Starting phenix.real_space_refine on Thu May 22 09:46:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arh_43782/05_2025/9arh_43782.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arh_43782/05_2025/9arh_43782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9arh_43782/05_2025/9arh_43782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arh_43782/05_2025/9arh_43782.map" model { file = "/net/cci-nas-00/data/ceres_data/9arh_43782/05_2025/9arh_43782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arh_43782/05_2025/9arh_43782.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.032 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: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 14690 2.51 5 N 3724 2.21 5 O 4242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22792 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 5695 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 36, 'TRANS': 765} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 659 Unresolved non-hydrogen angles: 805 Unresolved non-hydrogen dihedrals: 552 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 18, 'TRP:plan': 1, 'HIS:plan': 8, 'PHE:plan': 3, 'GLU:plan': 26, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 476 Chain: "B" Number of atoms: 5654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 5654 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 29, 'TRANS': 758} Chain breaks: 2 Unresolved non-hydrogen bonds: 587 Unresolved non-hydrogen angles: 712 Unresolved non-hydrogen dihedrals: 507 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 21, 'TYR:plan': 8, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 26, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 391 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: D, C, F Time building chain proxies: 22.42, per 1000 atoms: 0.98 Number of scatterers: 22792 At special positions: 0 Unit cell: (110.21, 145.52, 181.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 4242 8.00 N 3724 7.00 C 14690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.01 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=2.04 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=1.33 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=1.33 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 901 " - " ASN B 542 " " NAG D 901 " - " ASN D 542 " " NAG E 1 " - " ASN A 224 " " NAG F 1 " - " ASN C 224 " Time building additional restraints: 5.85 Conformation dependent library (CDL) restraints added in 3.0 seconds 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 34 sheets defined 42.6% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 70 through 81 Processing helix chain 'A' and resid 103 through 114 removed outlier: 4.727A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 removed outlier: 3.813A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 190 removed outlier: 3.667A pdb=" N LYS A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 245 through 260 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 297 through 317 Processing helix chain 'A' and resid 337 through 349 removed outlier: 4.019A pdb=" N LEU A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 492 Processing helix chain 'A' and resid 520 through 528 removed outlier: 3.516A pdb=" N GLY A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 601 removed outlier: 3.948A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 636 Processing helix chain 'A' and resid 647 through 673 removed outlier: 3.795A pdb=" N GLY A 659 " --> pdb=" O MET A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 Processing helix chain 'A' and resid 708 through 717 Processing helix chain 'A' and resid 718 through 728 removed outlier: 3.572A pdb=" N THR A 722 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS A 726 " --> pdb=" O THR A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.568A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 744 " --> pdb=" O GLN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 4.056A pdb=" N LYS A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 803 removed outlier: 4.263A pdb=" N GLN A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 813 Processing helix chain 'A' and resid 835 through 861 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 105 through 120 removed outlier: 4.315A pdb=" N ALA B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.564A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 209 through 224 removed outlier: 3.913A pdb=" N ASP B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 288 through 312 Processing helix chain 'B' and resid 323 through 330 removed outlier: 3.555A pdb=" N GLU B 326 " --> pdb=" O ASN B 323 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 460 through 472 removed outlier: 3.529A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 516 through 523 removed outlier: 4.237A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 576 removed outlier: 3.554A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 625 through 657 removed outlier: 3.930A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 657 " --> pdb=" O PHE B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 699 through 708 Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 772 through 787 Processing helix chain 'B' and resid 787 through 797 removed outlier: 4.001A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 843 Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 81 Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.726A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 156 removed outlier: 3.813A pdb=" N GLN C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 190 removed outlier: 3.667A pdb=" N LYS C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 Processing helix chain 'C' and resid 245 through 260 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 297 through 317 Processing helix chain 'C' and resid 337 through 