Starting phenix.real_space_refine on Sun Sep 13 05:50:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6aei_9615/09_2026/6aei_9615.cif Found real_map, /net/cci-nas-00/data/ceres_data/6aei_9615/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6aei_9615/09_2026/6aei_9615.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6aei_9615/09_2026/6aei_9615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6aei_9615/09_2026/6aei_9615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6aei_9615/09_2026/6aei_9615.map" model { file = "/net/cci-nas-00/data/ceres_data/6aei_9615/09_2026/6aei_9615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6aei_9615/09_2026/6aei_9615.cif" } 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-2.2.1-6174/lib/python3.11/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: 4.68, per 1000 atoms: 0.22 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: 1.65 Conformation dependent library (CDL) restraints added in 893.1 milliseconds 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: 0.48 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: 3.58 Time building geometry restraints manager: 2.28 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: 12127 17.24 - 34.47: 553 34.47 - 51.71: 142 51.71 - 68.94: 50 68.94 - 86.18: 12 Dihedral angle restraints: 12884 sinusoidal: 5304 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 12881 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.880 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 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 : 12.099 86.176 7944 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 : 0.833 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: 0.5429 time to fit residues: 415.0080 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 : 0.780 ------------------------------------------------------------------------------- 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... 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.165959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.130489 restraints weight = 23675.668| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.89 r_work: 0.3361 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 21643 Z= 0.149 Angle : 0.620 8.197 29326 Z= 0.328 Chirality : 0.040 0.236 3303 Planarity : 0.006 0.102 3610 Dihedral : 10.479 59.710 2993 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.98 % Favored : 96.87 % Rotamer: Outliers : 4.48 % Allowed : 11.90 % Favored : 83.62 % 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: -1.19 (0.15), residues: 2520 helix: -0.34 (0.11), residues: 1812 sheet: None (None), residues: 0 loop : -1.69 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 512 TYR 0.042 0.002 TYR B 58 PHE 0.024 0.002 PHE C 520 TRP 0.023 0.001 TRP A 327 HIS 0.008 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (21639) covalent geometry : angle 0.61915 / 0.33 (29318) SS BOND : bond 0.00249 / 0.13 ( 4) SS BOND : angle 2.06254 / 0.76 ( 8) hydrogen bonds : bond 0.04300 / 2.83 ( 1246) hydrogen bonds : angle 4.03676 / 2.80 ( 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 565 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 464 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.8612 (mtp) cc_final: 0.8323 (mtp) REVERT: A 172 HIS cc_start: 0.5042 (OUTLIER) cc_final: 0.4571 (m-70) REVERT: A 228 LYS cc_start: 0.8567 (tppt) cc_final: 0.8266 (tppp) REVERT: A 243 GLU cc_start: 0.8379 (tt0) cc_final: 0.7938 (tm-30) REVERT: A 250 LEU cc_start: 0.8937 (tm) cc_final: 0.8700 (tp) REVERT: A 262 SER cc_start: 0.9253 (OUTLIER) cc_final: 0.8932 (m) REVERT: A 266 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7505 (mm-30) REVERT: A 327 TRP cc_start: 0.7923 (p-90) cc_final: 0.7474 (p-90) REVERT: A 331 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7426 (tm) REVERT: A 335 MET cc_start: 0.7539 (mtt) cc_final: 0.7225 (mtt) REVERT: A 380 MET cc_start: 0.8328 (mtt) cc_final: 0.8120 (mtm) REVERT: A 416 TRP cc_start: 0.7944 (t-100) cc_final: 0.7206 (t-100) REVERT: A 442 MET cc_start: 0.8186 (ttt) cc_final: 0.7905 (ttm) REVERT: A 467 GLU cc_start: 0.8227 (pm20) cc_final: 0.8005 (pm20) REVERT: A 468 GLU cc_start: 0.8259 (tt0) cc_final: 0.7994 (tt0) REVERT: A 500 ASN cc_start: 0.8894 (t0) cc_final: 0.8631 (t0) REVERT: A 595 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7303 (mm-30) REVERT: A 630 LEU cc_start: 0.8410 (mt) cc_final: 0.8078 (mt) REVERT: A 652 ASP cc_start: 0.7783 (m-30) cc_final: 0.7438 (m-30) REVERT: B 44 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7735 (t0) REVERT: B 71 ARG cc_start: 0.8347 (mmm-85) cc_final: 0.8136 (mmm-85) REVERT: B 84 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7815 (mt-10) REVERT: B 195 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8361 (m) REVERT: B 215 ASP cc_start: 0.8409 (p0) cc_final: 0.8003 (p0) REVERT: B 222 ARG cc_start: 0.8088 (mtt180) cc_final: 0.7839 (mtm-85) REVERT: B 243 GLU cc_start: 0.8240 (tt0) cc_final: 0.7875 (tm-30) REVERT: B 247 GLN cc_start: 0.8895 (tt0) cc_final: 0.8568 (tt0) REVERT: B 266 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7574 (mt-10) REVERT: B 335 MET cc_start: 0.8060 (mtt) cc_final: 0.7814 (mtt) REVERT: B 548 ASP cc_start: 0.6550 (m-30) cc_final: 0.6165 (m-30) REVERT: B 623 MET cc_start: 0.8482 (ttm) cc_final: 0.8212 (ttm) REVERT: B 631 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.6867 (mp) REVERT: B 645 LYS cc_start: 0.9039 (mtpt) cc_final: 0.8730 (mtpt) REVERT: B 711 GLN cc_start: 0.8118 (mt0) cc_final: 0.7852 (mt0) REVERT: B 754 ARG cc_start: 0.7465 (ttt-90) cc_final: 0.6946 (ttt90) REVERT: C 84 GLU cc_start: 0.7677 (mp0) cc_final: 0.7272 (mm-30) REVERT: C 240 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: C 243 GLU cc_start: 0.8049 (tt0) cc_final: 0.7746 (tm-30) REVERT: C 266 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: C 380 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6478 (mpt) REVERT: C 471 MET cc_start: 0.6295 (ttp) cc_final: 0.6010 (ttm) REVERT: C 513 MET cc_start: 0.8077 (mtp) cc_final: 0.7630 (mtm) REVERT: C 519 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7581 (ttmt) REVERT: C 744 LYS cc_start: 0.7789 (mptm) cc_final: 0.7398 (mptp) REVERT: D 107 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7389 (mt-10) REVERT: D 230 LEU cc_start: 0.8078 (tp) cc_final: 0.7878 (tt) REVERT: D 243 GLU cc_start: 0.7774 (tt0) cc_final: 0.7529 (tt0) REVERT: D 266 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7735 (pt0) REVERT: D 291 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7452 (mptt) REVERT: D 369 CYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7500 (p) REVERT: D 468 GLU cc_start: 0.6531 (tt0) cc_final: 0.5801 (tm-30) REVERT: D 490 SER cc_start: 0.9055 (t) cc_final: 0.8782 (m) REVERT: D 506 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8658 (tp) REVERT: D 512 ARG cc_start: 0.8014 (mtp180) cc_final: 0.7694 (mtp180) REVERT: D 523 ILE cc_start: 0.7813 (mt) cc_final: 0.7570 (mt) REVERT: D 749 ASP cc_start: 0.7505 (m-30) cc_final: 0.7044 (m-30) outliers start: 101 outliers final: 23 residues processed: 527 average time/residue: 0.5329 time to fit residues: 325.1435 Evaluate side-chains 422 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 385 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 407 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 515 LEU 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 438 MET Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 638 GLU 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 732 SER Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 218 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 729 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 108 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 55 optimal weight: 0.0870 chunk 132 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 309 GLN A 563 ASN A 589 ASN A 625 ASN A 629 GLN B 258 GLN B 562 ASN B 662 ASN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.157138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.120968 restraints weight = 23083.982| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.90 r_work: 0.3070 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21643 Z= 0.142 Angle : 0.577 8.194 29326 Z= 0.304 Chirality : 0.040 0.187 3303 Planarity : 0.005 0.078 3610 Dihedral : 9.298 58.937 2983 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.82 % Favored : 97.02 % Rotamer: Outliers : 5.77 % Allowed : 14.51 % 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: 0.09 (0.16), residues: 2520 helix: 0.61 (0.12), residues: 1840 sheet: None (None), residues: 0 loop : -1.27 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 754 TYR 0.016 0.002 TYR B 524 PHE 0.031 0.002 PHE C 520 TRP 0.016 0.001 TRP A 410 HIS 0.008 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (21639) covalent geometry : angle 0.57636 / 0.30 (29318) SS BOND : bond 0.01523 / 0.75 ( 4) SS BOND : angle 1.93097 / 0.77 ( 8) hydrogen bonds : bond 0.04050 / 2.66 ( 1246) hydrogen bonds : angle 3.61242 / 2.51 ( 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 589 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 