_start: 0.7322 (m-30) cc_final: 0.7056 (m-30) outliers start: 17 outliers final: 5 residues processed: 661 average time/residue: 0.5669 time to fit residues: 429.9555 Evaluate side-chains 392 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 385 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.0970 chunk 71 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 153 ASN A 247 GLN A 258 GLN A 297 HIS A 298 GLN A 370 HIS A 443 ASN A 533 ASN A 536 ASN A 563 ASN A 573 GLN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN A 709 GLN A 731 ASN B 60 ASN B 64 ASN B 80 ASN B 82 ASN B 153 ASN B 154 ASN B 163 GLN B 192 HIS B 297 HIS B 298 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 HIS B 443 ASN B 473 HIS B 533 ASN B 536 ASN B 562 ASN B 709 GLN C 60 ASN C 64 ASN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN C 258 GLN C 297 HIS C 298 GLN C 306 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS C 443 ASN C 536 ASN C 537 GLN C 562 ASN C 573 GLN C 625 ASN C 662 ASN D 60 ASN D 64 ASN D 153 ASN D 258 GLN D 271 HIS D 297 HIS D 298 GLN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 HIS D 394 HIS D 500 ASN D 533 ASN D 536 ASN D 537 GLN D 573 GLN D 589 ASN D 625 ASN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.165917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.130060 restraints weight = 23695.907| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.90 r_work: 0.3223 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21643 Z= 0.148 Angle : 0.619 8.280 29326 Z= 0.326 Chirality : 0.040 0.242 3303 Planarity : 0.006 0.100 3610 Dihedral : 10.390 59.806 3225 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.06 % Favored : 96.79 % Rotamer: Outliers : 4.57 % Allowed : 12.03 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 2520 helix: -0.45 (0.11), residues: 1812 sheet: None (None), residues: 0 loop : -1.70 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 512 TYR 0.043 0.002 TYR B 58 PHE 0.021 0.002 PHE C 520 TRP 0.022 0.001 TRP A 327 HIS 0.008 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (21639) covalent geometry : angle 0.61797 / 0.33 (29318) SS BOND : bond 0.00333 / 0.16 ( 4) SS BOND : angle 2.16663 / 0.82 ( 8) hydrogen bonds : bond 0.04423 / 2.92 ( 1246) hydrogen bonds : angle 4.12783 / 2.87 ( 3648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 463 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 HIS cc_start: 0.5014 (OUTLIER) cc_final: 0.4535 (m-70) REVERT: A 228 LYS cc_start: 0.8445 (tppt) cc_final: 0.8121 (tppp) REVERT: A 243 GLU cc_start: 0.8057 (tt0) cc_final: 0.7633 (tm-30) REVERT: A 249 LYS cc_start: 0.8564 (mttt) cc_final: 0.8270 (mttp) REVERT: A 250 LEU cc_start: 0.8857 (tm) cc_final: 0.8604 (tp) REVERT: A 262 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8849 (m) REVERT: A 266 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7213 (mm-30) REVERT: A 327 TRP cc_start: 0.7916 (p-90) cc_final: 0.7476 (p-90) REVERT: A 331 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7544 (tm) REVERT: A 335 MET cc_start: 0.7485 (mtt) cc_final: 0.7154 (mtt) REVERT: A 380 MET cc_start: 0.8186 (mtt) cc_final: 0.7965 (mtm) REVERT: A 416 TRP cc_start: 0.7889 (t-100) cc_final: 0.7183 (t-100) REVERT: A 442 MET cc_start: 0.8098 (ttt) cc_final: 0.7814 (ttm) REVERT: A 468 GLU cc_start: 0.8184 (tt0) cc_final: 0.7967 (tt0) REVERT: A 500 ASN cc_start: 0.8806 (t0) cc_final: 0.8528 (t0) REVERT: A 595 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7152 (mm-30) REVERT: A 630 LEU cc_start: 0.8430 (mt) cc_final: 0.8130 (mt) REVERT: A 652 ASP cc_start: 0.7611 (m-30) cc_final: 0.7304 (m-30) REVERT: B 44 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7632 (t0) REVERT: B 84 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7676 (mt-10) REVERT: B 195 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8192 (m) REVERT: B 222 ARG cc_start: 0.7764 (mtt180) cc_final: 0.7543 (mtm-85) REVERT: B 243 GLU cc_start: 0.7942 (tt0) cc_final: 0.7631 (tm-30) REVERT: B 247 GLN cc_start: 0.8827 (tt0) cc_final: 0.8495 (tt0) REVERT: B 266 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7304 (mt-10) REVERT: B 335 MET cc_start: 0.7886 (mtt) cc_final: 0.7676 (mtt) REVERT: B 548 ASP cc_start: 0.6517 (m-30) cc_final: 0.6154 (m-30) REVERT: B 623 MET cc_start: 0.8259 (ttm) cc_final: 0.7975 (ttm) REVERT: B 631 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.6919 (mp) REVERT: B 645 LYS cc_start: 0.8922 (mtpt) cc_final: 0.8613 (mtpt) REVERT: B 711 GLN cc_start: 0.8027 (mt0) cc_final: 0.7773 (mt0) REVERT: B 754 ARG cc_start: 0.7284 (ttt-90) cc_final: 0.6789 (ttt90) REVERT: C 71 ARG cc_start: 0.7543 (ttt-90) cc_final: 0.7146 (ttt-90) REVERT: C 84 GLU cc_start: 0.7447 (mp0) cc_final: 0.6931 (mm-30) REVERT: C 240 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: C 243 GLU cc_start: 0.7761 (tt0) cc_final: 0.7463 (tm-30) REVERT: C 266 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: C 339 PHE cc_start: 0.7526 (m-80) cc_final: 0.7310 (m-10) REVERT: C 380 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6226 (mpt) REVERT: C 471 MET cc_start: 0.6216 (ttp) cc_final: 0.5932 (ttm) REVERT: C 513 MET cc_start: 0.8052 (mtp) cc_final: 0.7592 (mtm) REVERT: C 519 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7575 (ttmt) REVERT: C 744 LYS cc_start: 0.7675 (mptm) cc_final: 0.7270 (mptp) REVERT: D 107 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7266 (mt-10) REVERT: D 243 GLU cc_start: 0.7479 (tt0) cc_final: 0.7239 (tt0) REVERT: D 266 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7588 (pt0) REVERT: D 291 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7378 (mptt) REVERT: D 369 CYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7444 (p) REVERT: D 468 GLU cc_start: 0.6453 (tt0) cc_final: 0.5788 (tm-30) REVERT: D 490 SER cc_start: 0.8959 (t) cc_final: 0.8682 (m) REVERT: D 506 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8638 (tp) REVERT: D 512 ARG cc_start: 0.7947 (mtp180) cc_final: 0.7645 (mtp180) REVERT: D 523 ILE cc_start: 0.7776 (mt) cc_final: 0.7528 (mt) REVERT: D 745 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6626 (mt-10) REVERT: D 749 ASP cc_start: 0.7296 (m-30) cc_final: 0.6813 (m-30) outliers start: 103 outliers final: 26 residues processed: 527 average time/residue: 0.5445 time to fit residues: 330.6884 Evaluate side-chains 421 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 381 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 562 ASN Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 751 SER Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 729 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 108 optimal weight: 0.5980 chunk 250 optimal weight: 0.0010 chunk 55 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 106 optimal weight: 0.2980 chunk 148 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 563 ASN A 589 ASN A 625 ASN B 562 ASN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN D 154 ASN D 173 GLN D 306 ASN D 533 ASN D 563 ASN D 589 ASN D 594 HIS D 662 ASN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.159405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121530 restraints weight = 23107.831| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.99 r_work: 0.3114 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21643 Z= 0.140 Angle : 0.567 9.257 29326 Z= 0.301 Chirality : 0.039 0.147 3303 Planarity : 0.005 0.079 3610 Dihedral : 9.219 58.977 3215 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.90 % Favored : 96.94 % Rotamer: Outliers : 5.55 % Allowed : 14.74 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 2520 helix: 0.61 (0.12), residues: 1836 sheet: None (None), residues: 0 loop : -1.33 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 754 TYR 0.015 0.001 TYR B 524 PHE 0.029 0.002 PHE C 520 TRP 0.012 0.001 TRP A 410 HIS 0.006 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (21639) covalent geometry : angle 0.56656 / 0.30 (29318) SS BOND : bond 0.01839 / 0.91 ( 4) SS BOND : angle 1.71296 / 0.70 ( 8) hydrogen bonds : bond 0.03944 / 2.60 ( 1246) hydrogen bonds : angle 3.62679 / 2.52 ( 3648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 447 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7673 (tpp) REVERT: A 69 