349 removed outlier: 4.019A pdb=" N LEU C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 492 Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.516A pdb=" N GLY C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 601 removed outlier: 3.949A pdb=" N GLY C 588 " --> pdb=" O TRP C 584 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 594 " --> pdb=" O SER C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 636 Processing helix chain 'C' and resid 647 through 673 removed outlier: 3.795A pdb=" N GLY C 659 " --> pdb=" O MET C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 Processing helix chain 'C' and resid 708 through 717 Processing helix chain 'C' and resid 718 through 728 removed outlier: 3.572A pdb=" N THR C 722 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS C 726 " --> pdb=" O THR C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 744 removed outlier: 3.568A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP C 744 " --> pdb=" O GLN C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 764 removed outlier: 4.057A pdb=" N LYS C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 803 removed outlier: 4.264A pdb=" N GLN C 791 " --> pdb=" O SER C 787 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 813 Processing helix chain 'C' and resid 835 through 861 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 51 through 56 Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 105 through 120 removed outlier: 4.316A pdb=" N ALA D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.564A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 209 through 224 removed outlier: 3.913A pdb=" N ASP D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 288 through 312 Processing helix chain 'D' and resid 323 through 330 removed outlier: 3.555A pdb=" N GLU D 326 " --> pdb=" O ASN D 323 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 460 through 472 removed outlier: 3.529A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 523 removed outlier: 4.237A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 576 removed outlier: 3.553A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 579 No H-bonds generated for 'chain 'D' and resid 577 through 579' Processing helix chain 'D' and resid 601 through 612 Processing helix chain 'D' and resid 625 through 657 removed outlier: 3.929A pdb=" N ALA D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 655 " --> pdb=" O ALA D 651 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN D 656 " --> pdb=" O ALA D 652 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU D 657 " --> pdb=" O PHE D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 699 through 708 Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 732 through 742 Processing helix chain 'D' and resid 772 through 787 Processing helix chain 'D' and resid 787 through 797 removed outlier: 4.001A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 843 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 6.960A pdb=" N VAL A 27 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N THR A 63 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 91 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 163 removed outlier: 3.868A pdb=" N ILE A 163 " --> pdb=" O LYS A 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 removed outlier: 7.393A pdb=" N LEU A 166 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 292 removed outlier: 6.556A pdb=" N TYR A 372 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 387 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 374 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 383 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 389 " --> pdb=" O HIS A 392 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 361 removed outlier: 4.151A pdb=" N GLU A 360 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 498 through 499 removed outlier: 6.426A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 430 through 432 removed outlier: 3.621A pdb=" N TYR A 477 " --> pdb=" O TYR A 431 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 509 through 510 removed outlier: 3.792A pdb=" N GLU A 509 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 518 " --> pdb=" O GLU A 509 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 548 through 550 removed outlier: 3.866A pdb=" N MET A 783 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AB2, first strand: chain 'B' and resid 67 through 69 removed outlier: 8.245A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 67 through 69 removed outlier: 5.974A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA B 100 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 198 through 204 removed outlier: 7.723A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 229 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 231 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 341 through 344 removed outlier: 4.361A pdb=" N VAL B 342 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 349 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 344 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 406 through 408 removed outlier: 3.770A pdb=" N ASP B 477 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 408 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU B 478 " --> pdb=" O PRO B 435 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 420 " --> pdb=" O CYS B 456 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 458 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AB8, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.771A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 65 removed outlier: 6.959A pdb=" N VAL C 27 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N THR C 63 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 91 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 162 through 163 removed outlier: 3.868A pdb=" N ILE C 163 " --> pdb=" O LYS C 