459 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 66 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7503 (mmm) REVERT: A 79 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7073 (mm-30) REVERT: A 147 MET cc_start: 0.8530 (mtp) cc_final: 0.8176 (mtp) REVERT: A 172 HIS cc_start: 0.5048 (OUTLIER) cc_final: 0.4609 (m-70) REVERT: A 222 ARG cc_start: 0.8334 (mtt180) cc_final: 0.8012 (mtm-85) REVERT: A 228 LYS cc_start: 0.8544 (tppt) cc_final: 0.8325 (tppp) REVERT: A 243 GLU cc_start: 0.8101 (tt0) cc_final: 0.7628 (tm-30) REVERT: A 262 SER cc_start: 0.9200 (OUTLIER) cc_final: 0.8887 (m) REVERT: A 266 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7182 (mt-10) REVERT: A 331 LEU cc_start: 0.8104 (tp) cc_final: 0.7712 (tt) REVERT: A 335 MET cc_start: 0.7427 (mtt) cc_final: 0.6897 (mtt) REVERT: A 353 ARG cc_start: 0.7550 (mtm110) cc_final: 0.7130 (mtm-85) REVERT: A 380 MET cc_start: 0.8241 (mtt) cc_final: 0.7984 (mtm) REVERT: A 416 TRP cc_start: 0.8017 (t-100) cc_final: 0.7489 (t-100) REVERT: A 437 LEU cc_start: 0.8596 (tp) cc_final: 0.8335 (tp) REVERT: A 442 MET cc_start: 0.8087 (ttt) cc_final: 0.7874 (ttm) REVERT: A 468 GLU cc_start: 0.8267 (tt0) cc_final: 0.7988 (tt0) REVERT: A 470 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: A 500 ASN cc_start: 0.9080 (t0) cc_final: 0.8772 (t0) REVERT: A 595 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7465 (mm-30) REVERT: A 630 LEU cc_start: 0.8434 (mt) cc_final: 0.8104 (mt) REVERT: A 652 ASP cc_start: 0.7746 (m-30) cc_final: 0.7502 (m-30) REVERT: B 79 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7356 (pt0) REVERT: B 84 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7717 (mt-10) REVERT: B 222 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7763 (mtm-85) REVERT: B 243 GLU cc_start: 0.8114 (tt0) cc_final: 0.7705 (tm-30) REVERT: B 247 GLN cc_start: 0.8907 (tt0) cc_final: 0.8550 (tt0) REVERT: B 266 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7458 (mt-10) REVERT: B 394 HIS cc_start: 0.5612 (OUTLIER) cc_final: 0.5047 (m-70) REVERT: B 410 TRP cc_start: 0.8547 (OUTLIER) cc_final: 0.6360 (m-90) REVERT: B 436 ASN cc_start: 0.8475 (m-40) cc_final: 0.8116 (m110) REVERT: B 500 ASN cc_start: 0.9035 (t0) cc_final: 0.8821 (t0) REVERT: B 545 ARG cc_start: 0.7636 (mtp180) cc_final: 0.7344 (mpp80) REVERT: B 548 ASP cc_start: 0.7109 (m-30) cc_final: 0.6103 (m-30) REVERT: B 711 GLN cc_start: 0.8038 (mt0) cc_final: 0.7835 (mt0) REVERT: C 71 ARG cc_start: 0.7781 (tpp80) cc_final: 0.7532 (ttt-90) REVERT: C 81 GLU cc_start: 0.6506 (mt-10) cc_final: 0.6171 (mt-10) REVERT: C 191 ARG cc_start: 0.7629 (mtp-110) cc_final: 0.7104 (ttm-80) REVERT: C 240 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7372 (mt-10) REVERT: C 243 GLU cc_start: 0.7913 (tt0) cc_final: 0.7593 (tm-30) REVERT: C 300 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7937 (mp0) REVERT: C 380 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6486 (mpt) REVERT: C 513 MET cc_start: 0.8074 (mtp) cc_final: 0.7584 (mtm) REVERT: C 519 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8053 (ttmt) REVERT: C 744 LYS cc_start: 0.7790 (mptm) cc_final: 0.7352 (mptp) REVERT: D 37 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7985 (mp) REVERT: D 66 MET cc_start: 0.7645 (tpp) cc_final: 0.7235 (tpp) REVERT: D 71 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7473 (tpt-90) REVERT: D 194 ARG cc_start: 0.7716 (tpp-160) cc_final: 0.6811 (ttp-110) REVERT: D 225 TRP cc_start: 0.8534 (t-100) cc_final: 0.8312 (t-100) REVERT: D 243 GLU cc_start: 0.7941 (tt0) cc_final: 0.7579 (tm-30) REVERT: D 257 ASP cc_start: 0.8361 (m-30) cc_final: 0.8160 (m-30) REVERT: D 266 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7757 (pt0) REVERT: D 291 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7892 (mtpt) REVERT: D 335 MET cc_start: 0.7624 (mmm) cc_final: 0.7098 (mtm) REVERT: D 343 MET cc_start: 0.7622 (mmt) cc_final: 0.7324 (mpm) REVERT: D 369 CYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7984 (p) REVERT: D 422 MET cc_start: 0.5811 (OUTLIER) cc_final: 0.5601 (mmm) REVERT: D 490 SER cc_start: 0.9159 (t) cc_final: 0.8846 (m) REVERT: D 512 ARG cc_start: 0.7831 (mtp180) cc_final: 0.7509 (mtp180) REVERT: D 559 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7028 (tt0) REVERT: D 629 GLN cc_start: 0.8556 (mt0) cc_final: 0.8348 (mt0) REVERT: D 645 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8504 (mtpt) REVERT: D 744 LYS cc_start: 0.7889 (mptm) cc_final: 0.7588 (mptp) REVERT: D 745 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6234 (mt-10) outliers start: 130 outliers final: 36 residues processed: 528 average time/residue: 0.5497 time to fit residues: 335.0462 Evaluate side-chains 459 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 405 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 47 THR 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 369 CYS 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 514 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 567 THR 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 250 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 521 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 603 THR Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 757 VAL 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 240 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 496 LEU 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 71 ARG Chi-restraints excluded: chain D residue 96 VAL 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 369 CYS Chi-restraints excluded: chain D residue 422 MET 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: 1.9990 chunk 40 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 309 GLN A 507 GLN A 533 ASN A 537 GLN A 551 ASN A 589 ASN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 533 ASN C 562 ASN C 625 ASN D 80 ASN ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN D 308 GLN D 396 GLN D 507 GLN D 533 ASN D 589 ASN D 662 ASN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.144293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.107253 restraints weight = 22846.200| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.86 r_work: 0.2873 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 21643 Z= 0.248 Angle : 0.696 9.110 29326 Z= 0.360 Chirality : 0.044 0.244 3303 Planarity : 0.005 0.101 3610 Dihedral : 9.796 59.966 2980 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.61 % Favored : 96.23 % Rotamer: Outliers : 6.39 % Allowed : 15.93 % Favored : 77.67 % 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: 0.38 (0.16), residues: 2520 helix: 0.82 (0.12), residues: 1820 sheet: None (None), residues: 0 loop : -1.11 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 71 TYR 0.019 0.002 TYR B 524 PHE 0.029 0.003 PHE D 520 TRP 0.022 0.002 TRP A 327 HIS 0.006 0.001 HIS C 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.25 (21639) covalent geometry : angle 0.69533 / 0.36 (29318) SS BOND : bond 0.00976 / 0.49 ( 4) SS BOND : angle 1.17887 / 0.48 ( 8) hydrogen bonds : bond 0.04768 / 3.14 ( 1246) hydrogen bonds : angle 3.71591 / 2.58 ( 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 609 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 465 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 66 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7384 (mmm) REVERT: A 147 MET cc_start: 0.8916 (mtp) cc_final: 0.8576 (mtp) REVERT: A 172 HIS cc_start: 0.5776 (OUTLIER) cc_final: 0.4715 (m-70) REVERT: A 222 ARG cc_start: 0.8384 (mtt180) cc_final: 0.8059 (mtm-85) REVERT: A 243 GLU cc_start: 0.8289 (tt0) cc_final: 0.7847 (tm-30) REVERT: A 262 SER cc_start: 0.9181 (OUTLIER) cc_final: 0.8853 (m) REVERT: A 266 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7315 (mt-10) REVERT: A 331 LEU cc_start: 0.8198 (tp) cc_final: 0.7812 (tt) REVERT: A 335 MET cc_start: 0.7672 (mtt) cc_final: 0.7193 (mtm) REVERT: A 380 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8018 (mtm) REVERT: A 416 TRP cc_start: 0.8062 (t-100) cc_final: 0.7448 (t-100) REVERT: A 420 LYS cc_start: 0.7335 (ttmm) cc_final: 0.7119 (ttmm) REVERT: A 437 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8298 (tp) REVERT: A 468 GLU cc_start: 0.8459 (tt0) cc_final: 0.8000 (tt0) REVERT: A 470 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7660 (pt0) REVERT: A 500 ASN cc_start: 0.9066 (t0) cc_final: 0.8795 (t0) REVERT: A 595 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7884 (mm-30) REVERT: A 625 ASN cc_start: 0.8242 (m-40) cc_final: 0.7701 (m-40) REVERT: A 652 ASP cc_start: 0.7728 (m-30) cc_final: 0.7492 (m-30) REVERT: B 71 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.8438 (mmm-85) REVERT: B 81 GLU cc_start: 0.6327 (mt-10) cc_final: 0.6016 (mt-10) REVERT: B 84 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7771 (mt-10) REVERT: B 191 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7489 (ttm110) REVERT: B 222 ARG cc_start: 0.8292 (mtt180) cc_final: 0.7896 (mtm-85) REVERT: B 243 GLU cc_start: 0.8134 (tt0) cc_final: 0.7738 (tm-30) REVERT: B 247 GLN cc_start: 0.8866 (tt0) cc_final: 