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7517 (mt) REVERT: A 79 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: A 147 MET cc_start: 0.8390 (mtp) cc_final: 0.8143 (mtp) REVERT: A 172 HIS cc_start: 0.4980 (OUTLIER) cc_final: 0.4543 (m-70) REVERT: A 222 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7974 (mtm-85) REVERT: A 228 LYS cc_start: 0.8462 (tppt) cc_final: 0.8213 (tppp) REVERT: A 243 GLU cc_start: 0.8073 (tt0) cc_final: 0.7589 (tm-30) REVERT: A 262 SER cc_start: 0.9181 (OUTLIER) cc_final: 0.8838 (m) REVERT: A 266 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7119 (mt-10) REVERT: A 331 LEU cc_start: 0.8111 (tp) cc_final: 0.7726 (tt) REVERT: A 335 MET cc_start: 0.7454 (mtt) cc_final: 0.7119 (mtt) REVERT: A 380 MET cc_start: 0.8209 (mtt) cc_final: 0.7961 (mtm) REVERT: A 416 TRP cc_start: 0.7975 (t-100) cc_final: 0.7459 (t-100) REVERT: A 437 LEU cc_start: 0.8487 (tp) cc_final: 0.8215 (tp) REVERT: A 442 MET cc_start: 0.8040 (ttt) cc_final: 0.7839 (ttm) REVERT: A 468 GLU cc_start: 0.8293 (tt0) cc_final: 0.7747 (tt0) REVERT: A 500 ASN cc_start: 0.8959 (t0) cc_final: 0.8629 (t0) REVERT: A 516 ASP cc_start: 0.7947 (m-30) cc_final: 0.7743 (m-30) REVERT: A 595 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7380 (mm-30) REVERT: A 630 LEU cc_start: 0.8417 (mt) cc_final: 0.8152 (mt) REVERT: A 652 ASP cc_start: 0.7578 (m-30) cc_final: 0.7332 (m-30) REVERT: B 79 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7429 (pt0) REVERT: B 84 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7679 (mt-10) REVERT: B 222 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7683 (mtm-85) REVERT: B 232 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7852 (mtpt) REVERT: B 243 GLU cc_start: 0.8080 (tt0) cc_final: 0.7671 (tm-30) REVERT: B 247 GLN cc_start: 0.8884 (tt0) cc_final: 0.8536 (tt0) REVERT: B 266 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7386 (mt-10) REVERT: B 335 MET cc_start: 0.7809 (mtt) cc_final: 0.7603 (mtt) REVERT: B 394 HIS cc_start: 0.5550 (OUTLIER) cc_final: 0.4909 (m-70) REVERT: B 410 TRP cc_start: 0.8523 (OUTLIER) cc_final: 0.6604 (m-90) REVERT: B 500 ASN cc_start: 0.9012 (t0) cc_final: 0.8807 (t0) REVERT: B 548 ASP cc_start: 0.7126 (m-30) cc_final: 0.6451 (m-30) REVERT: B 711 GLN cc_start: 0.8010 (mt0) cc_final: 0.7792 (mt0) REVERT: C 81 GLU cc_start: 0.6491 (mt-10) cc_final: 0.5892 (mt-10) REVERT: C 191 ARG cc_start: 0.7543 (mtp-110) cc_final: 0.7069 (ttm-80) REVERT: C 230 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8030 (mt) REVERT: C 240 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: C 243 GLU cc_start: 0.7848 (tt0) cc_final: 0.7556 (tm-30) REVERT: C 339 PHE cc_start: 0.7580 (m-80) cc_final: 0.7359 (m-10) REVERT: C 380 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6387 (mpt) REVERT: C 513 MET cc_start: 0.7973 (mtp) cc_final: 0.7646 (mtm) REVERT: C 519 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7938 (ttmt) REVERT: C 744 LYS cc_start: 0.7731 (mptm) cc_final: 0.7296 (mptp) REVERT: C 745 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6586 (mt-10) REVERT: D 37 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7934 (mp) REVERT: D 66 MET cc_start: 0.7439 (tpp) cc_final: 0.7055 (tpp) REVERT: D 71 ARG cc_start: 0.7608 (ttt-90) cc_final: 0.7304 (tpt-90) REVERT: D 107 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7186 (mt-10) REVERT: D 225 TRP cc_start: 0.8507 (t-100) cc_final: 0.8285 (t-100) REVERT: D 230 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7975 (tp) REVERT: D 243 GLU cc_start: 0.7765 (tt0) cc_final: 0.7417 (tm-30) REVERT: D 257 ASP cc_start: 0.8340 (m-30) cc_final: 0.8135 (m-30) REVERT: D 266 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7719 (pt0) REVERT: D 291 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7337 (mptt) REVERT: D 335 MET cc_start: 0.7654 (mmm) cc_final: 0.7124 (mtm) REVERT: D 343 MET cc_start: 0.7604 (mmt) cc_final: 0.7101 (tpt) REVERT: D 359 PHE cc_start: 0.7736 (t80) cc_final: 0.7531 (t80) REVERT: D 369 CYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7913 (p) REVERT: D 380 MET cc_start: 0.7839 (mtm) cc_final: 0.7328 (mtt) REVERT: D 383 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7965 (mm) REVERT: D 422 MET cc_start: 0.5773 (OUTLIER) cc_final: 0.5462 (mmm) REVERT: D 490 SER cc_start: 0.9081 (t) cc_final: 0.8790 (m) REVERT: D 559 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: D 591 LYS cc_start: 0.8356 (tmmt) cc_final: 0.8143 (tmmt) REVERT: D 629 GLN cc_start: 0.8551 (mt0) cc_final: 0.8326 (mt0) REVERT: D 745 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6497 (mt-10) REVERT: D 749 ASP cc_start: 0.7241 (m-30) cc_final: 0.6932 (m-30) REVERT: D 752 SER cc_start: 0.8782 (p) cc_final: 0.8580 (p) outliers start: 125 outliers final: 33 residues processed: 513 average time/residue: 0.5487 time to fit residues: 324.1361 Evaluate side-chains 452 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 399 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 559 GLU Chi-restraints excluded: chain D residue 729 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 90 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 507 GLN A 537 GLN A 589 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 486 ASN B 507 GLN B 573 GLN B 594 HIS ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 192 HIS C 308 GLN C 500 ASN C 507 GLN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS D 247 GLN D 308 GLN D 396 GLN D 507 GLN D 533 ASN D 563 ASN D 589 ASN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.142041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.104801 restraints weight = 22925.403| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.84 r_work: 0.2851 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 21643 Z= 0.324 Angle : 0.763 8.980 29326 Z= 0.394 Chirality : 0.048 0.197 3303 Planarity : 0.006 0.106 3610 Dihedral : 10.195 59.859 3214 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.77 % Favored : 96.07 % Rotamer: Outliers : 6.44 % Allowed : 15.62 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.16), residues: 2520 helix: 0.60 (0.12), residues: 1820 sheet: None (None), residues: 0 loop : -1.17 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 466 TYR 0.021 0.003 TYR B 524 PHE 0.022 0.003 PHE C 341 TRP 0.023 0.002 TRP A 327 HIS 0.006 0.001 HIS B 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00784 / 0.32 (21639) covalent geometry : angle 0.76160 / 0.39 (29318) SS BOND : bond 0.01005 / 0.50 ( 4) SS BOND : angle 2.43350 / 1.04 ( 8) hydrogen bonds : bond 0.05259 / 3.45 ( 1246) hydrogen bonds : angle 3.84396 / 2.67 ( 3648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 481 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 66 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7416 (mmm) REVERT: A 67 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.6161 (m-30) REVERT: A 147 MET cc_start: 0.8995 (mtp) cc_final: 0.8675 (mtp) REVERT: A 172 HIS cc_start: 0.5756 (OUTLIER) cc_final: 0.4650 (m-70) REVERT: A 194 ARG cc_start: 0.8310 (tpp-160) cc_final: 0.6822 (ttm110) REVERT: A 222 ARG cc_start: 0.8524 (mtt180) cc_final: 0.8119 (mtm-85) REVERT: A 243 GLU cc_start: 0.8533 (tt0) cc_final: 0.8049 (tm-30) REVERT: A 262 SER cc_start: 0.9206 (OUTLIER) cc_final: 0.8887 (m) REVERT: A 266 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7610 (mt-10) REVERT: A 331 LEU cc_start: 0.8012 (tp) cc_final: 0.7658 (tt) REVERT: A 335 MET cc_start: 0.7812 (mtt) cc_final: 0.7292 (mtm) REVERT: A 380 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8086 (mtm) REVERT: A 416 TRP cc_start: 0.8136 (t-100) cc_final: 0.7465 (t-100) REVERT: A 437 LEU cc_start: 0.8597 (tp) cc_final: 0.8330 (tp) REVERT: A 468 GLU cc_start: 0.8579 (tt0) cc_final: 0.8190 (tt0) REVERT: A 500 ASN cc_start: 0.9210 (t0) cc_final: 0.8988 (t0) REVERT: A 595 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7984 (mm-30) REVERT: A 625 ASN cc_start: 0.8378 (m-40) cc_final: 0.7914 (m-40) REVERT: A 630 LEU cc_start: 0.8471 (mt) cc_final: 0.8221 (mt) REVERT: A 652 ASP cc_start: 0.8090 (m-30) cc_final: 0.7738 (m-30) REVERT: B 81 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6442 (mt-10) REVERT: B 84 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7931 (mt-10) REVERT: B 172 HIS cc_start: 0.5135 (OUTLIER) cc_final: 0.4912 (m-70) REVERT: B 222 ARG cc_start: 0.8501 (mtt180) cc_final: 0.8068 (mtm-85) REVERT: B 243 GLU cc_start: 0.8378 (tt0) cc_final: 0.7943 (tm-30) REVERT: B 247 GLN cc_start: 0.8942 (tt0) cc_final: 0.8595 (tt0) REVERT: B 266 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7784 (mt-10) REVERT: B 335 MET cc_start: 0.8040 (mtt) cc_final: 0.7745 (mtt) REVERT: B 359 PHE cc_start: 0.8529 (t80) cc_final: 0.8328 (t80) REVERT: B 369 CYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8083 (p) REVERT: B 436 ASN cc_start: 0.8836 (m-40) cc_final: 0.8454 (m-40) REVERT: B 471 MET cc_start: 0.7920 (ttp) cc_final: 0.7672 (tmm) REVERT: B 512 ARG cc_start: 0.8245 (mtp180) cc_final: 0.8042 (mtp180) REVERT: B 519 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.7987 (mtpm) REVERT: B 526 LEU cc_start: 0.8836 (tm) cc_final: 0.8502 (tt) REVERT: B 529 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8696 (mt) REVERT: B 634 HIS cc_start: 0.7963 (m170) cc_final: 0.7725 (m90) REVERT: B 709 GLN cc_start: 0.7774 (tt0) cc_final: 0.7458 (tt0) REVERT: B 729 ILE cc_start: 0.7873 (pp) cc_final: 0.7568 (mt) REVERT: C 81 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6640 (mt-10) REVERT: C 84 GLU cc_start: 0.8040 (mp0) cc_final: 0.7544 (mt-10) REVERT: C 87 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7898 (mt-10) REVERT: C 190 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8579 (tt) REVERT: C 240 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: C 243 GLU cc_start: 0.8495 (tt0) cc_final: 0.8086 (tm-30) REVERT: C 266 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: C 380 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.6982 (mpt) REVERT: C 395 VAL cc_start: 0.8554 (t) cc_final: 0.8346 (t) REVERT: C 436 ASN cc_start: 0.8379 (m-40) cc_final: 0.7961 (m110) REVERT: C 450 ILE cc_start: 0.8039 (mm) cc_final: 0.7815 (mt) REVERT: C 454 ILE cc_start: 0.8139 (mm) cc_final: 0.7871 (mt) REVERT: C 468 GLU cc_start: 0.7009 (tt0) cc_final: 0.6702 (tm-30) REVERT: C 490 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.8905 (m) REVERT: C 519 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8531 (ptmt) REVERT: C 529 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8660 (mt) REVERT: C 591 LYS cc_start: 0.8182 (mttt) cc_final: 0.7720 (tmmt) REVERT: C 595 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8211 (mt-10) REVERT: C 729 ILE cc_start: 0.8147 (pp) cc_final: 0.7893 (mt) REVERT: C 744 LYS cc_start: 0.8007 (mptm) cc_final: 0.7634 (mptp) REVERT: C 745 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7295 (mt-10) REVERT: C 756 GLU cc_start: 0.8240 (tt0) cc_final: 0.8033 (tt0) REVERT: D 71 ARG cc_start: 0.8026 (ttt-90) cc_final: 0.7441 (ttt180) REVERT: D 214 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8094 (mm-30) REVERT: D 225 TRP cc_start: 0.8923 (t-100) cc_final: 0.8672 (t-100) REVERT: D 243 GLU cc_start: 0.8400 (tt0) cc_final: 0.7975 (tm-30) REVERT: D 266 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: D 291 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8331 (mtpt) REVERT: D 335 MET cc_start: 0.7969 (mmm) cc_final: 0.7362 (mtm) REVERT: D 343 MET cc_start: 0.7691 (mmt) cc_final: 0.7310 (mpm) REVERT: D 359 PHE cc_start: 0.7984 (t80) cc_final: 0.7557 (t80) REVERT: D 369 CYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8152 (p) REVERT: D 410 TRP cc_start: 0.8704 (OUTLIER) cc_final: 0.7779 (m-90) REVERT: D 436 ASN cc_start: 0.8667 (m-40) cc_final: 0.8083 (m110) REVERT: D 508 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8250 (mm) REVERT: D 553 CYS cc_start: 0.7639 (t) cc_final: 0.7218 (t) REVERT: D 559 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: D 587 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8578 (m) REVERT: D 591 LYS cc_start: 0.8548 (tmmt) cc_final: 0.8235 (ttmm) REVERT: D 595 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8104 (mm-30) REVERT: D 747 LYS cc_start: 0.8452 (mttt) cc_final: 0.8103 (mtmt) outliers start: 145 outliers final: 51 residues processed: 561 average time/residue: 0.5445 time to fit residues: 351.7381 Evaluate side-chains 492 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 418 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 508 ILE Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 751 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 519 LYS Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 559 GLU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 729 ILE Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 751 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 142 optimal weight: 0.0980 chunk 167 optimal weight: 0.2980 chunk 232 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 241 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 198 optimal weight: 0.0670 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 533 ASN A 589 ASN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS B 500 ASN B 589 ASN B 709 GLN C 82 ASN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS C 533 ASN C 625 ASN C 662 ASN C 748 GLN D 192 HIS D 533 ASN D 589 ASN D 625 ASN D 629 GLN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.147847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.110302 restraints weight = 22530.657| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.96 r_work: 0.2972 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.6092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21643 Z= 0.118 Angle : 0.560 10.433 29326 Z= 0.294 Chirality : 0.039 0.145 3303 Planarity : 0.005 0.098 3610 Dihedral : 9.406 59.906 3214 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.86 % Favored : 96.98 % Rotamer: Outliers : 5.33 % Allowed : 19.31 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2520 helix: 1.23 (0.12), residues: 1824 sheet: None (None), residues: 0 loop : -1.18 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 71 TYR 0.034 0.001 TYR B 58 PHE 0.019 0.001 PHE C 520 TRP 0.027 0.001 TRP D 327 HIS 0.005 0.001 HIS A 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (21639) covalent geometry : angle 0.55886 / 0.29 (29318) SS BOND : bond 0.00156 / 0.08 ( 4) SS BOND : angle 2.20164 / 0.74 ( 8) hydrogen bonds : bond 0.03878 / 2.53 ( 1246) hydrogen bonds : angle 3.46162 / 2.40 ( 3648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 448 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7271 (mmm) REVERT: A 172 HIS cc_start: 0.5432 (OUTLIER) cc_final: 0.4561 (m-70) REVERT: A 194 ARG cc_start: 0.8250 (tpp-160) cc_final: 0.6688 (ttm110) REVERT: A 222 ARG cc_start: 0.8446 (mtt180) cc_final: 0.8002 (mtm-85) REVERT: A 243 GLU cc_start: 0.8376 (tt0) cc_final: 0.7882 (tm-30) REVERT: A 266 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7405 (mt-10) REVERT: A 331 LEU cc_start: 0.7978 (tp) cc_final: 0.7615 (tt) REVERT: A 335 MET cc_start: 0.7615 (mtt) cc_final: 0.7129 (mtm) REVERT: A 343 MET cc_start: 0.7952 (tpt) cc_final: 0.7725 (tpt) REVERT: A 380 MET cc_start: 0.8375 (mtt) cc_final: 0.8065 (mtm) REVERT: A 436 ASN cc_start: 0.8926 (m-40) cc_final: 0.8718 (m-40) REVERT: A 442 MET cc_start: 0.8255 (ttt) cc_final: 0.8014 (ttm) REVERT: A 468 GLU cc_start: 0.8391 (tt0) cc_final: 0.7879 (tt0) REVERT: A 470 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7506 (pt0) REVERT: A 500 ASN cc_start: 0.9090 (t0) cc_final: 0.8837 (t0) REVERT: A 587 VAL cc_start: 0.8681 (t) cc_final: 0.8283 (m) REVERT: A 595 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7783 (mm-30) REVERT: A 625 ASN cc_start: 0.8165 (m-40) cc_final: 0.7721 (m-40) REVERT: A 630 LEU cc_start: 0.8401 (mt) cc_final: 0.8163 (mt) REVERT: A 652 ASP cc_start: 0.7827 (m-30) cc_final: 0.7544 (m-30) REVERT: A 711 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: B 84 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7852 (mt-10) REVERT: B 172 HIS cc_start: 0.4669 (OUTLIER) cc_final: 0.4428 (m-70) REVERT: B 191 ARG cc_start: 0.7862 (mtp-110) cc_final: 0.7631 (ttm110) REVERT: B 222 ARG cc_start: 0.8396 (mtt180) cc_final: 0.7921 (mtm-85) REVERT: B 243 GLU cc_start: 0.8334 (tt0) cc_final: 0.7890 (tm-30) REVERT: B 247 GLN cc_start: 0.8888 (tt0) cc_final: 0.8518 (tt0) REVERT: B 266 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7465 (mt-10) REVERT: B 335 MET cc_start: 0.7925 (mtt) cc_final: 0.7515 (mtt) REVERT: B 410 TRP cc_start: 0.8647 (OUTLIER) cc_final: 0.7672 (m-90) REVERT: B 436 ASN cc_start: 0.8813 (m-40) cc_final: 0.8385 (m110) REVERT: B 526 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8483 (tt) REVERT: B 529 LEU cc_start: 0.8879 (mm) cc_final: 0.8608 (mt) REVERT: B 554 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7855 (tttp) REVERT: B 631 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7213 (mt) REVERT: B 634 HIS cc_start: 0.7811 (m170) cc_final: 0.6748 (t70) REVERT: B 715 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7982 (mm-30) REVERT: C 71 ARG cc_start: 0.8039 (ttt-90) cc_final: 0.7718 (mmm-85) REVERT: C 84 GLU cc_start: 0.8087 (mp0) cc_final: 0.7664 (mt-10) REVERT: C 106 LYS cc_start: 0.8235 (mtpm) cc_final: 0.7966 (ttmm) REVERT: C 191 ARG cc_start: 0.8080 (mtp-110) cc_final: 0.7183 (ttm170) REVERT: C 240 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: C 243 GLU cc_start: 0.8325 (tt0) cc_final: 0.7906 (tm-30) REVERT: C 319 PHE cc_start: 0.6511 (m-10) cc_final: 0.6164 (m-10) REVERT: C 380 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.6958 (mpt) REVERT: C 395 VAL cc_start: 0.8456 (t) cc_final: 0.8240 (t) REVERT: C 454 ILE cc_start: 0.8084 (mm) cc_final: 0.7860 (mt) REVERT: C 519 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8389 (ttmt) REVERT: C 529 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8564 (mt) REVERT: C 591 LYS cc_start: 0.8026 (mttt) cc_final: 0.7693 (tmmt) REVERT: C 645 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8615 (mtpt) REVERT: C 744 LYS cc_start: 0.7849 (mptm) cc_final: 0.7501 (mptp) REVERT: D 71 ARG cc_start: 0.7975 (ttt-90) cc_final: 0.7756 (mmm-85) REVERT: D 96 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7978 (t) REVERT: D 225 TRP cc_start: 0.8767 (t-100) cc_final: 0.8548 (t-100) REVERT: D 240 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: D 243 GLU cc_start: 0.8206 (tt0) cc_final: 0.7773 (tm-30) REVERT: D 291 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8099 (mppt) REVERT: D 343 MET cc_start: 0.7470 (mmt) cc_final: 0.7088 (mpm) REVERT: D 359 PHE cc_start: 0.7757 (t80) cc_final: 0.7382 (t80) REVERT: D 369 CYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8010 (p) REVERT: D 410 TRP cc_start: 0.8445 (OUTLIER) cc_final: 0.7445 (m-90) REVERT: D 422 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.6161 (mmm) REVERT: D 436 ASN cc_start: 0.8526 (m-40) cc_final: 0.8061 (m-40) REVERT: D 508 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8250 (mm) REVERT: D 520 PHE cc_start: 0.8493 (t80) cc_final: 0.7921 (t80) REVERT: D 553 CYS cc_start: 0.7448 (t) cc_final: 0.7008 (t) REVERT: D 559 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7985 (tt0) REVERT: D 587 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8492 (m) REVERT: D 591 LYS cc_start: 0.8451 (tmmt) cc_final: 0.8191 (ttmm) REVERT: D 595 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8017 (mm-30) REVERT: D 645 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8590 (mtpt) REVERT: D 747 LYS cc_start: 0.8367 (mttt) cc_final: 0.8078 (mtmt) outliers start: 120 outliers final: 33 residues processed: 504 average time/residue: 0.5605 time to fit residues: 324.6777 Evaluate side-chains 473 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 419 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 587 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 67 optimal weight: 0.0170 chunk 116 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 236 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN A 533 ASN A 589 ASN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 625 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 536 ASN C 562 ASN C 625 ASN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN D 533 ASN D 589 ASN D 625 ASN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN ** D 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.148064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.109900 restraints weight = 22549.763| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.94 r_work: 0.2960 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.6227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21643 Z= 0.123 Angle : 0.548 10.529 29326 Z= 0.285 Chirality : 0.039 0.143 3303 Planarity : 0.004 0.100 3610 Dihedral : 8.709 59.654 3212 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 5.06 % Allowed : 20.02 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.17), residues: 2520 helix: 1.53 (0.12), residues: 1828 sheet: None (None), residues: 0 loop : -1.11 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 71 TYR 0.030 0.001 TYR B 58 PHE 0.015 0.001 PHE B 341 TRP 0.021 0.001 TRP D 327 HIS 0.004 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (21639) covalent geometry : angle 0.54739 / 0.28 (29318) SS BOND : bond 0.00351 / 0.17 ( 4) SS BOND : angle 1.75850 / 0.62 ( 8) hydrogen bonds : bond 0.03798 / 2.49 ( 1246) hydrogen bonds : angle 3.38635 / 2.34 ( 3648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 442 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 PHE cc_start: 0.8226 (t80) cc_final: 0.7879 (t80) REVERT: A 172 HIS cc_start: 0.5659 (OUTLIER) cc_final: 0.4729 (m-70) REVERT: A 173 GLN cc_start: 0.4388 (OUTLIER) cc_final: 0.3967 (tt0) REVERT: A 194 ARG cc_start: 0.8354 (tpp-160) cc_final: 0.8123 (tpt170) REVERT: A 222 ARG cc_start: 0.8538 (mtt180) cc_final: 0.8121 (mtm-85) REVERT: A 243 GLU cc_start: 0.8416 (tt0) cc_final: 0.7962 (tm-30) REVERT: A 246 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8119 (tp40) REVERT: A 262 SER cc_start: 0.9106 (OUTLIER) cc_final: 0.8849 (m) REVERT: A 266 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7576 (mt-10) REVERT: A 331 LEU cc_start: 0.7974 (tp) cc_final: 0.7607 (tt) REVERT: A 335 MET cc_start: 0.7675 (mtt) cc_final: 0.7195 (mtm) REVERT: A 343 MET cc_start: 0.8033 (tpt) cc_final: 0.7800 (tpt) REVERT: A 380 MET cc_start: 0.8379 (mtt) cc_final: 0.8078 (mtm) REVERT: A 436 ASN cc_start: 0.8797 (m-40) cc_final: 0.8590 (m-40) REVERT: A 438 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8235 (ttt) REVERT: A 442 MET cc_start: 0.8275 (ttt) cc_final: 0.8050 (ttm) REVERT: A 468 GLU cc_start: 0.8313 (tt0) cc_final: 0.7835 (tt0) REVERT: A 470 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: A 500 ASN cc_start: 0.9115 (t0) cc_final: 0.8855 (t0) REVERT: A 587 VAL cc_start: 0.8775 (t) cc_final: 0.8299 (m) REVERT: A 595 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8042 (mm-30) REVERT: A 652 ASP cc_start: 0.7803 (m-30) cc_final: 0.7553 (m-30) REVERT: B 84 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7922 (mt-10) REVERT: B 191 ARG cc_start: 0.7948 (mtp-110) cc_final: 0.7719 (ttm110) REVERT: B 222 ARG cc_start: 0.8495 (mtt180) cc_final: 0.8046 (mtm-85) REVERT: B 243 GLU cc_start: 0.8290 (tt0) cc_final: 0.7855 (tm-30) REVERT: B 247 GLN cc_start: 0.8911 (tt0) cc_final: 0.8591 (tt0) REVERT: B 266 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7572 (mm-30) REVERT: B 335 MET cc_start: 0.7940 (mtt) cc_final: 0.7621 (mtt) REVERT: B 404 GLU cc_start: 0.5861 (mm-30) cc_final: 0.5186 (tm-30) REVERT: B 436 ASN cc_start: 0.8865 (m-40) cc_final: 0.8459 (m110) REVERT: B 526 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8522 (tt) REVERT: B 529 LEU cc_start: 0.8943 (mm) cc_final: 0.8722 (mt) REVERT: B 559 GLU cc_start: 0.8094 (tt0) cc_final: 0.7841 (tt0) REVERT: B 631 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7357 (mt) REVERT: B 634 HIS cc_start: 0.7903 (m170) cc_final: 0.6890 (t70) REVERT: B 709 GLN cc_start: 0.7787 (tt0) cc_final: 0.7470 (tt0) REVERT: C 71 ARG cc_start: 0.8083 (ttt-90) cc_final: 0.7812 (mmm-85) REVERT: C 79 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7843 (pt0) REVERT: C 84 GLU cc_start: 0.8167 (mp0) cc_final: 0.7745 (mt-10) REVERT: C 106 LYS cc_start: 0.8283 (mtpm) cc_final: 0.8012 (ttmm) REVERT: C 190 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8381 (tt) REVERT: C 191 ARG cc_start: 0.8103 (mtp-110) cc_final: 0.7229 (ttm170) REVERT: C 240 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: C 243 GLU cc_start: 0.8388 (tt0) cc_final: 0.7966 (tm-30) REVERT: C 266 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7850 (mp0) REVERT: C 380 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.6986 (mpt) REVERT: C 395 VAL cc_start: 0.8547 (t) cc_final: 0.8328 (t) REVERT: C 436 ASN cc_start: 0.8496 (m-40) cc_final: 0.7981 (m110) REVERT: C 454 ILE cc_start: 0.8059 (mm) cc_final: 0.7845 (mt) REVERT: C 519 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8445 (ttmt) REVERT: C 529 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8580 (mt) REVERT: C 558 CYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6320 (t) REVERT: C 591 LYS cc_start: 0.8032 (mttt) cc_final: 0.7687 (tmmt) REVERT: C 595 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7919 (mm-30) REVERT: C 645 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8750 (mtpt) REVERT: C 744 LYS cc_start: 0.7986 (mptm) cc_final: 0.7621 (mptp) REVERT: D 71 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7659 (mmm-85) REVERT: D 75 LEU cc_start: 0.8597 (mp) cc_final: 0.8396 (mt) REVERT: D 194 ARG cc_start: 0.8281 (tpp-160) cc_final: 0.6896 (ttp-110) REVERT: D 225 TRP cc_start: 0.8793 (t-100) cc_final: 0.8569 (t-100) REVERT: D 240 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: D 243 GLU cc_start: 0.8297 (tt0) cc_final: 0.7879 (tm-30) REVERT: D 291 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8142 (mppt) REVERT: D 343 MET cc_start: 0.7639 (mmt) cc_final: 0.7302 (mpm) REVERT: D 359 PHE cc_start: 0.7739 (t80) cc_final: 0.7328 (t80) REVERT: D 369 CYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7959 (p) REVERT: D 410 TRP cc_start: 0.8459 (OUTLIER) cc_final: 0.7489 (m-90) REVERT: D 422 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.6215 (mmm) REVERT: D 436 ASN cc_start: 0.8591 (m-40) cc_final: 0.8174 (m110) REVERT: D 471 MET cc_start: 0.8307 (ttm) cc_final: 0.8050 (tmm) REVERT: D 508 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8219 (mm) REVERT: D 553 CYS cc_start: 0.7508 (t) cc_final: 0.7040 (t) REVERT: D 559 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: D 591 LYS cc_start: 0.8445 (tmmt) cc_final: 0.8234 (tttm) REVERT: D 645 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8727 (mtpt) REVERT: D 747 LYS cc_start: 0.8422 (mttt) cc_final: 0.8130 (mtmt) outliers start: 114 outliers final: 41 residues processed: 497 average time/residue: 0.5748 time to fit residues: 327.8607 Evaluate side-chains 484 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 420 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 559 GLU Chi-restraints excluded: chain D residue 652 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 134 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 249 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 221 optimal weight: 0.5980 chunk 150 optimal weight: 0.0570 chunk 170 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 562 ASN A 589 ASN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 625 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS C 533 ASN C 536 ASN C 562 ASN C 625 ASN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN D 589 ASN D 625 ASN D 629 GLN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN ** D 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.148405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.112093 restraints weight = 22602.966| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.87 r_work: 0.2926 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21643 Z= 0.118 Angle : 0.544 11.646 29326 Z= 0.280 Chirality : 0.038 0.143 3303 Planarity : 0.004 0.103 3610 Dihedral : 8.388 58.482 3212 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.82 % Favored : 97.02 % Rotamer: Outliers : 4.66 % Allowed : 21.39 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.17), residues: 2520 helix: 1.63 (0.12), residues: 1840 sheet: None (None), residues: 0 loop : -0.99 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 71 TYR 0.022 0.001 TYR B 58 PHE 0.016 0.001 PHE C 341 TRP 0.017 0.001 TRP D 327 HIS 0.004 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (21639) covalent geometry : angle 0.54384 / 0.28 (29318) SS BOND : bond 0.00419 / 0.21 ( 4) SS BOND : angle 1.30044 / 0.48 ( 8) hydrogen bonds : bond 0.03699 / 2.42 ( 1246) hydrogen bonds : angle 3.35405 / 2.32 ( 3648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 433 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7758 (mm-30) REVERT: A 136 PHE cc_start: 0.8137 (t80) cc_final: 0.7852 (t80) REVERT: A 172 HIS cc_start: 0.5443 (OUTLIER) cc_final: 0.4629 (m-70) REVERT: A 173 GLN cc_start: 0.4275 (OUTLIER) cc_final: 0.3924 (tt0) REVERT: A 194 ARG cc_start: 0.8241 (tpp-160) cc_final: 0.8014 (tpt170) REVERT: A 222 ARG cc_start: 0.8411 (mtt180) cc_final: 0.8084 (mtm-85) REVERT: A 243 GLU cc_start: 0.8223 (tt0) cc_final: 0.7786 (tm-30) REVERT: A 262 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8808 (m) REVERT: A 266 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7366 (mm-30) REVERT: A 331 LEU cc_start: 0.8041 (tp) cc_final: 0.7654 (tt) REVERT: A 335 MET cc_start: 0.7545 (mtt) cc_final: 0.7072 (mtm) REVERT: A 343 MET cc_start: 0.8023 (tpt) cc_final: 0.7780 (tpt) REVERT: A 380 MET cc_start: 0.8214 (mtt) cc_final: 0.7897 (mtm) REVERT: A 436 ASN cc_start: 0.8804 (m-40) cc_final: 0.8588 (m-40) REVERT: A 438 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8101 (ttt) REVERT: A 442 MET cc_start: 0.8214 (ttt) cc_final: 0.8005 (ttm) REVERT: A 468 GLU cc_start: 0.8164 (tt0) cc_final: 0.7733 (tt0) REVERT: A 470 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: A 500 ASN cc_start: 0.9065 (t0) cc_final: 0.8807 (t0) REVERT: A 587 VAL cc_start: 0.8727 (t) cc_final: 0.8263 (m) REVERT: B 84 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7814 (mt-10) REVERT: B 136 PHE cc_start: 0.8109 (t80) cc_final: 0.7847 (t80) REVERT: B 191 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.7134 (ttm-80) REVERT: B 222 ARG cc_start: 0.8358 (mtt180) cc_final: 0.7961 (mtm-85) REVERT: B 243 GLU cc_start: 0.8095 (tt0) cc_final: 0.7690 (tm-30) REVERT: B 247 GLN cc_start: 0.8858 (tt0) cc_final: 0.8537 (tt0) REVERT: B 266 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7351 (mm-30) REVERT: B 335 MET cc_start: 0.7965 (mtt) cc_final: 0.7606 (mtt) REVERT: B 404 GLU cc_start: 0.5918 (mm-30) cc_final: 0.5082 (tm-30) REVERT: B 436 ASN cc_start: 0.8892 (m-40) cc_final: 0.8475 (m110) REVERT: B 526 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8500 (tt) REVERT: B 529 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8610 (mt) REVERT: B 631 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7403 (mt) REVERT: B 634 HIS cc_start: 0.7757 (m170) cc_final: 0.6933 (t70) REVERT: B 709 GLN cc_start: 0.7792 (tt0) cc_final: 0.7520 (tt0) REVERT: C 71 ARG cc_start: 0.8120 (ttt-90) cc_final: 0.7848 (mmm-85) REVERT: C 79 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7752 (pt0) REVERT: C 84 GLU cc_start: 0.8013 (mp0) cc_final: 0.7657 (mt-10) REVERT: C 106 LYS cc_start: 0.8248 (mtpm) cc_final: 0.8003 (ttmm) REVERT: C 136 PHE cc_start: 0.8198 (t80) cc_final: 0.7985 (t80) REVERT: C 191 ARG cc_start: 0.7943 (mtp-110) cc_final: 0.7197 (ttm170) REVERT: C 240 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: C 243 GLU cc_start: 0.8171 (tt0) cc_final: 0.7772 (tm-30) REVERT: C 369 CYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7905 (p) REVERT: C 395 VAL cc_start: 0.8488 (t) cc_final: 0.8275 (t) REVERT: C 436 ASN cc_start: 0.8511 (m-40) cc_final: 0.7935 (m110) REVERT: C 519 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8387 (ttmt) REVERT: C 529 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8524 (mt) REVERT: C 558 CYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6101 (t) REVERT: C 591 LYS cc_start: 0.8154 (mttt) cc_final: 0.7841 (tmmt) REVERT: C 645 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8641 (mtpt) REVERT: C 744 LYS cc_start: 0.7924 (mptm) cc_final: 0.7542 (mptp) REVERT: D 194 ARG cc_start: 0.8128 (tpp-160) cc_final: 0.6766 (ttp-110) REVERT: D 225 TRP cc_start: 0.8712 (t-100) cc_final: 0.8500 (t-100) REVERT: D 243 GLU cc_start: 0.8119 (tt0) cc_final: 0.7722 (tm-30) REVERT: D 266 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7648 (mp0) REVERT: D 291 