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 216 through 217 removed outlier: 7.394A pdb=" N LEU C 166 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 289 through 292 removed outlier: 6.557A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 383 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN C 389 " --> pdb=" O HIS C 392 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 360 through 361 removed outlier: 4.150A pdb=" N GLU C 360 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 498 through 499 removed outlier: 6.426A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 430 through 432 removed outlier: 3.621A pdb=" N TYR C 477 " --> pdb=" O TYR C 431 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 509 through 510 removed outlier: 3.792A pdb=" N GLU C 509 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 518 " --> pdb=" O GLU C 509 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 548 through 550 removed outlier: 3.866A pdb=" N MET C 783 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AD1, first strand: chain 'D' and resid 67 through 69 removed outlier: 8.246A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 67 through 69 removed outlier: 5.974A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 198 through 204 removed outlier: 7.723A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 229 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR D 231 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 341 through 344 removed outlier: 4.361A pdb=" N VAL D 342 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 349 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE D 344 " --> pdb=" O ARG D 347 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 406 through 408 removed outlier: 3.770A pdb=" N ASP D 477 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE D 408 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU D 478 " --> pdb=" O PRO D 435 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU D 420 " --> pdb=" O CYS D 456 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS D 458 " --> pdb=" O ILE D 418 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 508 through 509 Processing sheet with id=AD7, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.771A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 1016 hydrogen bonds defined for protein. 2964 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: 8.67 Time building geometry restraints manager: 6.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.20: 268 1.20 - 1.36: 7195 1.36 - 1.51: 7095 1.51 - 1.67: 8494 1.67 - 1.82: 228 Bond restraints: 23280 Sorted by residual: bond pdb=" C PRO C 553 " pdb=" O PRO C 553 " ideal model delta sigma weight residual 1.233 1.047 0.186 1.23e-02 6.61e+03 2.29e+02 bond pdb=" C PRO A 553 " pdb=" O PRO A 553 " ideal model delta sigma weight residual 1.233 1.048 0.185 1.23e-02 6.61e+03 2.27e+02 bond pdb=" C LYS C 555 " pdb=" O LYS C 555 " ideal model delta sigma weight residual 1.234 1.059 0.175 1.22e-02 6.72e+03 2.05e+02 bond pdb=" C LYS A 555 " pdb=" O LYS A 555 " ideal model delta sigma weight residual 1.234 1.060 0.174 1.22e-02 6.72e+03 2.05e+02 bond pdb=" C ALA D 636 " pdb=" O ALA D 636 " ideal model delta sigma weight residual 1.236 1.064 0.172 1.25e-02 6.40e+03 1.90e+02 ... (remaining 23275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.71: 31335 5.71 - 11.42: 469 11.42 - 17.13: 40 17.13 - 22.84: 14 22.84 - 28.55: 4 Bond angle restraints: 31862 Sorted by residual: angle pdb=" C PHE D 653 " pdb=" CA PHE D 653 " pdb=" CB PHE D 653 " ideal model delta sigma weight residual 110.79 82.24 28.55 1.68e+00 3.54e-01 2.89e+02 angle pdb=" C PHE B 653 " pdb=" CA PHE B 653 " pdb=" CB PHE B 653 " ideal model delta sigma weight residual 110.79 82.27 28.52 1.68e+00 3.54e-01 2.88e+02 angle pdb=" C TYR A 668 " pdb=" CA TYR A 668 " pdb=" CB TYR A 668 " ideal model delta sigma weight residual 110.88 89.71 21.17 1.57e+00 4.06e-01 1.82e+02 angle pdb=" C TYR C 668 " pdb=" CA TYR C 668 " pdb=" CB TYR C 668 " ideal model delta sigma weight residual 110.88 89.72 21.16 1.57e+00 4.06e-01 1.82e+02 angle pdb=" CA PHE C 630 " pdb=" C PHE C 630 " pdb=" O PHE C 630 " ideal model delta sigma weight residual 120.55 106.78 13.77 1.06e+00 8.90e-01 1.69e+02 ... (remaining 31857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 12738 17.63 - 35.27: 696 35.27 - 52.90: 207 52.90 - 70.54: 81 70.54 - 88.17: 10 Dihedral angle restraints: 13732 sinusoidal: 4536 harmonic: 9196 Sorted by residual: dihedral pdb=" C PHE A 759 " pdb=" N PHE A 759 " pdb=" CA PHE A 759 " pdb=" CB PHE A 759 " ideal model delta harmonic sigma weight residual -122.60 -157.99 35.39 0 2.50e+00 1.60e-01 2.00e+02 dihedral pdb=" C PHE C 759 " pdb=" N PHE C 759 " pdb=" CA PHE C 759 " pdb=" CB PHE C 759 " ideal model delta harmonic sigma weight residual -122.60 -157.98 35.38 0 2.50e+00 1.60e-01 2.00e+02 dihedral pdb=" N THR C 669 " pdb=" C THR C 669 " pdb=" CA THR C 669 " pdb=" CB THR C 669 " ideal model delta harmonic sigma weight residual 123.40 155.96 -32.56 0 2.50e+00 1.60e-01 1.70e+02 ... (remaining 13729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.278: 3755 0.278 - 0.557: 107 0.557 - 0.835: 6 0.835 - 1.113: 8 1.113 - 1.392: 8 Chirality restraints: 3884 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.24 -1.16 2.00e-02 2.50e+03 3.39e+03 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.24 -1.16 2.00e-02 2.50e+03 3.38e+03 chirality pdb=" CA PHE A 759 " pdb=" N PHE A 759 " pdb=" C PHE A 759 " pdb=" CB PHE A 759 " both_signs ideal model delta sigma weight residual False 2.51 1.12 1.39 2.00e-01 2.50e+01 4.84e+01 ... (remaining 3881 not shown) Planarity restraints: 4026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 580 " -0.040 2.00e-02 2.50e+03 7.71e-02 5.95e+01 pdb=" C GLN A 580 " 0.134 2.00e-02 2.50e+03 pdb=" O GLN A 580 " -0.048 2.00e-02 2.50e+03 pdb=" N SER A 581 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 