0.8524 (tt0) REVERT: B 266 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7417 (mt-10) REVERT: B 335 MET cc_start: 0.7871 (mtt) cc_final: 0.7624 (mtt) REVERT: B 359 PHE cc_start: 0.8465 (t80) cc_final: 0.8244 (t80) REVERT: B 410 TRP cc_start: 0.8666 (OUTLIER) cc_final: 0.7178 (m-90) REVERT: B 436 ASN cc_start: 0.8844 (m-40) cc_final: 0.8497 (m-40) REVERT: B 438 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7922 (ttt) REVERT: B 500 ASN cc_start: 0.9107 (t0) cc_final: 0.8877 (t0) REVERT: B 519 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7871 (mtpm) REVERT: B 529 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8549 (mt) REVERT: B 545 ARG cc_start: 0.8417 (mtp180) cc_final: 0.7916 (mtm110) REVERT: B 554 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8440 (tttp) REVERT: B 711 GLN cc_start: 0.8314 (mt0) cc_final: 0.8100 (mt0) REVERT: B 715 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7892 (mm-30) REVERT: B 729 ILE cc_start: 0.7783 (pp) cc_final: 0.7534 (mt) REVERT: C 71 ARG cc_start: 0.8124 (tpp80) cc_final: 0.7901 (mmm-85) REVERT: C 84 GLU cc_start: 0.7785 (mp0) cc_final: 0.7436 (mt-10) REVERT: C 106 LYS cc_start: 0.8420 (mtpm) cc_final: 0.8115 (ttmt) REVERT: C 190 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8477 (tt) REVERT: C 191 ARG cc_start: 0.7928 (mtp-110) cc_final: 0.7357 (ttm-80) REVERT: C 240 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: C 243 GLU cc_start: 0.8199 (tt0) cc_final: 0.7834 (tm-30) REVERT: C 266 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: C 380 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.6783 (mpt) REVERT: C 382 LEU cc_start: 0.8227 (tp) cc_final: 0.7978 (mt) REVERT: C 450 ILE cc_start: 0.8156 (mm) cc_final: 0.7902 (mt) REVERT: C 454 ILE cc_start: 0.8007 (mm) cc_final: 0.7708 (mt) REVERT: C 490 SER cc_start: 0.9288 (OUTLIER) cc_final: 0.8760 (m) REVERT: C 519 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8386 (ttmt) REVERT: C 529 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8615 (mt) REVERT: C 595 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7614 (mt-10) REVERT: C 729 ILE cc_start: 0.8084 (pp) cc_final: 0.7870 (mt) REVERT: C 744 LYS cc_start: 0.7989 (mptm) cc_final: 0.7617 (mptp) REVERT: C 756 GLU cc_start: 0.8119 (tt0) cc_final: 0.7884 (tt0) REVERT: D 71 ARG cc_start: 0.7955 (ttt-90) cc_final: 0.7649 (mmm160) REVERT: D 223 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8722 (tp) REVERT: D 240 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: D 243 GLU cc_start: 0.8191 (tt0) cc_final: 0.7804 (tm-30) REVERT: D 291 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8296 (mtpt) REVERT: D 335 MET cc_start: 0.7900 (mmm) cc_final: 0.7421 (mtm) REVERT: D 343 MET cc_start: 0.7529 (mmt) cc_final: 0.7202 (mpm) REVERT: D 369 CYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8090 (p) REVERT: D 410 TRP cc_start: 0.8562 (OUTLIER) cc_final: 0.7853 (m-90) REVERT: D 436 ASN cc_start: 0.8540 (m-40) cc_final: 0.8102 (m-40) REVERT: D 508 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8232 (mm) REVERT: D 553 CYS cc_start: 0.7153 (t) cc_final: 0.6659 (t) REVERT: D 587 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8876 (m) REVERT: D 591 LYS cc_start: 0.8578 (tmmt) cc_final: 0.8259 (ttmm) REVERT: D 595 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7763 (mm-30) REVERT: D 747 LYS cc_start: 0.8363 (mttt) cc_final: 0.8018 (mtmt) outliers start: 144 outliers final: 50 residues processed: 539 average time/residue: 0.5463 time to fit residues: 339.4424 Evaluate side-chains 495 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 420 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 96 VAL 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 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 437 LEU Chi-restraints excluded: chain A residue 470 GLU 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 656 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 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 490 SER Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 547 ILE 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 656 THR Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 75 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 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 490 SER 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 98 ASP Chi-restraints excluded: chain D residue 223 LEU 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 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 514 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 519 LYS 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: 0.9980 chunk 167 optimal weight: 0.0070 chunk 232 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 241 optimal weight: 0.5980 chunk 190 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 533 ASN A 589 ASN A 629 GLN ** 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 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS C 533 ASN C 562 ASN C 625 ASN D 82 ASN D 533 ASN D 552 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.147439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.111501 restraints weight = 22602.175| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.85 r_work: 0.2920 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21643 Z= 0.133 Angle : 0.575 10.446 29326 Z= 0.299 Chirality : 0.039 0.142 3303 Planarity : 0.005 0.100 3610 Dihedral : 9.213 59.802 2980 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.98 % Favored : 96.87 % Rotamer: Outliers : 5.64 % Allowed : 18.51 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.90 (0.17), residues: 2520 helix: 1.26 (0.12), residues: 1824 sheet: None (None), residues: 0 loop : -1.12 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 512 TYR 0.037 0.001 TYR D 348 PHE 0.017 0.002 PHE C 520 TRP 0.022 0.001 TRP A 327 HIS 0.005 0.001 HIS A 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (21639) covalent geometry : angle 0.57238 / 0.30 (29318) SS BOND : bond 0.00537 / 0.27 ( 4) SS BOND : angle 3.32815 / 1.05 ( 8) hydrogen bonds : bond 0.03969 / 2.60 ( 1246) hydrogen bonds : angle 3.47447 / 2.41 ( 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 564 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 437 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 66 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7280 (mmm) REVERT: A 147 MET cc_start: 0.8784 (mtp) cc_final: 0.8474 (mtp) REVERT: A 172 HIS cc_start: 0.5556 (OUTLIER) cc_final: 0.4655 (m-70) REVERT: A 222 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7947 (mtm-85) REVERT: A 243 GLU cc_start: 0.8230 (tt0) cc_final: 0.7761 (tm-30) REVERT: A 246 GLN cc_start: 0.8248 (tp-100) cc_final: 0.7964 (mp10) REVERT: A 262 SER cc_start: 0.9095 (OUTLIER) cc_final: 0.8812 (m) REVERT: A 266 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 331 LEU cc_start: 0.8085 (tp) cc_final: 0.7700 (tt) REVERT: A 335 MET cc_start: 0.7535 (mtt) cc_final: 0.7039 (mtm) REVERT: A 343 MET cc_start: 0.7908 (tpt) cc_final: 0.7661 (tpt) REVERT: A 380 MET cc_start: 0.8275 (mtt) cc_final: 0.7969 (mtm) REVERT: A 438 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8173 (ttt) REVERT: A 442 MET cc_start: 0.8283 (ttt) cc_final: 0.8006 (ttm) REVERT: A 468 GLU cc_start: 0.8273 (tt0) cc_final: 0.7899 (tt0) REVERT: A 470 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7605 (pt0) REVERT: A 500 ASN cc_start: 0.9058 (t0) cc_final: 0.8778 (t0) REVERT: A 587 VAL cc_start: 0.8647 (t) cc_final: 0.8253 (m) REVERT: A 595 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7853 (mm-30) REVERT: A 652 ASP cc_start: 0.7611 (m-30) cc_final: 0.7365 (m-30) REVERT: A 711 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8245 (mt0) REVERT: B 84 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7794 (mt-10) REVERT: B 191 ARG cc_start: 0.7720 (mtp-110) cc_final: 0.7511 (ttm110) REVERT: B 222 ARG cc_start: 0.8219 (mtt180) cc_final: 0.7821 (mtm-85) REVERT: B 243 GLU cc_start: 0.8149 (tt0) cc_final: 0.7725 (tm-30) REVERT: B 247 GLN cc_start: 0.8830 (tt0) cc_final: 0.8471 (tt0) REVERT: B 266 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7386 (mt-10) REVERT: B 436 ASN cc_start: 0.8789 (m-40) cc_final: 0.8380 (m110) REVERT: B 500 ASN cc_start: 0.9109 (t0) cc_final: 0.8863 (t0) REVERT: B 529 LEU cc_start: 0.8773 (mm) cc_final: 0.8508 (mt) REVERT: B 545 ARG cc_start: 0.8105 (mtp180) cc_final: 0.7828 (mtm110) REVERT: B 548 ASP cc_start: 0.7776 (m-30) cc_final: 0.6763 (m-30) REVERT: B 554 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7790 (tttp) REVERT: B 631 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7352 (mt) REVERT: B 715 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7934 (mm-30) REVERT: C 71 ARG cc_start: 0.8102 (tpp80) cc_final: 0.7639 (mmm-85) REVERT: C 84 GLU cc_start: 0.8006 (mp0) cc_final: 0.7604 (mt-10) REVERT: C 106 LYS cc_start: 0.8309 (mtpm) cc_final: 0.8005 (ttmt) REVERT: C 191 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7409 (ttm-80) REVERT: C 240 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: C 243 GLU cc_start: 0.8103 (tt0) cc_final: 