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8137 (mppt) REVERT: D 343 MET cc_start: 0.7372 (mmt) cc_final: 0.7126 (mpm) REVERT: D 359 PHE cc_start: 0.7769 (t80) cc_final: 0.7417 (t80) REVERT: D 369 CYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7942 (p) REVERT: D 422 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6360 (mmm) REVERT: D 436 ASN cc_start: 0.8586 (m-40) cc_final: 0.8166 (m110) REVERT: D 471 MET cc_start: 0.8271 (ttm) cc_final: 0.8031 (tmm) REVERT: D 508 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8180 (mm) REVERT: D 520 PHE cc_start: 0.8464 (t80) cc_final: 0.7985 (t80) REVERT: D 553 CYS cc_start: 0.7177 (t) cc_final: 0.6700 (t) REVERT: D 559 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: D 645 LYS cc_start: 0.8934 (mtpt) cc_final: 0.8602 (mtpt) REVERT: D 747 LYS cc_start: 0.8363 (mttt) cc_final: 0.8015 (mtmt) outliers start: 105 outliers final: 45 residues processed: 482 average time/residue: 0.5708 time to fit residues: 316.7478 Evaluate side-chains 486 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 421 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 559 GLU Chi-restraints excluded: chain D residue 652 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 174 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 173 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 562 ASN A 589 ASN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN B 533 ASN B 625 ASN B 735 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN C 533 ASN C 625 ASN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN D 589 ASN D 625 ASN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.146633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.108225 restraints weight = 22583.534| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.97 r_work: 0.2937 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.6485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21643 Z= 0.137 Angle : 0.574 12.621 29326 Z= 0.291 Chirality : 0.039 0.152 3303 Planarity : 0.004 0.107 3610 Dihedral : 8.305 59.948 3212 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.13 % Favored : 96.71 % Rotamer: Outliers : 4.97 % Allowed : 21.66 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.17), residues: 2520 helix: 1.68 (0.12), residues: 1832 sheet: None (None), residues: 0 loop : -0.97 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 71 TYR 0.017 0.001 TYR A 586 PHE 0.017 0.002 PHE B 341 TRP 0.015 0.001 TRP B 472 HIS 0.004 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (21639) covalent geometry : angle 0.57358 / 0.29 (29318) SS BOND : bond 0.00446 / 0.22 ( 4) SS BOND : angle 1.34418 / 0.50 ( 8) hydrogen bonds : bond 0.03821 / 2.50 ( 1246) hydrogen bonds : angle 3.36563 / 2.33 ( 3648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 433 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 172 HIS cc_start: 0.5414 (OUTLIER) cc_final: 0.4590 (m-70) REVERT: A 173 GLN cc_start: 0.4322 (OUTLIER) cc_final: 0.3901 (tt0) REVERT: A 194 ARG cc_start: 0.8338 (tpp-160) cc_final: 0.8127 (tpt170) REVERT: A 222 ARG cc_start: 0.8561 (mtt180) cc_final: 0.8157 (mtm-85) REVERT: A 243 GLU cc_start: 0.8403 (tt0) cc_final: 0.7924 (tm-30) REVERT: A 262 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8835 (m) REVERT: A 266 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7570 (mm-30) REVERT: A 331 LEU cc_start: 0.7926 (tp) cc_final: 0.7589 (tt) REVERT: A 335 MET cc_start: 0.7587 (mtt) cc_final: 0.7098 (mtm) REVERT: A 343 MET cc_start: 0.8024 (tpt) cc_final: 0.7770 (tpt) REVERT: A 380 MET cc_start: 0.8278 (mtt) cc_final: 0.7954 (mtm) REVERT: A 436 ASN cc_start: 0.8763 (m-40) cc_final: 0.8558 (m-40) REVERT: A 438 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8126 (ttt) REVERT: A 442 MET cc_start: 0.8266 (ttt) cc_final: 0.8014 (ttm) REVERT: A 468 GLU cc_start: 0.8179 (tt0) cc_final: 0.7736 (tt0) REVERT: A 470 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: A 500 ASN cc_start: 0.9128 (t0) cc_final: 0.8863 (t0) REVERT: B 84 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7912 (mt-10) REVERT: B 136 PHE cc_start: 0.8333 (t80) cc_final: 0.7919 (t80) REVERT: B 172 HIS cc_start: 0.4806 (OUTLIER) cc_final: 0.4555 (m-70) REVERT: B 190 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8376 (tt) REVERT: B 191 ARG cc_start: 0.7928 (mtp-110) cc_final: 0.7164 (ttm-80) REVERT: B 222 ARG cc_start: 0.8519 (mtt180) cc_final: 0.8063 (mtm-85) REVERT: B 243 GLU cc_start: 0.8306 (tt0) cc_final: 0.7872 (tm-30) REVERT: B 247 GLN cc_start: 0.8912 (tt0) cc_final: 0.8588 (tt0) REVERT: B 266 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7623 (mm-30) REVERT: B 335 MET cc_start: 0.8038 (mtt) cc_final: 0.7677 (mtt) REVERT: B 404 GLU cc_start: 0.5907 (mm-30) cc_final: 0.5153 (tm-30) REVERT: B 436 ASN cc_start: 0.8869 (m-40) cc_final: 0.8507 (m-40) REVERT: B 519 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8151 (mtpm) REVERT: B 526 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8518 (tt) REVERT: B 529 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8646 (mt) REVERT: B 554 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8247 (tttp) REVERT: B 631 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7411 (mt) REVERT: B 634 HIS cc_start: 0.7868 (m170) cc_final: 0.6879 (t70) REVERT: B 709 GLN cc_start: 0.7865 (tt0) cc_final: 0.7555 (tt0) REVERT: B 745 GLU cc_start: 0.7213 (mt-10) cc_final: 0.7001 (mt-10) REVERT: C 38 SER cc_start: 0.8492 (t) cc_final: 0.8268 (t) REVERT: C 71 ARG cc_start: 0.8031 (ttt-90) cc_final: 0.7746 (mmm-85) REVERT: C 79 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7889 (pt0) REVERT: C 84 GLU cc_start: 0.8224 (mp0) cc_final: 0.7766 (mt-10) REVERT: C 106 LYS cc_start: 0.8299 (mtpm) cc_final: 0.8054 (ttmm) REVERT: C 136 PHE cc_start: 0.8294 (t80) cc_final: 0.7994 (t80) REVERT: C 190 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8383 (tt) REVERT: C 191 ARG cc_start: 0.8076 (mtp-110) cc_final: 0.7169 (ttm170) REVERT: C 240 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: C 243 GLU cc_start: 0.8390 (tt0) cc_final: 0.7959 (tm-30) REVERT: C 369 CYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7989 (p) REVERT: C 380 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7804 (mtt) REVERT: C 395 VAL cc_start: 0.8522 (t) cc_final: 0.8308 (t) REVERT: C 421 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6770 (tm-30) REVERT: C 436 ASN cc_start: 0.8521 (m-40) cc_final: 0.7989 (m110) REVERT: C 519 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8418 (ttmt) REVERT: C 529 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8569 (mt) REVERT: C 645 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8702 (mtpt) REVERT: C 744 LYS cc_start: 0.7916 (mptm) cc_final: 0.7543 (mptp) REVERT: C 756 GLU cc_start: 0.7808 (tt0) cc_final: 0.7485 (tt0) REVERT: D 194 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.6635 (ttp-110) REVERT: D 243 GLU cc_start: 0.8325 (tt0) cc_final: 0.7886 (tm-30) REVERT: D 266 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7816 (mp0) REVERT: D 291 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8190 (mppt) REVERT: D 335 MET cc_start: 0.7886 (mmm) cc_final: 0.7339 (mtm) REVERT: D 343 MET cc_start: 0.7458 (mmt) cc_final: 0.7193 (mpm) REVERT: D 359 PHE cc_start: 0.7815 (t80) cc_final: 0.7413 (t80) REVERT: D 369 CYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8205 (p) REVERT: D 422 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.6358 (mmm) REVERT: D 436 ASN cc_start: 0.8677 (m-40) cc_final: 0.8288 (m110) REVERT: D 470 GLU cc_start: 0.7408 (pt0) cc_final: 0.7141 (tt0) REVERT: D 508 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8136 (mm) REVERT: D 551 ASN cc_start: 0.8345 (m110) cc_final: 0.8055 (m-40) REVERT: D 553 CYS cc_start: 0.7570 (t) cc_final: 0.7116 (t) REVERT: D 559 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: D 747 LYS cc_start: 0.8394 (mttt) cc_final: 0.8067 (mtmt) outliers start: 112 outliers final: 50 residues processed: 490 average time/residue: 0.5678 time to fit residues: 319.4825 Evaluate side-chains 497 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 423 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 747 LYS Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 