580 " 0.040 2.00e-02 2.50e+03 7.71e-02 5.95e+01 pdb=" C GLN C 580 " -0.133 2.00e-02 2.50e+03 pdb=" O GLN C 580 " 0.048 2.00e-02 2.50e+03 pdb=" N SER C 581 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 800 " -0.035 2.00e-02 2.50e+03 7.37e-02 5.43e+01 pdb=" C SER A 800 " 0.127 2.00e-02 2.50e+03 pdb=" O SER A 800 " -0.048 2.00e-02 2.50e+03 pdb=" N HIS A 801 " -0.045 2.00e-02 2.50e+03 ... (remaining 4023 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 50 2.37 - 3.00: 13160 3.00 - 3.63: 32473 3.63 - 4.27: 46024 4.27 - 4.90: 76699 Nonbonded interactions: 168406 Sorted by model distance: nonbonded pdb=" O SER B 469 " pdb=" O VAL B 472 " model vdw 1.736 3.040 nonbonded pdb=" O SER D 469 " pdb=" O VAL D 472 " model vdw 1.737 3.040 nonbonded pdb=" O VAL B 538 " pdb=" CG1 VAL B 749 " model vdw 1.739 3.460 nonbonded pdb=" O VAL D 538 " pdb=" CG1 VAL D 749 " model vdw 1.740 3.460 nonbonded pdb=" O TRP B 391 " pdb=" N ARG B 393 " model vdw 1.826 3.120 ... (remaining 168401 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: 0.12 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue 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: 1.730 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: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 60.230 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 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 : 0.015 0.696 23304 Z= 1.005 Angle : 1.644 44.435 31916 Z= 1.098 Chirality : 0.114 1.392 3884 Planarity : 0.010 0.078 4022 Dihedral : 12.971 88.170 7738 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.36 % Favored : 92.26 % Rotamer: Outliers : 8.98 % Allowed : 10.36 % Favored : 80.66 % Cbeta Deviations : 2.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.13), residues: 3152 helix: -0.48 (0.13), residues: 1280 sheet: -3.06 (0.23), residues: 334 loop : -3.42 (0.13), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP B 610 HIS 0.021 0.002 HIS C 801 PHE 0.071 0.003 PHE D 642 TYR 0.071 0.002 TYR C 732 ARG 0.008 0.001 ARG C 743 Details of bonding type rmsd link_NAG-ASN : bond 0.00099 ( 4) link_NAG-ASN : angle 1.01149 ( 12) link_BETA1-4 : bond 0.06427 ( 2) link_BETA1-4 : angle 17.92924 ( 6) hydrogen bonds : bond 0.19079 ( 1010) hydrogen bonds : angle 7.68136 ( 2964) SS BOND : bond 0.23217 ( 18) SS BOND : angle 11.22464 ( 36) covalent geometry : bond 0.01349 (23280) covalent geometry : angle 1.58252 (31862) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 471 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8654 (tp) REVERT: A 660 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7614 (t80) REVERT: A 662 MET cc_start: 0.8701 (tmt) cc_final: 0.7306 (tmm) REVERT: B 358 MET cc_start: 0.7283 (mmm) cc_final: 0.7016 (mmt) REVERT: B 563 PHE cc_start: 0.7574 (t80) cc_final: 0.6750 (m-10) REVERT: B 796 TRP cc_start: 0.8651 (m100) cc_final: 0.8325 (m100) REVERT: C 342 PHE cc_start: 0.6547 (t80) cc_final: 0.6117 (t80) REVERT: C 628 MET cc_start: 0.8692 (tmm) cc_final: 0.7785 (tmm) REVERT: C 635 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8694 (tp) REVERT: C 660 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7611 (t80) REVERT: C 662 MET cc_start: 0.8589 (tmt) cc_final: 0.7145 (tmm) REVERT: C 806 MET cc_start: 0.8759 (mmm) cc_final: 0.7229 (mmt) REVERT: D 358 MET cc_start: 0.7011 (mmm) cc_final: 0.6790 (mmt) REVERT: D 563 PHE cc_start: 0.7829 (t80) cc_final: 0.6824 (m-10) REVERT: D 631 MET cc_start: 0.7278 (tpt) cc_final: 0.6958 (tpp) REVERT: D 796 TRP cc_start: 0.8579 (m100) cc_final: 0.8101 (m100) outliers start: 196 outliers final: 127 residues processed: 646 average time/residue: 0.3051 time to fit residues: 318.6939 Evaluate side-chains 454 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 323 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 479 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 784 ARG Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 816 TYR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 392 PRO Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 578 PRO Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 630 PHE Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 660 PHE Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain C residue 730 HIS Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 784 ARG Chi-restraints excluded: chain C residue 787 SER Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 392 PRO Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 795 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 40.0000 chunk 239 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 81 optimal weight: 0.0670 chunk 161 optimal weight: 30.0000 chunk 127 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 184 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 414 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN A 542 ASN A 803 ASN A 824 ASN B 180 GLN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN B 703 HIS ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 414 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 GLN C 671 ASN C 803 ASN C 824 ASN ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.221857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.191981 restraints weight = 26378.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.185061 restraints weight = 29966.