0.7703 (tm-30) REVERT: C 380 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.6706 (mpt) REVERT: C 395 VAL cc_start: 0.8370 (t) cc_final: 0.8134 (t) REVERT: C 450 ILE cc_start: 0.8025 (mm) cc_final: 0.7787 (mt) REVERT: C 454 ILE cc_start: 0.7998 (mm) cc_final: 0.7736 (mt) REVERT: C 508 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8157 (mm) REVERT: C 519 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8368 (ttmt) REVERT: C 529 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8513 (mt) REVERT: C 744 LYS cc_start: 0.7854 (mptm) cc_final: 0.7477 (mptp) REVERT: C 756 GLU cc_start: 0.8012 (tt0) cc_final: 0.7741 (tt0) REVERT: D 66 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.6934 (mtm) REVERT: D 223 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8719 (tp) REVERT: D 240 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: D 243 GLU cc_start: 0.8059 (tt0) cc_final: 0.7651 (tm-30) REVERT: D 291 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8059 (mppt) REVERT: D 335 MET cc_start: 0.7838 (mmm) cc_final: 0.7365 (mtm) REVERT: D 343 MET cc_start: 0.7475 (mmt) cc_final: 0.7127 (mpm) REVERT: D 359 PHE cc_start: 0.7990 (t80) cc_final: 0.7768 (t80) REVERT: D 369 CYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8026 (p) REVERT: D 410 TRP cc_start: 0.8424 (OUTLIER) cc_final: 0.7675 (m-90) REVERT: D 422 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.6095 (mmm) REVERT: D 436 ASN cc_start: 0.8459 (m-40) cc_final: 0.7983 (m-40) REVERT: D 508 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8180 (mm) REVERT: D 553 CYS cc_start: 0.7104 (t) cc_final: 0.6629 (t) REVERT: D 559 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: D 587 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8735 (m) REVERT: D 595 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7727 (mm-30) REVERT: D 645 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8581 (mtpt) REVERT: D 744 LYS cc_start: 0.8097 (mptt) cc_final: 0.7423 (mptp) REVERT: D 747 LYS cc_start: 0.8294 (mttt) cc_final: 0.7951 (mtmt) outliers start: 127 outliers final: 51 residues processed: 497 average time/residue: 0.5292 time to fit residues: 303.8472 Evaluate side-chains 486 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 412 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 96 VAL 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 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 521 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 656 THR 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 86 MET Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 631 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 B residue 758 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 508 ILE 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 66 MET Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 223 LEU 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 394 HIS 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 514 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 559 GLU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 729 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 67 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 236 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 ASN A 533 ASN A 584 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 533 ASN B 625 ASN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 536 ASN C 562 ASN C 625 ASN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.146385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.108738 restraints weight = 22511.789| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.92 r_work: 0.2912 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.6194 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= 0.144 Angle : 0.570 10.160 29326 Z= 0.295 Chirality : 0.040 0.136 3303 Planarity : 0.005 0.104 3610 Dihedral : 8.940 59.821 2980 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.45 % Favored : 96.39 % Rotamer: Outliers : 5.86 % Allowed : 18.95 % Favored : 75.19 % 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: 1.15 (0.17), residues: 2520 helix: 1.46 (0.12), residues: 1828 sheet: None (None), residues: 0 loop : -1.09 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 71 TYR 0.035 0.002 TYR B 58 PHE 0.016 0.002 PHE C 341 TRP 0.019 0.001 TRP A 327 HIS 0.004 0.001 HIS A 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (21639) covalent geometry : angle 0.56894 / 0.29 (29318) SS BOND : bond 0.00393 / 0.19 ( 4) SS BOND : angle 2.29252 / 0.75 ( 8) hydrogen bonds : bond 0.03960 / 2.59 ( 1246) hydrogen bonds : angle 3.41767 / 2.36 ( 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 574 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 442 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 71 ARG cc_start: 0.8311 (mmm160) cc_final: 0.8006 (mmm-85) REVERT: A 136 PHE cc_start: 0.8382 (t80) cc_final: 0.8086 (t80) REVERT: A 147 MET cc_start: 0.8966 (mtp) cc_final: 0.8644 (mtp) REVERT: A 172 HIS cc_start: 0.5784 (OUTLIER) cc_final: 0.4919 (m-70) REVERT: A 173 GLN cc_start: 0.4457 (OUTLIER) cc_final: 0.3955 (tt0) REVERT: A 194 ARG cc_start: 0.8391 (tpp-160) cc_final: 0.6800 (ttm110) REVERT: A 222 ARG cc_start: 0.8567 (mtt180) cc_final: 0.8150 (mtm-85) REVERT: A 243 GLU cc_start: 0.8471 (tt0) cc_final: 0.7995 (tm-30) REVERT: A 246 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8145 (mp10) REVERT: A 262 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8875 (m) REVERT: A 266 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7645 (mt-10) REVERT: A 331 LEU cc_start: 0.7962 (tp) cc_final: 0.7674 (tt) REVERT: A 335 MET cc_start: 0.7632 (mtt) cc_final: 0.7157 (mtt) REVERT: A 343 MET cc_start: 0.7955 (tpt) cc_final: 0.7716 (tpt) REVERT: A 380 MET cc_start: 0.8428 (mtt) cc_final: 0.8128 (mtm) REVERT: A 438 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8152 (ttt) REVERT: A 468 GLU cc_start: 0.8366 (tt0) cc_final: 0.7896 (tt0) REVERT: A 470 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: A 500 ASN cc_start: 0.9157 (t0) cc_final: 0.8901 (t0) REVERT: A 595 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8027 (mm-30) REVERT: A 652 ASP cc_start: 0.7830 (m-30) cc_final: 0.7556 (m-30) REVERT: B 84 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7949 (mt-10) REVERT: B 172 HIS cc_start: 0.4636 (OUTLIER) cc_final: 0.4424 (m-70) REVERT: B 190 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8433 (tt) REVERT: B 191 ARG cc_start: 0.7997 (mtp-110) cc_final: 0.7770 (ttm110) REVERT: B 222 ARG cc_start: 0.8533 (mtt180) cc_final: 0.8087 (mtm-85) REVERT: B 243 GLU cc_start: 0.8293 (tt0) cc_final: 0.7850 (tm-30) REVERT: B 247 GLN cc_start: 0.8937 (tt0) cc_final: 0.8611 (tt0) REVERT: B 266 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7641 (mm-30) REVERT: B 436 ASN cc_start: 0.8889 (m-40) cc_final: 0.8489 (m110) REVERT: B 500 ASN cc_start: 0.9232 (t0) cc_final: 0.9018 (t0) REVERT: B 519 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8199 (mtpm) REVERT: B 529 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8628 (mt) REVERT: B 631 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7416 (mt) REVERT: C 84 GLU cc_start: 0.8214 (mp0) cc_final: 0.7782 (mt-10) REVERT: C 106 LYS cc_start: 0.8353 (mtpm) cc_final: 0.8081 (ttmt) REVERT: C 190 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8428 (tt) REVERT: C 191 ARG cc_start: 0.8152 (mtp-110) cc_final: 0.7263 (ttm170) REVERT: C 240 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: C 243 GLU cc_start: 0.8413 (tt0) cc_final: 0.8001 (tm-30) REVERT: C 257 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8258 (m-30) REVERT: C 266 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7989 (mp0) REVERT: C 380 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.6995 (mpt) REVERT: C 395 VAL cc_start: 0.8407 (t) cc_final: 0.8179 (t) REVERT: C 421 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6810 (tm-30) REVERT: C 436 ASN cc_start: 0.8481 (m-40) cc_final: 0.7986 (m110) REVERT: C 454 ILE cc_start: 0.8052 (mm) cc_final: 0.7831 (mt) REVERT: C 508 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8231 (mm) REVERT: C 519 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8436 (ttmt) REVERT: C 529 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8596 (mt) REVERT: C 558 CYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6400 (t) REVERT: C 744 LYS cc_start: 0.7963 (mptm) cc_final: 0.7581 (mptp) REVERT: C 756 GLU cc_start: 0.8203 (tt0) cc_final: 0.7977 (tt0) REVERT: D 66 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.6986 (mtm) REVERT: D 194 ARG cc_start: 0.8353 (tpp-160) cc_final: 0.6946 (ttp-110) REVERT: D 223 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8776 (tp) REVERT: D 243 GLU cc_start: 0.8369 (tt0) cc_final: 0.7945 (tm-30) REVERT: D 266 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7909 (mp0) REVERT: D 291 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8156 (mppt) REVERT: D 343 MET cc_start: 0.7560 (mmt) cc_final: 0.7228 (mpm) REVERT: D 359 PHE cc_start: 0.8024 (t80) cc_final: 0.7732 (t80) REVERT: D 369 CYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8048 (p) REVERT: D 410 TRP cc_start: 0.8476 (OUTLIER) cc_final: 0.7586 (m-90) REVERT: D 422 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6300 (mmm) REVERT: D 436 ASN cc_start: 0.8596 (m-40) cc_final: 0.8183 (m110) REVERT: D 508 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8203 (mm) REVERT: D 553 CYS cc_start: 0.7624 (t) cc_final: 0.7186 (t) REVERT: D 559 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: D 587 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8781 (m) REVERT: D 595 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7970 (mm-30) REVERT: D 744 LYS cc_start: 0.8121 (mptt) cc_final: 0.7454 (mptp) REVERT: D 747 LYS cc_start: 0.8436 (mttt) cc_final: 0.8137 (mtmt) outliers start: 132 outliers final: 53 residues processed: 510 average time/residue: 0.5677 time to fit residues: 333.8092 Evaluate side-chains 501 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 420 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 246 GLN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 262 SER 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 637 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 86 MET 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 394 HIS 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 562 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 656 THR 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 B residue 758 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 75 LEU 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 250 LEU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 508 ILE 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 558 CYS Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 223 LEU 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 394 HIS 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 514 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 559 GLU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 729 ILE 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: 0.6980 chunk 127 optimal weight: 0.7980 chunk 249 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 221 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 436 ASN 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 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS C 396 GLN C 533 ASN C 536 ASN C 562 ASN C 625 ASN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.147168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109791 restraints weight = 22542.491| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.95 r_work: 0.2971 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.6299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21643 Z= 0.128 Angle : 0.566 12.155 29326 Z= 0.289 Chirality : 0.039 0.142 3303 Planarity : 0.005 0.105 3610 Dihedral : 8.674 59.799 2980 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.75 % Rotamer: Outliers : 5.46 % Allowed : 20.64 % Favored : 73.90 % 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: 1.34 (0.17), residues: 2520 helix: 1.61 (0.12), residues: 1828 sheet: None (None), residues: 0 loop : -1.02 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 71 TYR 0.032 0.001 TYR D 348 PHE 0.016 0.002 PHE B 341 TRP 0.016 0.001 TRP A 327 HIS 0.004 0.001 HIS A 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (21639) covalent geometry : angle 0.56585 / 0.29 (29318) SS BOND : bond 0.00397 / 0.20 ( 4) SS BOND : angle 1.67083 / 0.56 ( 8) hydrogen bonds : bond 0.03767 / 2.47 ( 1246) hydrogen bonds : angle 3.36606 / 2.33 ( 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 564 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 441 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 67 ASP cc_start: 0.6537 (OUTLIER) cc_final: 0.5738 (m-30) REVERT: A 79 GLU cc_start: 0.7370 (pt0) cc_final: 0.7102 (mt-10) REVERT: A 136 PHE cc_start: 0.8261 (t80) cc_final: 0.7832 (t80) REVERT: A 147 MET cc_start: 0.8902 (mtp) cc_final: 0.8557 (mtp) REVERT: A 172 HIS cc_start: 0.5564 (OUTLIER) cc_final: 0.4845 (m-70) REVERT: A 173 GLN cc_start: 0.4387 (OUTLIER) cc_final: 0.3990 (tt0) REVERT: A 194 ARG cc_start: 0.8325 (tpp-160) cc_final: 0.8069 (tpt170) REVERT: A 222 ARG cc_start: 0.8479 (mtt180) cc_final: 0.8078 (mtm-85) REVERT: A 243 GLU cc_start: 0.8380 (tt0) cc_final: 0.7901 (tm-30) REVERT: A 246 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8063 (mp10) REVERT: A 262 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8851 (m) REVERT: A 266 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7536 (mt-10) REVERT: A 331 LEU cc_start: 0.7932 (tp) cc_final: 0.7576 (tt) REVERT: A 335 MET cc_start: 0.7586 (mtt) cc_final: 0.7112 (mtm) REVERT: A 343 MET cc_start: 0.7927 (tpt) cc_final: 0.7679 (tpt) REVERT: A 380 MET cc_start: 0.8299 (mtt) cc_final: 0.7974 (mtm) REVERT: A 438 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8123 (ttt) REVERT: A 442 MET cc_start: 0.8309 (ttt) cc_final: 0.8040 (ttm) REVERT: A 468 GLU cc_start: 0.8330 (tt0) cc_final: 0.7937 (tt0) REVERT: A 470 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: A 500 ASN cc_start: 0.9114 (t0) cc_final: 0.8844 (t0) REVERT: A 587 VAL cc_start: 0.8577 (t) cc_final: 0.8198 (m) REVERT: A 595 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7946 (mm-30) REVERT: A 652 ASP cc_start: 0.7755 (m-30) cc_final: 0.7497 (m-30) REVERT: A 711 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: B 84 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7869 (mt-10) REVERT: B 136 PHE cc_start: 0.8270 (t80) cc_final: 0.7953 (t80) REVERT: B 172 HIS cc_start: 0.4621 (OUTLIER) cc_final: 0.4397 (m-70) REVERT: B 190 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8407 (tt) REVERT: B 191 ARG cc_start: 0.7896 (mtp-110) cc_final: 0.7181 (ttm-80) REVERT: B 222 ARG cc_start: 0.8470 (mtt180) cc_final: 0.8020 (mtm-85) REVERT: B 243 GLU cc_start: 0.8239 (tt0) cc_final: 0.7791 (tm-30) REVERT: B 247 GLN cc_start: 0.8894 (tt0) cc_final: 0.8557 (tt0) REVERT: B 266 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7503 (mm-30) REVERT: B 404 GLU cc_start: 0.5905 (mm-30) cc_final: 0.5215 (tm-30) REVERT: B 436 ASN cc_start: 0.8880 (m-40) cc_final: 0.8469 (m110) REVERT: B 500 ASN cc_start: 0.9204 (t0) cc_final: 0.8977 (t0) REVERT: B 529 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8598 (mt) REVERT: B 634 HIS cc_start: 0.7840 (m170) cc_final: 0.6829 (t70) REVERT: C 84 GLU cc_start: 0.8134 (mp0) cc_final: 0.7690 (mt-10) REVERT: C 106 LYS cc_start: 0.8269 (mtpm) cc_final: 0.8030 (ttmm) REVERT: C 190 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8387 (tt) REVERT: C 191 ARG cc_start: 0.8048 (mtp-110) cc_final: 0.7243 (ttm170) REVERT: C 240 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: C 243 GLU cc_start: 0.8328 (tt0) cc_final: 0.7913 (tm-30) REVERT: C 257 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8164 (m-30) REVERT: C 266 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7782 (mp0) REVERT: C 343 MET cc_start: 0.7261 (mmt) cc_final: 0.7029 (tpt) REVERT: C 380 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.6912 (mpt) REVERT: C 395 VAL cc_start: 0.8402 (t) cc_final: 0.8182 (t) REVERT: C 421 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6716 (tm-30) REVERT: C 436 ASN cc_start: 0.8533 (m-40) cc_final: 0.8001 (m110) REVERT: C 454 ILE cc_start: 0.8003 (mm) cc_final: 0.7802 (mt) REVERT: C 508 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8147 (mm) REVERT: C 519 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8404 (ttmt) REVERT: C 529 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8533 (mt) REVERT: C 558 CYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6300 (t) REVERT: C 744 LYS cc_start: 0.7965 (mptm) cc_final: 0.7579 (mptp) REVERT: C 756 GLU cc_start: 0.8073 (tt0) cc_final: 0.7866 (tt0) REVERT: D 66 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6956 (mtm) REVERT: D 194 ARG cc_start: 0.8147 (tpp-160) cc_final: 0.6651 (ttp-110) REVERT: D 223 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8829 (tp) REVERT: D 243 GLU cc_start: 0.8314 (tt0) cc_final: 0.7879 (tm-30) REVERT: D 266 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7780 (mp0) REVERT: D 291 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8132 (mppt) REVERT: D 335 MET cc_start: 0.7901 (mmm) cc_final: 0.7370 (mtm) REVERT: D 343 MET cc_start: 0.7521 (mmt) cc_final: 0.7257 (mpm) REVERT: D 359 PHE cc_start: 0.8004 (t80) cc_final: 0.7725 (t80) REVERT: D 369 CYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8075 (p) REVERT: D 410 TRP cc_start: 0.8386 (OUTLIER) cc_final: 0.7394 (m-90) REVERT: D 422 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6252 (mmm) REVERT: D 436 ASN cc_start: 0.8587 (m-40) cc_final: 0.8187 (m110) REVERT: D 470 GLU cc_start: 0.7328 (pt0) cc_final: 0.7063 (tt0) REVERT: D 508 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8130 (mm) REVERT: D 553 CYS cc_start: 0.7516 (t) cc_final: 0.7077 (t) REVERT: D 559 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: D 587 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8754 (m) REVERT: D 744 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7462 (mptp) REVERT: D 747 