562 ASN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 559 GLU Chi-restraints excluded: chain D residue 652 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 54 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 242 optimal weight: 0.0020 chunk 247 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 232 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 562 ASN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 552 ASN B 589 ASN B 625 ASN B 735 ASN B 742 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 625 ASN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN D 552 ASN D 589 ASN D 625 ASN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.147151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.109447 restraints weight = 22526.264| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.06 r_work: 0.2962 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.6594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21643 Z= 0.130 Angle : 0.561 11.540 29326 Z= 0.287 Chirality : 0.039 0.149 3303 Planarity : 0.004 0.112 3610 Dihedral : 8.137 59.832 3212 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.06 % Favored : 96.79 % Rotamer: Outliers : 3.95 % Allowed : 23.12 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.17), residues: 2520 helix: 1.74 (0.12), residues: 1828 sheet: None (None), residues: 0 loop : -0.93 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 71 TYR 0.018 0.001 TYR A 586 PHE 0.016 0.002 PHE B 341 TRP 0.018 0.001 TRP B 472 HIS 0.004 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (21639) covalent geometry : angle 0.56056 / 0.29 (29318) SS BOND : bond 0.00521 / 0.26 ( 4) SS BOND : angle 1.32636 / 0.51 ( 8) hydrogen bonds : bond 0.03767 / 2.46 ( 1246) hydrogen bonds : angle 3.37150 / 2.34 ( 3648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 442 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 136 PHE cc_start: 0.7993 (t80) cc_final: 0.7686 (t80) REVERT: A 172 HIS cc_start: 0.5390 (OUTLIER) cc_final: 0.4661 (m-70) REVERT: A 173 GLN cc_start: 0.4362 (OUTLIER) cc_final: 0.3976 (tt0) REVERT: A 194 ARG cc_start: 0.8320 (tpp-160) cc_final: 0.8097 (tpt170) REVERT: A 222 ARG cc_start: 0.8516 (mtt180) cc_final: 0.8108 (mtm-85) REVERT: A 243 GLU cc_start: 0.8360 (tt0) cc_final: 0.7877 (tm-30) REVERT: A 262 SER cc_start: 0.9074 (OUTLIER) cc_final: 0.8815 (m) REVERT: A 266 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7539 (mm-30) REVERT: A 331 LEU cc_start: 0.7919 (tp) cc_final: 0.7582 (tt) REVERT: A 335 MET cc_start: 0.7567 (mtt) cc_final: 0.7073 (mtm) REVERT: A 343 MET cc_start: 0.8021 (tpt) cc_final: 0.7766 (tpt) REVERT: A 380 MET cc_start: 0.8281 (mtt) cc_final: 0.7972 (mtm) REVERT: A 404 GLU cc_start: 0.5882 (tm-30) cc_final: 0.5603 (tm-30) REVERT: A 436 ASN cc_start: 0.8744 (m-40) cc_final: 0.8535 (m-40) REVERT: A 438 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8095 (ttt) REVERT: A 442 MET cc_start: 0.8350 (ttt) cc_final: 0.8096 (ttm) REVERT: A 470 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: A 500 ASN cc_start: 0.9121 (t0) cc_final: 0.8846 (t0) REVERT: A 587 VAL cc_start: 0.8692 (t) cc_final: 0.8258 (m) REVERT: B 84 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7871 (mt-10) REVERT: B 136 PHE cc_start: 0.8265 (t80) cc_final: 0.7876 (t80) REVERT: B 191 ARG cc_start: 0.7910 (mtp-110) cc_final: 0.7128 (ttm-80) REVERT: B 222 ARG cc_start: 0.8503 (mtt180) cc_final: 0.8039 (mtm-85) REVERT: B 243 GLU cc_start: 0.8267 (tt0) cc_final: 0.7827 (tm-30) REVERT: B 247 GLN cc_start: 0.8888 (tt0) cc_final: 0.8564 (tt0) REVERT: B 266 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7557 (mm-30) REVERT: B 335 MET cc_start: 0.7985 (mtt) cc_final: 0.7599 (mtt) REVERT: B 404 GLU cc_start: 0.5913 (mm-30) cc_final: 0.5290 (tm-30) REVERT: B 436 ASN cc_start: 0.8865 (m-40) cc_final: 0.8505 (m-40) REVERT: B 472 TRP cc_start: 0.8681 (m100) cc_final: 0.8471 (m100) REVERT: B 526 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8419 (tt) REVERT: B 529 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8616 (mt) REVERT: B 634 HIS cc_start: 0.7836 (m170) cc_final: 0.6944 (t70) REVERT: B 709 GLN cc_start: 0.7795 (tt0) cc_final: 0.7401 (tt0) REVERT: C 38 SER cc_start: 0.8473 (t) cc_final: 0.8255 (t) REVERT: C 71 ARG cc_start: 0.8029 (ttt-90) cc_final: 0.7750 (mmm-85) REVERT: C 79 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7854 (pt0) REVERT: C 84 GLU cc_start: 0.8226 (mp0) cc_final: 0.7770 (mt-10) REVERT: C 106 LYS cc_start: 0.8285 (mtpm) cc_final: 0.8016 (ttmm) REVERT: C 136 PHE cc_start: 0.8278 (t80) cc_final: 0.7951 (t80) REVERT: C 190 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8359 (tt) REVERT: C 191 ARG cc_start: 0.8059 (mtp-110) cc_final: 0.7177 (ttm-80) REVERT: C 240 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: C 243 GLU cc_start: 0.8292 (tt0) cc_final: 0.7852 (tm-30) REVERT: C 369 CYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8002 (p) REVERT: C 395 VAL cc_start: 0.8507 (t) cc_final: 0.8288 (t) REVERT: C 421 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6607 (tm-30) REVERT: C 436 ASN cc_start: 0.8582 (m-40) cc_final: 0.8054 (m110) REVERT: C 519 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8351 (ttmt) REVERT: C 529 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8538 (mt) REVERT: C 744 LYS cc_start: 0.7888 (mptm) cc_final: 0.7517 (mptp) REVERT: C 756 GLU cc_start: 0.7747 (tt0) cc_final: 0.7469 (tt0) REVERT: D 136 PHE cc_start: 0.8231 (t80) cc_final: 0.7932 (t80) REVERT: D 194 ARG cc_start: 0.8164 (tpp-160) cc_final: 0.6585 (ttp-110) REVERT: D 243 GLU cc_start: 0.8313 (tt0) cc_final: 0.7861 (tm-30) REVERT: D 266 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7764 (mp0) REVERT: D 291 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8226 (mppt) REVERT: D 335 MET cc_start: 0.7951 (mmm) cc_final: 0.7379 (mtm) REVERT: D 343 MET cc_start: 0.7440 (mmt) cc_final: 0.7169 (mpm) REVERT: D 359 PHE cc_start: 0.7788 (t80) cc_final: 0.7408 (t80) REVERT: D 369 CYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8176 (p) REVERT: D 422 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6312 (mmm) REVERT: D 436 ASN cc_start: 0.8676 (m-40) cc_final: 0.8290 (m110) REVERT: D 470 GLU cc_start: 0.7402 (pt0) cc_final: 0.7132 (tt0) REVERT: D 490 SER cc_start: 0.9281 (t) cc_final: 0.8943 (m) REVERT: D 508 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8085 (mm) REVERT: D 551 ASN cc_start: 0.8353 (m110) cc_final: 0.8065 (m-40) REVERT: D 553 CYS cc_start: 0.7519 (t) cc_final: 0.7068 (t) REVERT: D 559 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: D 744 LYS cc_start: 0.8090 (mptt) cc_final: 0.7458 (mptp) REVERT: D 747 LYS cc_start: 0.8371 (mttt) cc_final: 0.8047 (mtmt) outliers start: 89 outliers final: 45 residues processed: 483 average time/residue: 0.5715 time to fit residues: 316.1044 Evaluate side-chains 487 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 424 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 747 LYS Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 562 ASN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 394 HIS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 559 GLU Chi-restraints excluded: chain D residue 652 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 114 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 221 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 562 ASN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 589 ASN B 625 ASN B 735 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS C 533 ASN C 625 ASN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN D 552 ASN D 589 ASN D 625 ASN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.146039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.110910 restraints weight = 22995.913| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.74 r_work: 0.3040 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21643 Z= 0.136 Angle : 0.571 11.096 29326 Z= 0.292 Chirality : 0.039 0.151 3303 Planarity : 0.004 0.114 3610 Dihedral : 8.046 58.448 3212 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.75 % Rotamer: Outliers : 3.28 % Allowed : 23.92 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.17), residues: 2520 helix: 1.76 (0.12), residues: 1828 sheet: None (None), residues: 0 loop : -0.91 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 71 TYR 0.018 0.001 TYR A 586 PHE 0.016 0.002 PHE B 341 TRP 0.016 0.001 TRP B 472 HIS 0.004 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (21639) covalent geometry : angle 0.57011 / 0.29 (29318) SS BOND : bond 0.00428 / 0.21 ( 4) SS BOND : angle 1.58425 / 0.60 ( 8) hydrogen bonds : bond 0.03807 / 2.50 ( 1246) hydrogen bonds : angle 3.38176 / 2.34 ( 3648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 426 time to evaluate : 0.808 Fit side-chains REVERT: A 136 PHE cc_start: 0.8109 (t80) cc_final: 0.7731 (t80) REVERT: A 172 HIS cc_start: 0.5472 (OUTLIER) cc_final: 0.4709 (m-70) REVERT: A 173 GLN cc_start: 0.4451 (OUTLIER) cc_final: 0.4082 (tt0) REVERT: A 191 ARG cc_start: 0.8173 (mtp-110) cc_final: 0.7288 (ttm170) REVERT: A 194 ARG cc_start: 0.8319 (tpp-160) cc_final: 0.8097 (tpt170) REVERT: A 222 ARG cc_start: 0.8530 (mtt180) cc_final: 0.8156 (mtm-85) REVERT: A 243 GLU cc_start: 0.8362 (tt0) cc_final: 0.7922 (tm-30) REVERT: A 262 SER cc_start: 0.9109 (OUTLIER) cc_final: 0.8841 (m) REVERT: A 266 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7560 (mm-30) REVERT: A 331 LEU cc_start: 0.8052 (tp) cc_final: 0.7671 (tt) REVERT: A 335 MET cc_start: 0.7592 (mtt) cc_final: 0.7121 (mtm) REVERT: A 380 MET cc_start: 0.8293 (mtt) cc_final: 0.7986 (mtm) REVERT: A 404 GLU cc_start: 0.5965 (tm-30) cc_final: 0.5675 (tm-30) REVERT: A 436 ASN cc_start: 0.8775 (m-40) cc_final: 0.8570 (m-40) REVERT: A 438 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8147 (ttt) REVERT: A 442 MET cc_start: 0.8271 (ttt) cc_final: 0.8015 (ttm) REVERT: A 470 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: A 500 ASN cc_start: 0.9126 (t0) cc_final: 0.8864 (t0) REVERT: A 587 VAL cc_start: 0.8745 (t) cc_final: 0.8348 (m) REVERT: B 47 THR cc_start: 0.8578 (p) cc_final: 0.8169 (t) REVERT: B 81 GLU cc_start: 0.7000 (mp0) cc_final: 0.6678 (mp0) REVERT: B 84 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7822 (mt-10) REVERT: B 136 PHE cc_start: 0.8314 (t80) cc_final: 0.8016 (t80) REVERT: B 190 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8412 (tt) REVERT: B 191 ARG cc_start: 0.7952 (mtp-110) cc_final: 0.7220 (ttm-80) REVERT: B 222 ARG cc_start: 0.8482 (mtt180) cc_final: 0.8067 (mtm-85) REVERT: B 243 GLU cc_start: 0.8270 (tt0) cc_final: 0.7847 (tm-30) REVERT: B 247 GLN cc_start: 0.8882 (tt0) cc_final: 0.8575 (tt0) REVERT: B 266 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7529 (mm-30) REVERT: B 335 MET cc_start: 0.8000 (mtt) cc_final: 0.7611 (mtt) REVERT: B 380 MET cc_start: 0.8191 (mpt) cc_final: 0.7726 (mtm) REVERT: B 404 GLU cc_start: 0.6141 (mm-30) cc_final: 0.5674 (tm-30) REVERT: B 436 ASN cc_start: 0.8885 (m-40) cc_final: 0.8524 (m-40) REVERT: B 519 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8199 (mtpm) REVERT: B 526 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8474 (tt) REVERT: B 529 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8629 (mt) REVERT: B 631 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7693 (mt) REVERT: B 634 HIS cc_start: 0.7915 (m170) cc_final: 0.6988 (t70) REVERT: B 709 GLN cc_start: 0.7828 (tt0) cc_final: 0.7445 (tt0) REVERT: C 38 SER cc_start: 0.8535 (t) cc_final: 0.8311 (t) REVERT: C 71 ARG cc_start: 0.8036 (ttt-90) cc_final: 0.7809 (mmm-85) REVERT: C 79 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7846 (pt0) REVERT: C 81 GLU cc_start: 0.6384 (mt-10) cc_final: 0.6116 (mp0) REVERT: C 84 GLU cc_start: 0.8226 (mp0) cc_final: 0.7810 (mt-10) REVERT: C 106 LYS cc_start: 0.8251 (mtpm) cc_final: 0.8001 (ttmt) REVERT: C 190 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8415 (tt) REVERT: C 191 ARG cc_start: 0.8073 (mtp-110) cc_final: 0.7214 (ttm170) REVERT: C 240 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: C 243 GLU cc_start: 0.8294 (tt0) cc_final: 0.7874 (tm-30) REVERT: C 369 CYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8003 (p) REVERT: C 380 MET cc_start: 0.8155 (mpt) cc_final: 0.7786 (mtm) REVERT: C 395 VAL cc_start: 0.8606 (t) cc_final: 0.8395 (t) REVERT: C 421 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6665 (tm-30) REVERT: C 436 ASN cc_start: 0.8619 (m-40) cc_final: 0.8106 (m110) REVERT: C 519 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8369 (ttmt) REVERT: C 529 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8563 (mt) REVERT: C 744 LYS cc_start: 0.8070 (mptm) cc_final: 0.7726 (mptp) REVERT: C 745 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6984 (mt-10) REVERT: C 756 GLU cc_start: 0.7761 (tt0) cc_final: 0.7488 (tt0) REVERT: D 81 GLU cc_start: 0.6928 (mt-10) cc_final: 0.5740 (mp0) REVERT: D 191 ARG cc_start: 0.8189 (mtp-110) cc_final: 0.7336 (ttm-80) REVERT: D 194 ARG cc_start: 0.8214 (tpp-160) cc_final: 0.6656 (ttp-110) REVERT: D 243 GLU cc_start: 0.8336 (tt0) cc_final: 0.7897 (tm-30) REVERT: D 266 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7791 (mp0) REVERT: D 291 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8268 (mppt) REVERT: D 335 MET cc_start: 0.8016 (mmm) cc_final: 0.7469 (mtm) REVERT: D 343 MET cc_start: 0.7295 (mmt) cc_final: 0.7004 (mpm) REVERT: D 359 PHE cc_start: 0.7850 (t80) cc_final: 0.7473 (t80) REVERT: D 369 CYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8149 (p) REVERT: D 422 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6349 (mmm) REVERT: D 436 ASN cc_start: 0.8706 (m-40) cc_final: 0.8378 (m110) REVERT: D 508 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8078 (mm) REVERT: D 551 ASN cc_start: 0.8346 (m110) cc_final: 0.8084 (m-40) REVERT: D 553 CYS cc_start: 0.7569 (t) cc_final: 0.7128 (t) REVERT: D 559 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: D 624 MET cc_start: 0.8149 (mtt) cc_final: 0.7680 (mtt) REVERT: D 744 LYS cc_start: 0.8163 (mptt) cc_final: 0.7519 (mptp) REVERT: D 747 LYS cc_start: 0.8438 (mttt) cc_final: 0.8139 (mtmt) outliers start: 74 outliers final: 45 residues processed: 462 average time/residue: 0.5786 time to fit residues: 305.6821 Evaluate side-chains 484 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 418 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 747 LYS Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 369 CYS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 562 ASN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 559 GLU Chi-restraints excluded: chain D residue 652 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 239 optimal weight: 0.9990 chunk 243 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 250 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 562 ASN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 589 ASN B 625 ASN B 735 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS C 533 ASN C 625 ASN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 533 ASN D 552 ASN D 589 ASN D 625 ASN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN D 742 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.144714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110770 restraints weight = 23283.570| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.69 r_work: 0.2966 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.6768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21643 Z= 0.146 Angle : 0.580 11.618 29326 Z= 0.296 Chirality : 0.039 0.137 3303 Planarity : 0.004 0.114 3610 Dihedral : 8.072 58.548 3212 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.02 % Favored : 96.83 % Rotamer: Outliers : 3.95 % Allowed : 23.52 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.17), residues: 2520 helix: 1.74 (0.12), residues: 1828 sheet: None (None), residues: 0 loop : -0.90 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 71 TYR 0.017 0.001 TYR A 586 PHE 0.017 0.002 PHE B 341 TRP 0.014 0.001 TRP C 472 HIS 0.004 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (21639) covalent geometry : angle 0.57969 / 0.30 (29318) SS BOND : bond 0.00388 / 0.19 ( 4) SS BOND : angle 1.49761 / 0.56 ( 8) hydrogen bonds : bond 0.03885 / 2.54 ( 1246) hydrogen bonds : angle 3.41507 / 2.37 ( 3648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8507.78 seconds wall clock time: 145 minutes 21.58 seconds (8721.58 seconds total)