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.185767 restraints weight = 36957.469| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23304 Z= 0.159 Angle : 0.669 8.789 31916 Z= 0.355 Chirality : 0.046 0.232 3884 Planarity : 0.005 0.057 4022 Dihedral : 9.547 73.935 3694 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.20 % Favored : 92.61 % Rotamer: Outliers : 7.15 % Allowed : 17.00 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.14), residues: 3152 helix: 0.30 (0.14), residues: 1330 sheet: -2.93 (0.22), residues: 370 loop : -2.91 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 391 HIS 0.009 0.001 HIS D 61 PHE 0.029 0.002 PHE C 554 TYR 0.018 0.001 TYR A 668 ARG 0.009 0.001 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 4) link_NAG-ASN : angle 1.44911 ( 12) link_BETA1-4 : bond 0.00381 ( 2) link_BETA1-4 : angle 1.16919 ( 6) hydrogen bonds : bond 0.04856 ( 1010) hydrogen bonds : angle 5.30535 ( 2964) SS BOND : bond 0.00487 ( 18) SS BOND : angle 1.58121 ( 36) covalent geometry : bond 0.00356 (23280) covalent geometry : angle 0.66690 (31862) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 321 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLN cc_start: 0.9202 (pp30) cc_final: 0.8997 (pp30) REVERT: A 675 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8521 (t80) REVERT: A 730 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.8108 (p-80) REVERT: A 743 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.8038 (mtm180) REVERT: A 801 HIS cc_start: 0.8815 (OUTLIER) cc_final: 0.7667 (t-90) REVERT: B 358 MET cc_start: 0.7849 (mmm) cc_final: 0.7608 (mmt) REVERT: B 563 PHE cc_start: 0.7865 (t80) cc_final: 0.7134 (m-10) REVERT: B 796 TRP cc_start: 0.8806 (m100) cc_final: 0.8542 (m100) REVERT: C 342 PHE cc_start: 0.7235 (t80) cc_final: 0.6691 (t80) REVERT: C 557 GLN cc_start: 0.9152 (pp30) cc_final: 0.8947 (pp30) REVERT: C 675 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8350 (t80) REVERT: C 723 MET cc_start: 0.7836 (tmm) cc_final: 0.7481 (tmm) REVERT: C 730 HIS cc_start: 0.8499 (OUTLIER) cc_final: 0.8141 (p-80) REVERT: C 743 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7910 (mtm180) REVERT: D 207 MET cc_start: 0.5467 (mmm) cc_final: 0.4865 (mmt) REVERT: D 307 MET cc_start: 0.3977 (OUTLIER) cc_final: 0.3498 (mmm) REVERT: D 358 MET cc_start: 0.7626 (mmm) cc_final: 0.7219 (mmt) REVERT: D 563 PHE cc_start: 0.8044 (t80) cc_final: 0.7220 (m-10) outliers start: 156 outliers final: 96 residues processed: 457 average time/residue: 0.2902 time to fit residues: 223.0555 Evaluate side-chains 410 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 306 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 784 ARG Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 840 HIS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 730 HIS Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 784 ARG Chi-restraints excluded: chain C residue 787 SER Chi-restraints excluded: chain C residue 797 ILE Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 786 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 31 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 287 optimal weight: 0.0570 chunk 315 optimal weight: 3.9990 chunk 279 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 108 optimal weight: 30.0000 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 171 HIS ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 GLN B 127 HIS B 703 HIS C 171 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 792 GLN ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.230740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.194421 restraints weight = 29276.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.186525 restraints weight = 33195.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.189143 restraints weight = 41704.203| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23304 Z= 0.175 Angle : 0.647 9.037 31916 Z= 0.343 Chirality : 0.046 0.196 3884 Planarity : 0.005 0.057 4022 Dihedral : 8.277 67.137 3561 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.22 % Favored : 91.69 % Rotamer: Outliers : 7.33 % Allowed : 17.19 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.15), residues: 3152 helix: 0.90 (0.15), residues: 1306 sheet: -2.66 (0.25), residues: 322 loop : -2.73 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 610 HIS 0.005 0.001 HIS B 703 PHE 0.027 0.002 PHE A 554 TYR 0.015 0.001 TYR C 732 ARG 0.006 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 4) link_NAG-ASN : angle 1.32469 ( 12) link_BETA1-4 : bond 0.00709 ( 2) link_BETA1-4 : angle 1.24738 ( 6) hydrogen bonds : bond 0.04587 ( 1010) hydrogen bonds : angle 4.89379 ( 2964) SS BOND : bond 0.00490 ( 18) SS BOND : angle 1.66855 ( 36) covalent geometry : bond 0.00409 (23280) covalent geometry : angle 0.64460 (31862) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 321 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6984 (ttm) REVERT: A 730 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.8128 (p-80) REVERT: A 743 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.8005 (mtm180) REVERT: B 358 MET cc_start: 0.8150 (mmm) cc_final: 0.7904 (mpp) REVERT: B 563 PHE cc_start: 0.7994 (t80) cc_final: 0.7741 (t80) REVERT: B 643 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8082 (tt) REVERT: B 664 SER cc_start: 0.7861 (t) cc_final: 0.7550 (p) REVERT: C 723 MET cc_start: 0.7877 (tmm) cc_final: 0.7569 (tmm) REVERT: C 743 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7954 (mtm180) REVERT: D 112 LEU cc_start: 0.8894 (mm) cc_final: 0.8525 (tp) REVERT: D 207 MET cc_start: 0.5561 (mmm) cc_final: 0.4974 (mmt) REVERT: D 307 MET cc_start: 0.4146 (OUTLIER) cc_final: 0.3624 (mmm) REVERT: D 358 MET cc_start: 0.8065 (mmm) cc_final: 0.7818 (mpp) REVERT: D 563 PHE cc_start: 0.8177 (t80) cc_final: 0.7063 (m-10) REVERT: D 643 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8236 (tt) REVERT: D 664 SER cc_start: 0.7601 (t) cc_final: 0.7277 (p) REVERT: D 789 MET cc_start: 0.8333 (tpp) cc_final: 0.7956 (tpp) REVERT: D 796 TRP cc_start: 0.8799 (m100) cc_final: 0.8512 (m100) outliers start: 160 outliers final: 112 residues processed: 449 average time/residue: 0.2746 time to fit residues: 206.7386 Evaluate side-chains 413 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 294 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 784 ARG Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 784 ARG Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 786 ASP Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 835 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 306 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 282 optimal weight: 0.0970 chunk 190 optimal weight: 6.9990 chunk 303 optimal weight: 10.0000 chunk 313 optimal weight: 0.0980 chunk 172 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 HIS C 426 GLN D 127 HIS D 145 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.234398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.197393 restraints weight = 29630.