LYS cc_start: 0.8398 (mttt) cc_final: 0.8106 (mtmt) outliers start: 123 outliers final: 50 residues processed: 497 average time/residue: 0.5511 time to fit residues: 315.8081 Evaluate side-chains 505 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 426 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 69 LEU 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 246 GLN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 262 SER 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 711 GLN Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 521 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 575 LEU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 747 LYS Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 VAL 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 257 ASP Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 508 ILE 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 568 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN 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 410 TRP 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 521 LEU 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 652 ASP Chi-restraints excluded: chain D residue 729 ILE Chi-restraints excluded: chain D residue 744 LYS Chi-restraints excluded: chain D residue 756 GLU 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: 1.9990 chunk 240 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 173 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 B 735 ASN ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 625 ASN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN 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 = 0.3579 r_free = 0.3579 target = 0.146443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.107501 restraints weight = 22583.821| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.96 r_work: 0.2936 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.6433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21643 Z= 0.136 Angle : 0.575 12.206 29326 Z= 0.292 Chirality : 0.039 0.141 3303 Planarity : 0.004 0.108 3610 Dihedral : 8.524 59.563 2980 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.17 % Favored : 96.67 % Rotamer: Outliers : 5.06 % Allowed : 21.13 % Favored : 73.81 % 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: 1.42 (0.17), residues: 2520 helix: 1.66 (0.12), residues: 1828 sheet: None (None), residues: 0 loop : -0.97 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 71 TYR 0.030 0.001 TYR D 348 PHE 0.016 0.002 PHE B 341 TRP 0.017 0.001 TRP B 472 HIS 0.004 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (21639) covalent geometry : angle 0.57432 / 0.29 (29318) SS BOND : bond 0.00449 / 0.22 ( 4) SS BOND : angle 1.57848 / 0.54 ( 8) hydrogen bonds : bond 0.03802 / 2.49 ( 1246) hydrogen bonds : angle 3.36839 / 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 556 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 442 time to evaluate : 0.970 Fit side-chains REVERT: A 79 GLU cc_start: 0.7417 (pt0) cc_final: 0.6993 (mt-10) REVERT: A 147 MET cc_start: 0.8893 (mtp) cc_final: 0.8504 (mtp) REVERT: A 172 HIS cc_start: 0.5401 (OUTLIER) cc_final: 0.4596 (m-70) REVERT: A 173 GLN cc_start: 0.4310 (OUTLIER) cc_final: 0.3891 (tt0) REVERT: A 194 ARG cc_start: 0.8289 (tpp-160) cc_final: 0.8073 (tpt170) REVERT: A 222 ARG cc_start: 0.8511 (mtt180) cc_final: 0.8096 (mtm-85) REVERT: A 243 GLU cc_start: 0.8356 (tt0) cc_final: 0.7852 (tm-30) REVERT: A 246 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: A 262 SER cc_start: 0.9068 (OUTLIER) cc_final: 0.8808 (m) REVERT: A 266 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7528 (mm-30) REVERT: A 331 LEU cc_start: 0.7872 (tp) cc_final: 0.7506 (tt) REVERT: A 335 MET cc_start: 0.7541 (mtt) cc_final: 0.7060 (mtm) REVERT: A 343 MET cc_start: 0.7989 (tpt) cc_final: 0.7724 (tpt) REVERT: A 380 MET cc_start: 0.8272 (mtt) cc_final: 0.7932 (mtm) REVERT: A 404 GLU cc_start: 0.6095 (tm-30) cc_final: 0.5876 (tm-30) REVERT: A 436 ASN cc_start: 0.8620 (m-40) cc_final: 0.8385 (m-40) REVERT: A 438 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8110 (ttt) REVERT: A 442 MET cc_start: 0.8265 (ttt) cc_final: 0.7983 (ttm) REVERT: A 468 GLU cc_start: 0.8301 (tt0) cc_final: 0.7866 (tt0) REVERT: A 470 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: A 500 ASN cc_start: 0.9122 (t0) cc_final: 0.8838 (t0) REVERT: A 537 GLN cc_start: 0.8851 (tp40) cc_final: 0.8614 (tp40) REVERT: A 587 VAL cc_start: 0.8611 (t) cc_final: 0.8188 (m) REVERT: A 595 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7998 (mm-30) REVERT: A 711 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: B 71 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.8043 (mmm-85) REVERT: B 84 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7855 (mt-10) REVERT: B 136 PHE cc_start: 0.8274 (t80) cc_final: 0.7947 (t80) REVERT: B 172 HIS cc_start: 0.4779 (OUTLIER) cc_final: 0.4545 (m-70) REVERT: B 190 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8348 (tt) REVERT: B 191 ARG cc_start: 0.7891 (mtp-110) cc_final: 0.7116 (ttm-80) REVERT: B 222 ARG cc_start: 0.8464 (mtt180) cc_final: 0.7987 (mtm-85) REVERT: B 243 GLU cc_start: 0.8256 (tt0) cc_final: 0.7796 (tm-30) REVERT: B 247 GLN cc_start: 0.8892 (tt0) cc_final: 0.8559 (tt0) REVERT: B 266 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7521 (mm-30) REVERT: B 404 GLU cc_start: 0.5982 (mm-30) cc_final: 0.5335 (tm-30) REVERT: B 436 ASN cc_start: 0.8866 (m-40) cc_final: 0.8481 (m-40) REVERT: B 500 ASN cc_start: 0.9216 (t0) cc_final: 0.8975 (t0) REVERT: B 529 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8562 (mt) REVERT: B 631 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7646 (mt) REVERT: C 84 GLU cc_start: 0.8167 (mp0) cc_final: 0.7708 (mt-10) REVERT: C 106 LYS cc_start: 0.8302 (mtpm) cc_final: 0.8018 (ttmm) REVERT: C 190 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8381 (tt) REVERT: C 191 ARG cc_start: 0.8043 (mtp-110) cc_final: 0.7129 (ttm170) REVERT: C 240 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: C 243 GLU cc_start: 0.8320 (tt0) cc_final: 0.7885 (tm-30) REVERT: C 257 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: C 319 PHE cc_start: 0.6538 (m-10) cc_final: 0.6297 (m-10) REVERT: C 380 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7687 (mtt) REVERT: C 395 VAL cc_start: 0.8496 (t) cc_final: 0.8272 (t) REVERT: C 421 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6730 (tm-30) REVERT: C 436 ASN cc_start: 0.8519 (m-40) cc_final: 0.7980 (m110) REVERT: C 508 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8116 (mm) REVERT: C 519 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8358 (ptpp) REVERT: C 529 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8512 (mt) REVERT: C 595 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7897 (mm-30) REVERT: C 744 LYS cc_start: 0.7887 (mptm) cc_final: 0.7479 (mptp) REVERT: C 745 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6994 (mt-10) REVERT: D 66 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.6984 (mtm) REVERT: D 81 GLU cc_start: 0.7104 (mt-10) cc_final: 0.5931 (mp0) REVERT: D 194 ARG cc_start: 0.8146 (tpp-160) cc_final: 0.6576 (ttp-110) REVERT: D 223 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8798 (tp) REVERT: D 243 GLU cc_start: 0.8348 (tt0) cc_final: 0.7886 (tm-30) REVERT: D 291 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8136 (mppt) REVERT: D 343 MET cc_start: 0.7492 (mmt) cc_final: 0.7231 (mpm) REVERT: D 359 PHE cc_start: 0.7980 (t80) cc_final: 0.7671 (t80) REVERT: D 369 CYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8097 (p) REVERT: D 422 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6292 (mmm) REVERT: D 436 ASN cc_start: 0.8587 (m-40) cc_final: 0.8205 (m110) REVERT: D 470 GLU cc_start: 0.7421 (pt0) cc_final: 0.7106 (tt0) REVERT: D 508 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8060 (mm) REVERT: D 551 ASN cc_start: 0.8336 (m110) cc_final: 0.8098 (m-40) REVERT: D 553 CYS cc_start: 0.7614 (t) cc_final: 0.7187 (t) REVERT: D 559 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: D 587 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8754 (m) REVERT: D 645 LYS cc_start: 0.9026 (mtpt) cc_final: 0.8667 (mtpt) REVERT: D 744 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7408 (mptp) REVERT: D 747 LYS cc_start: 0.8363 (mttt) cc_final: 0.8072 (mtmt) outliers start: 114 outliers final: 54 residues processed: 497 average time/residue: 0.5399 time to fit residues: 309.3557 Evaluate side-chains 507 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 426 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER 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 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 246 GLN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 262 SER 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 A residue 656 THR Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 514 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 575 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 747 LYS Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 96 VAL 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 257 ASP Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 508 ILE 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 66 MET Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN 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 378 LEU 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 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 587 VAL Chi-restraints excluded: chain D residue 729 ILE Chi-restraints excluded: chain D residue 744 LYS Chi-restraints excluded: chain D residue 756 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 54 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 176 optimal weight: 0.1980 chunk 242 optimal weight: 0.8980 chunk 247 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 232 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 625 ASN C 742 ASN ** D 64 ASN ** 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 D 742 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.146755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.110308 restraints weight = 22570.325| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.85 r_work: 0.2918 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.6539 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= 0.131 Angle : 0.573 14.026 29326 Z= 0.292 Chirality : 0.039 0.139 3303 Planarity : 0.004 0.112 3610 Dihedral : 8.384 59.373 2980 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.86 % Favored : 96.98 % Rotamer: Outliers : 4.93 % Allowed : 22.02 % Favored : 73.06 % 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: 1.49 (0.17), residues: 2520 helix: 1.71 (0.12), residues: 1828 sheet: None (None), residues: 0 loop : -0.95 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 71 TYR 0.034 0.001 TYR B 58 PHE 0.015 0.002 PHE D 520 TRP 0.021 0.001 TRP B 472 HIS 0.004 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (21639) covalent geometry : angle 0.57204 / 0.29 (29318) SS BOND : bond 0.00314 / 0.15 ( 4) SS BOND : angle 1.59927 / 0.55 ( 8) hydrogen bonds : bond 0.03754 / 2.45 ( 1246) hydrogen bonds : angle 3.36906 / 2.33 ( 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 548 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 437 time to evaluate : 0.825 Fit side-chains REVERT: A 136 PHE cc_start: 0.8007 (t80) cc_final: 0.7764 (t80) REVERT: A 147 MET cc_start: 0.8841 (mtp) cc_final: 0.8461 (mtp) REVERT: A 172 HIS cc_start: 0.5393 (OUTLIER) cc_final: 0.4662 (m-70) REVERT: A 173 GLN cc_start: 0.4322 (OUTLIER) cc_final: 0.4008 (tt0) REVERT: A 194 ARG cc_start: 0.8148 (tpp-160) cc_final: 0.7936 (tpt170) REVERT: A 222 ARG cc_start: 0.8361 (mtt180) cc_final: 0.8017 (mtm-85) REVERT: A 243 GLU cc_start: 0.8165 (tt0) cc_final: 0.7718 (tm-30) REVERT: A 246 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: A 262 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8792 (m) REVERT: A 266 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7292 (mm-30) REVERT: A 331 LEU cc_start: 0.7978 (tp) cc_final: 0.7602 (tt) REVERT: A 335 MET cc_start: 0.7492 (mtt) cc_final: 0.7037 (mtm) REVERT: A 343 MET cc_start: 0.7941 (tpt) cc_final: 0.7670 (tpt) REVERT: A 380 MET cc_start: 0.8233 (mtt) cc_final: 0.7913 (mtm) REVERT: A 404 GLU cc_start: 0.6167 (tm-30) cc_final: 0.5897 (tm-30) REVERT: A 438 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8073 (ttt) REVERT: A 442 MET cc_start: 0.8225 (ttt) cc_final: 0.7951 (ttm) REVERT: A 468 GLU cc_start: 0.8261 (tt0) cc_final: 0.7823 (tt0) REVERT: A 470 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: A 500 ASN cc_start: 0.9076 (t0) cc_final: 0.8793 (t0) REVERT: A 537 GLN cc_start: 0.8759 (tp40) cc_final: 0.8516 (tp40) REVERT: A 587 VAL cc_start: 0.8588 (t) cc_final: 0.8206 (m) REVERT: A 595 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7882 (mm-30) REVERT: A 711 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8245 (mt0) REVERT: B 71 ARG cc_start: 0.8346 (mmm-85) cc_final: 0.8113 (mmm-85) REVERT: B 84 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7786 (mt-10) REVERT: B 136 PHE cc_start: 0.8275 (t80) cc_final: 0.8013 (t80) REVERT: B 172 HIS cc_start: 0.4760 (OUTLIER) cc_final: 0.4522 (m-70) REVERT: B 190 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8345 (tt) REVERT: B 191 ARG cc_start: 0.7777 (mtp-110) cc_final: 0.7084 (ttm-80) REVERT: B 222 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7911 (mtm-85) REVERT: B 243 GLU cc_start: 0.8033 (tt0) cc_final: 0.7594 (tm-30) REVERT: B 247 GLN cc_start: 0.8847 (tt0) cc_final: 0.8535 (tt0) REVERT: B 266 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7300 (mm-30) REVERT: B 404 GLU cc_start: 0.6012 (mm-30) cc_final: 0.5303 (tm-30) REVERT: B 436 ASN cc_start: 0.8887 (m-40) cc_final: 0.8522 (m-40) REVERT: B 490 SER cc_start: 0.9169 (OUTLIER) cc_final: 0.8693 (m) REVERT: B 500 ASN cc_start: 0.9139 (t0) cc_final: 0.8904 (t0) REVERT: B 529 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8537 (mt) REVERT: B 631 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7764 (mt) REVERT: B 756 GLU cc_start: 0.8134 (tt0) cc_final: 0.7853 (tt0) REVERT: C 84 GLU cc_start: 0.7909 (mp0) cc_final: 0.7521 (mt-10) REVERT: C 106 LYS cc_start: 0.8254 (mtpm) cc_final: 0.8024 (ttmm) REVERT: C 190 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8373 (tt) REVERT: C 191 ARG cc_start: 0.7891 (mtp-110) cc_final: 0.7140 (ttm170) REVERT: C 240 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: C 243 GLU cc_start: 0.8105 (tt0) cc_final: 0.7693 (tm-30) REVERT: C 257 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8033 (m-30) REVERT: C 395 VAL cc_start: 0.8554 (t) cc_final: 0.8327 (t) REVERT: C 436 ASN cc_start: 0.8542 (m-40) cc_final: 0.8039 (m110) REVERT: C 490 SER cc_start: 0.9181 (OUTLIER) cc_final: 0.8835 (m) REVERT: C 508 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8101 (mm) REVERT: C 519 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8170 (mtpm) REVERT: C 529 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8491 (mt) REVERT: C 744 LYS cc_start: 0.7851 (mptm) cc_final: 0.7511 (mptp) REVERT: D 66 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6998 (mtm) REVERT: D 194 ARG cc_start: 0.8004 (tpp-160) cc_final: 0.6496 (ttp-110) REVERT: D 223 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8757 (tp) REVERT: D 243 GLU cc_start: 0.8175 (tt0) cc_final: 0.7720 (tm-30) REVERT: D 266 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7528 (mp0) REVERT: D 291 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8199 (mppt) REVERT: D 343 MET cc_start: 0.7331 (mmt) cc_final: 0.7086 (mpm) REVERT: D 359 PHE cc_start: 0.7876 (t80) cc_final: 0.7559 (t80) REVERT: D 369 CYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8142 (p) REVERT: D 422 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6393 (mmm) REVERT: D 436 ASN cc_start: 0.8682 (m-40) cc_final: 0.8298 (m110) REVERT: D 508 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8057 (mm) REVERT: D 551 ASN cc_start: 0.8266 (m110) cc_final: 0.8032 (m-40) REVERT: D 553 CYS cc_start: 0.7213 (t) cc_final: 0.6754 (t) REVERT: D 559 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: D 587 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8766 (m) REVERT: D 645 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8591 (mtpt) REVERT: D 744 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7594 (mptp) REVERT: D 747 LYS cc_start: 0.8350 (mttt) cc_final: 0.8018 (mtmt) outliers start: 111 outliers final: 55 residues processed: 493 average time/residue: 0.5269 time to fit residues: 300.7398 Evaluate side-chains 507 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 424 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER 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 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 246 GLN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 378 LEU 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 A residue 656 THR Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 514 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 575 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 508 ILE 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 66 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 223 LEU 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 378 LEU 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 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 587 VAL Chi-restraints excluded: chain D residue 729 ILE Chi-restraints excluded: chain D residue 744 LYS Chi-restraints excluded: chain D residue 756 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 114 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 204 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 221 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 209 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN A 562 ASN A 589 ASN A 629 GLN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 625 ASN B 735 ASN ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 625 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 Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.146181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.112160 