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.190294 restraints weight = 32102.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.191864 restraints weight = 42509.413| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23304 Z= 0.120 Angle : 0.596 7.690 31916 Z= 0.313 Chirality : 0.044 0.200 3884 Planarity : 0.004 0.055 4022 Dihedral : 7.684 60.863 3540 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.58 % Favored : 92.29 % Rotamer: Outliers : 6.42 % Allowed : 18.84 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.15), residues: 3152 helix: 1.18 (0.15), residues: 1306 sheet: -2.38 (0.26), residues: 322 loop : -2.56 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 391 HIS 0.006 0.001 HIS B 703 PHE 0.021 0.001 PHE B 351 TYR 0.017 0.001 TYR B 239 ARG 0.006 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 4) link_NAG-ASN : angle 1.30018 ( 12) link_BETA1-4 : bond 0.00828 ( 2) link_BETA1-4 : angle 1.13973 ( 6) hydrogen bonds : bond 0.03762 ( 1010) hydrogen bonds : angle 4.60013 ( 2964) SS BOND : bond 0.00339 ( 18) SS BOND : angle 1.50777 ( 36) covalent geometry : bond 0.00259 (23280) covalent geometry : angle 0.59353 (31862) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 320 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.6734 (m-70) cc_final: 0.6495 (m-70) REVERT: A 730 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.7935 (p-80) REVERT: B 358 MET cc_start: 0.8059 (mmm) cc_final: 0.7825 (mpp) REVERT: B 508 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7557 (tpt) REVERT: B 664 SER cc_start: 0.7886 (t) cc_final: 0.7513 (p) REVERT: C 219 ASP cc_start: 0.7112 (t0) cc_final: 0.6911 (t0) REVERT: C 261 MET cc_start: 0.7646 (tpp) cc_final: 0.6983 (tpp) REVERT: C 342 PHE cc_start: 0.7289 (t80) cc_final: 0.6838 (t80) REVERT: C 557 GLN cc_start: 0.9188 (pp30) cc_final: 0.8868 (pp30) REVERT: C 723 MET cc_start: 0.7812 (tmm) cc_final: 0.7565 (tmm) REVERT: C 743 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7946 (mtm180) REVERT: D 112 LEU cc_start: 0.8986 (mm) cc_final: 0.8746 (tp) REVERT: D 207 MET cc_start: 0.5607 (mmm) cc_final: 0.5138 (mmt) REVERT: D 307 MET cc_start: 0.3998 (OUTLIER) cc_final: 0.3494 (mmm) REVERT: D 358 MET cc_start: 0.8018 (mmm) cc_final: 0.7749 (mpp) REVERT: D 563 PHE cc_start: 0.8274 (t80) cc_final: 0.7197 (m-10) REVERT: D 664 SER cc_start: 0.7546 (t) cc_final: 0.7201 (p) REVERT: D 796 TRP cc_start: 0.8720 (m100) cc_final: 0.8453 (m100) REVERT: D 818 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7558 (ptm) outliers start: 140 outliers final: 91 residues processed: 434 average time/residue: 0.2690 time to fit residues: 196.6963 Evaluate side-chains 386 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 290 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 818 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 288 optimal weight: 0.4980 chunk 240 optimal weight: 2.9990 chunk 154 optimal weight: 0.0970 chunk 82 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS B 127 HIS B 491 ASN B 703 HIS C 730 HIS D 127 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.232964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.203687 restraints weight = 29331.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.200895 restraints weight = 51709.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.202033 restraints weight = 54342.263| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23304 Z= 0.138 Angle : 0.612 8.048 31916 Z= 0.321 Chirality : 0.044 0.196 3884 Planarity : 0.004 0.058 4022 Dihedral : 7.283 59.696 3520 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.09 % Favored : 91.78 % Rotamer: Outliers : 6.55 % Allowed : 18.97 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 3152 helix: 1.31 (0.15), residues: 1306 sheet: -2.31 (0.26), residues: 322 loop : -2.47 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 584 HIS 0.007 0.001 HIS B 703 PHE 0.021 0.001 PHE B 351 TYR 0.016 0.001 TYR B 239 ARG 0.006 0.000 ARG A 716 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 4) link_NAG-ASN : angle 1.31634 ( 12) link_BETA1-4 : bond 0.00729 ( 2) link_BETA1-4 : angle 1.31119 ( 6) hydrogen bonds : bond 0.03858 ( 1010) hydrogen bonds : angle 4.54024 ( 2964) SS BOND : bond 0.00483 ( 18) SS BOND : angle 1.60404 ( 36) covalent geometry : bond 0.00317 (23280) covalent geometry : angle 0.60972 (31862) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 299 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 730 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7885 (p-80) REVERT: B 207 MET cc_start: 0.5781 (mmm) cc_final: 0.5146 (mmt) REVERT: B 664 SER cc_start: 0.7564 (t) cc_final: 0.7318 (p) REVERT: C 723 MET cc_start: 0.7800 (tmm) cc_final: 0.7551 (tmm) REVERT: C 743 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7922 (mtm180) REVERT: C 839 MET cc_start: 0.6974 (ppp) cc_final: 0.6665 (ppp) REVERT: D 207 MET cc_start: 0.5614 (mmm) cc_final: 0.5132 (mmt) REVERT: D 307 MET cc_start: 0.4046 (OUTLIER) cc_final: 0.3683 (mmm) REVERT: D 563 PHE cc_start: 0.8311 (t80) cc_final: 0.7067 (m-10) REVERT: D 631 MET cc_start: 0.6809 (tpt) cc_final: 0.6432 (tpt) REVERT: D 664 SER cc_start: 0.7328 (t) cc_final: 0.7123 (p) REVERT: D 778 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8044 (tt) REVERT: D 796 TRP cc_start: 0.8838 (m100) cc_final: 0.8638 (m100) REVERT: D 818 MET cc_start: 0.8129 (ptm) cc_final: 0.7857 (ptm) outliers start: 143 outliers final: 115 residues processed: 413 average time/residue: 0.2576 time to fit residues: 182.6028 Evaluate side-chains 404 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 285 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 632 TRP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 240 optimal weight: 30.0000 chunk 89 optimal weight: 0.7980 chunk 82 optimal weight: 0.0570 chunk 234 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 238 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS B 180 GLN B 703 HIS D 127 HIS D 145 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.233499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.202773 restraints weight = 29275.