restraints weight = 22949.775| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.70 r_work: 0.2985 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.6635 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= 0.131 Angle : 0.577 14.187 29326 Z= 0.293 Chirality : 0.039 0.159 3303 Planarity : 0.004 0.115 3610 Dihedral : 8.279 59.429 2980 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.17 % Favored : 96.67 % Rotamer: Outliers : 4.53 % Allowed : 22.50 % Favored : 72.97 % 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 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 71 TYR 0.035 0.001 TYR B 58 PHE 0.019 0.002 PHE B 520 TRP 0.022 0.001 TRP B 472 HIS 0.004 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (21639) covalent geometry : angle 0.57669 / 0.29 (29318) SS BOND : bond 0.00418 / 0.21 ( 4) SS BOND : angle 1.84645 / 0.65 ( 8) hydrogen bonds : bond 0.03752 / 2.45 ( 1246) hydrogen bonds : angle 3.36118 / 2.33 ( 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 527 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 425 time to evaluate : 0.841 Fit side-chains REVERT: A 147 MET cc_start: 0.8932 (mtp) cc_final: 0.8582 (mtp) REVERT: A 172 HIS cc_start: 0.5425 (OUTLIER) cc_final: 0.4783 (m-70) REVERT: A 173 GLN cc_start: 0.4343 (OUTLIER) cc_final: 0.3989 (tt0) REVERT: A 194 ARG cc_start: 0.8236 (tpp-160) cc_final: 0.8002 (tpt170) REVERT: A 222 ARG cc_start: 0.8461 (mtt180) cc_final: 0.8050 (mtm-85) REVERT: A 243 GLU cc_start: 0.8259 (tt0) cc_final: 0.7697 (tm-30) REVERT: A 246 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: A 262 SER cc_start: 0.9054 (OUTLIER) cc_final: 0.8781 (m) REVERT: A 266 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7463 (mm-30) REVERT: A 331 LEU cc_start: 0.7957 (tp) cc_final: 0.7593 (tt) REVERT: A 335 MET cc_start: 0.7522 (mtt) cc_final: 0.7059 (mtm) REVERT: A 343 MET cc_start: 0.7989 (tpt) cc_final: 0.7787 (tpt) REVERT: A 380 MET cc_start: 0.8240 (mtt) cc_final: 0.7906 (mtm) REVERT: A 404 GLU cc_start: 0.6072 (tm-30) cc_final: 0.5784 (tm-30) REVERT: A 438 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8099 (ttt) REVERT: A 442 MET cc_start: 0.8222 (ttt) cc_final: 0.7974 (ttm) REVERT: A 468 GLU cc_start: 0.8277 (tt0) cc_final: 0.7826 (tt0) REVERT: A 470 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: A 500 ASN cc_start: 0.9118 (t0) cc_final: 0.8812 (t0) REVERT: A 587 VAL cc_start: 0.8625 (t) cc_final: 0.8205 (m) REVERT: A 595 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7932 (mm-30) REVERT: A 711 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8253 (mt0) REVERT: B 71 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.8057 (mmm-85) REVERT: B 84 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7852 (mt-10) REVERT: B 136 PHE cc_start: 0.8285 (t80) cc_final: 0.8015 (t80) REVERT: B 172 HIS cc_start: 0.4784 (OUTLIER) cc_final: 0.4530 (m-70) REVERT: B 190 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8340 (tt) REVERT: B 191 ARG cc_start: 0.7867 (mtp-110) cc_final: 0.7107 (ttm-80) REVERT: B 222 ARG cc_start: 0.8389 (mtt180) cc_final: 0.7942 (mtm-85) REVERT: B 243 GLU cc_start: 0.8178 (tt0) cc_final: 0.7708 (tm-30) REVERT: B 247 GLN cc_start: 0.8847 (tt0) cc_final: 0.8520 (tt0) REVERT: B 266 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7438 (mm-30) REVERT: B 380 MET cc_start: 0.8149 (mpt) cc_final: 0.7624 (mtm) REVERT: B 404 GLU cc_start: 0.6143 (mm-30) cc_final: 0.5700 (tm-30) REVERT: B 436 ASN cc_start: 0.8853 (m-40) cc_final: 0.8482 (m-40) REVERT: B 490 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.8745 (m) REVERT: B 500 ASN cc_start: 0.9187 (t0) cc_final: 0.8927 (t0) REVERT: B 529 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8522 (mt) REVERT: B 631 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7781 (mt) REVERT: B 756 GLU cc_start: 0.8210 (tt0) cc_final: 0.7944 (tt0) REVERT: C 84 GLU cc_start: 0.7936 (mp0) cc_final: 0.7556 (mt-10) REVERT: C 106 LYS cc_start: 0.8292 (mtpm) cc_final: 0.7987 (ttmm) REVERT: C 190 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8367 (tt) REVERT: C 191 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.7092 (ttm170) REVERT: C 240 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: C 243 GLU cc_start: 0.8182 (tt0) cc_final: 0.7744 (tm-30) REVERT: C 257 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8103 (m-30) REVERT: C 380 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7692 (mtm) REVERT: C 395 VAL cc_start: 0.8544 (t) cc_final: 0.8321 (t) REVERT: C 436 ASN cc_start: 0.8562 (m-40) cc_final: 0.8069 (m110) REVERT: C 490 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8865 (m) REVERT: C 508 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8063 (mm) REVERT: C 519 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8181 (mtpm) REVERT: C 529 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8525 (mt) REVERT: C 744 LYS cc_start: 0.7867 (mptm) cc_final: 0.7535 (mptp) REVERT: C 756 GLU cc_start: 0.7746 (tt0) cc_final: 0.7310 (tt0) REVERT: D 66 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6992 (mtm) REVERT: D 191 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7179 (ttm-80) REVERT: D 194 ARG cc_start: 0.8095 (tpp-160) cc_final: 0.6529 (ttp-110) REVERT: D 223 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8748 (tp) REVERT: D 243 GLU cc_start: 0.8308 (tt0) cc_final: 0.7831 (tm-30) REVERT: D 291 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8223 (mppt) REVERT: D 359 PHE cc_start: 0.7870 (t80) cc_final: 0.7509 (t80) REVERT: D 369 CYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8186 (p) REVERT: D 412 LEU cc_start: 0.8414 (mm) cc_final: 0.8172 (mt) REVERT: D 422 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6444 (mmm) REVERT: D 436 ASN cc_start: 0.8651 (m-40) cc_final: 0.8279 (m110) REVERT: D 508 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7984 (mm) REVERT: D 551 ASN cc_start: 0.8347 (m110) cc_final: 0.8065 (m-40) REVERT: D 553 CYS cc_start: 0.7600 (t) cc_final: 0.7155 (t) REVERT: D 559 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: D 744 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7495 (mptp) REVERT: D 747 LYS cc_start: 0.8416 (mttt) cc_final: 0.8081 (mtmt) outliers start: 102 outliers final: 56 residues processed: 473 average time/residue: 0.5554 time to fit residues: 302.7853 Evaluate side-chains 498 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 414 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 246 GLN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 378 LEU 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 A residue 656 THR Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 747 LYS 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 96 VAL Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 514 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 575 LEU Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 508 ILE 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 66 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 223 LEU 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 378 LEU 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 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 Chi-restraints excluded: chain D residue 729 ILE Chi-restraints excluded: chain D residue 744 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 239 optimal weight: 0.0670 chunk 243 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 252 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 250 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN A 562 ASN A 589 ASN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 625 ASN B 735 ASN ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 625 ASN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 533 ASN D 552 ASN D 589 ASN ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.144485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.111851 restraints weight = 23318.461| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.70 r_work: 0.2972 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.6763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21643 Z= 0.150 Angle : 0.602 14.346 29326 Z= 0.304 Chirality : 0.040 0.159 3303 Planarity : 0.005 0.114 3610 Dihedral : 8.329 59.771 2980 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 4.44 % Allowed : 22.86 % Favored : 72.70 % 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: 1.53 (0.17), residues: 2520 helix: 1.72 (0.12), residues: 1828 sheet: None (None), residues: 0 loop : -0.87 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 71 TYR 0.035 0.002 TYR B 58 PHE 0.016 0.002 PHE B 341 TRP 0.024 0.001 TRP B 472 HIS 0.004 0.001 HIS D 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (21639) covalent geometry : angle 0.60128 / 0.30 (29318) SS BOND : bond 0.00427 / 0.21 ( 4) SS BOND : angle 1.83971 / 0.64 ( 8) hydrogen bonds : bond 0.03902 / 2.55 ( 1246) hydrogen bonds : angle 3.40223 / 2.36 ( 3648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8011.80 seconds wall clock time: 137 minutes 21.89 seconds (8241.89 seconds total)