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.198994 restraints weight = 54627.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.200558 restraints weight = 52245.441| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23304 Z= 0.129 Angle : 0.604 7.899 31916 Z= 0.315 Chirality : 0.044 0.215 3884 Planarity : 0.004 0.060 4022 Dihedral : 7.139 59.831 3518 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.06 % Favored : 91.88 % Rotamer: Outliers : 6.69 % Allowed : 20.21 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.15), residues: 3152 helix: 1.37 (0.15), residues: 1308 sheet: -2.27 (0.26), residues: 322 loop : -2.41 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 197 HIS 0.008 0.001 HIS B 703 PHE 0.025 0.001 PHE D 351 TYR 0.027 0.001 TYR C 266 ARG 0.004 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00080 ( 4) link_NAG-ASN : angle 1.33239 ( 12) link_BETA1-4 : bond 0.00556 ( 2) link_BETA1-4 : angle 1.29154 ( 6) hydrogen bonds : bond 0.03730 ( 1010) hydrogen bonds : angle 4.47493 ( 2964) SS BOND : bond 0.00406 ( 18) SS BOND : angle 1.38965 ( 36) covalent geometry : bond 0.00289 (23280) covalent geometry : angle 0.60159 (31862) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 291 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 730 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.7803 (p-80) REVERT: B 207 MET cc_start: 0.5731 (mmm) cc_final: 0.5105 (mmt) REVERT: B 664 SER cc_start: 0.7604 (t) cc_final: 0.7349 (p) REVERT: B 778 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8287 (tt) REVERT: C 723 MET cc_start: 0.7779 (tmm) cc_final: 0.7537 (tmm) REVERT: C 743 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7917 (mtm180) REVERT: C 839 MET cc_start: 0.6967 (ppp) cc_final: 0.6672 (ppp) REVERT: D 112 LEU cc_start: 0.8310 (tp) cc_final: 0.8087 (tp) REVERT: D 207 MET cc_start: 0.5565 (mmm) cc_final: 0.5098 (mmt) REVERT: D 307 MET cc_start: 0.4041 (OUTLIER) cc_final: 0.3680 (mmm) REVERT: D 563 PHE cc_start: 0.8301 (t80) cc_final: 0.7151 (m-10) REVERT: D 664 SER cc_start: 0.7355 (t) cc_final: 0.7126 (p) REVERT: D 818 MET cc_start: 0.8211 (ptm) cc_final: 0.7990 (ptm) outliers start: 146 outliers final: 119 residues processed: 405 average time/residue: 0.2600 time to fit residues: 180.3709 Evaluate side-chains 408 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 285 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 629 TRP Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 629 TRP Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 321 CYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 191 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 262 optimal weight: 0.9990 chunk 222 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 13 optimal weight: 0.0060 chunk 2 optimal weight: 30.0000 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS B 180 GLN B 357 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.224729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.203171 restraints weight = 28898.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.194644 restraints weight = 32426.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.193685 restraints weight = 39058.190| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23304 Z= 0.122 Angle : 0.600 9.218 31916 Z= 0.311 Chirality : 0.044 0.194 3884 Planarity : 0.004 0.061 4022 Dihedral : 6.860 59.629 3514 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.09 % Favored : 91.85 % Rotamer: Outliers : 6.28 % Allowed : 20.81 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 3152 helix: 1.54 (0.15), residues: 1292 sheet: -2.14 (0.26), residues: 322 loop : -2.38 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 197 HIS 0.014 0.001 HIS D 127 PHE 0.027 0.001 PHE D 351 TYR 0.027 0.001 TYR A 266 ARG 0.004 0.000 ARG A 716 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 4) link_NAG-ASN : angle 1.31889 ( 12) link_BETA1-4 : bond 0.00518 ( 2) link_BETA1-4 : angle 1.31191 ( 6) hydrogen bonds : bond 0.03598 ( 1010) hydrogen bonds : angle 4.41389 ( 2964) SS BOND : bond 0.00501 ( 18) SS BOND : angle 1.10657 ( 36) covalent geometry : bond 0.00271 (23280) covalent geometry : angle 0.59845 (31862) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 287 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 730 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.7619 (p-80) REVERT: B 207 MET cc_start: 0.5640 (mmm) cc_final: 0.5064 (mmt) REVERT: B 664 SER cc_start: 0.7488 (t) cc_final: 0.7240 (p) REVERT: B 778 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8258 (tt) REVERT: C 723 MET cc_start: 0.7815 (tmm) cc_final: 0.7558 (tmm) REVERT: C 743 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7930 (mtm180) REVERT: C 839 MET cc_start: 0.7075 (ppp) cc_final: 0.6760 (ppp) REVERT: D 112 LEU cc_start: 0.8245 (tp) cc_final: 0.7987 (tp) REVERT: D 207 MET cc_start: 0.5778 (mmm) cc_final: 0.5413 (mmt) REVERT: D 664 SER cc_start: 0.7351 (t) cc_final: 0.7111 (p) REVERT: D 789 MET cc_start: 0.8224 (tpp) cc_final: 0.7875 (tpp) outliers start: 137 outliers final: 115 residues processed: 397 average time/residue: 0.2602 time to fit residues: 178.2099 Evaluate side-chains 401 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 283 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 321 CYS Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 116 optimal weight: 0.0570 chunk 35 optimal weight: 0.0000 chunk 228 optimal weight: 0.5980 chunk 287 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 237 optimal weight: 5.9990 chunk 314 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 overall best weight: 0.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS B 180 GLN D 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.235242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.206370 restraints weight = 29258.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.203029 restraints weight = 50144.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.204057 restraints weight = 52492.390| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23304 Z= 0.114 Angle : 0.593 8.709 31916 Z= 0.306 Chirality : 0.043 0.218 3884 Planarity : 0.004 0.072 4022 Dihedral : 6.503 59.845 3504 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.90 % Favored : 92.04 % Rotamer: Outliers : 5.27 % Allowed : 21.81 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 3152 helix: 1.62 (0.15), residues: 1294 sheet: -2.04 (0.26), residues: 322 loop : -2.32 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 197 HIS 0.016 0.001 HIS B 127 PHE 0.027 0.001 PHE D 351 TYR 0.018 0.001 TYR B 239 ARG 0.004 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 4) link_NAG-ASN : angle 1.31114 ( 12) link_BETA1-4 : bond 0.00405 ( 2) link_BETA1-4 : angle 1.28413 ( 6) hydrogen bonds : bond 0.03404 ( 1010) hydrogen bonds : angle 4.34305 ( 2964) SS BOND : bond 0.00291 ( 18) SS BOND : angle 0.95936 ( 36) covalent geometry : bond 0.00245 (23280) covalent geometry : angle 0.59225 (31862) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 295 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 730 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7534 (p-80) REVERT: B 207 MET cc_start: 0.5782 (mmm) cc_final: 0.5261 (mmt) REVERT: B 664 SER cc_start: 0.7547 (t) cc_final: 0.7262 (p) REVERT: B 778 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8300 (tt) REVERT: C 839 MET cc_start: 0.6998 (ppp) cc_final: 0.6718 (ppp) REVERT: D 112 LEU cc_start: 0.8388 (tp) cc_final: 0.8118 (tp) REVERT: D 207 MET cc_start: 0.5767 (mmm) cc_final: 0.5402 (mmt) REVERT: D 664 SER cc_start: 0.7486 (t) cc_final: 0.7218 (p) REVERT: D 789 MET cc_start: 0.8256 (tpp) cc_final: 0.7933 (tpp) outliers start: 115 outliers final: 96 residues processed: 385 average time/residue: 0.2549 time to fit residues: 169.5285 Evaluate side-chains 382 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 284 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 321 CYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 140 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 300 optimal weight: 4.9990 chunk 262 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 285 optimal weight: 0.8980 chunk 200 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS B 180 GLN D 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.224632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.202671 restraints weight = 28855.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.195336 restraints weight = 34568.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.193992 restraints weight = 40575.195| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23304 Z= 0.133 Angle : 0.614 8.496 31916 Z= 0.317 Chirality : 0.044 0.233 3884 Planarity : 0.004 0.065 4022 Dihedral : 6.360 59.970 3496 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.34 % Favored : 91.59 % Rotamer: Outliers : 5.45 % Allowed : 21.95 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3152 helix: 1.63 (0.15), residues: 1294 sheet: -2.07 (0.26), residues: 322 loop : -2.30 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 584 HIS 0.015 0.001 HIS D 127 PHE 0.025 0.001 PHE D 351 TYR 0.017 0.001 TYR B 239 ARG 0.003 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 4) link_NAG-ASN : angle 1.33338 ( 12) link_BETA1-4 : bond 0.00446 ( 2) link_BETA1-4 : angle 1.31115 ( 6) hydrogen bonds : bond 0.03557 ( 1010) hydrogen bonds : angle 4.34344 ( 2964) SS BOND : bond 0.00413 ( 18) SS BOND : angle 1.64360 ( 36) covalent geometry : bond 0.00306 (23280) covalent geometry : angle 0.61078 (31862) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 287 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 730 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7566 (p-80) REVERT: B 207 MET cc_start: 0.5811 (mmm) cc_final: 0.5292 (mmt) REVERT: B 664 SER cc_start: 0.7502 (t) cc_final: 0.7238 (p) REVERT: C 839 MET cc_start: 0.7060 (ppp) cc_final: 0.6778 (ppp) REVERT: D 112 LEU cc_start: 0.8257 (tp) cc_final: 0.7991 (tp) REVERT: D 207 MET cc_start: 0.5745 (mmm) cc_final: 0.5403 (mmt) REVERT: D 664 SER cc_start: 0.7336 (t) cc_final: 0.7085 (p) outliers start: 119 outliers final: 105 residues processed: 381 average time/residue: 0.2666 time to fit residues: 172.9900 Evaluate side-chains 390 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 284 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 321 CYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 177 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 chunk 312 optimal weight: 0.4980 chunk 94 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 271 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS B 180 GLN D 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.232632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.194767 restraints weight = 29225.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.189624 restraints weight = 31718.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.191240 restraints weight = 46513.458| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23304 Z= 0.144 Angle : 0.631 9.883 31916 Z= 0.326 Chirality : 0.044 0.228 3884 Planarity : 0.004 0.068 4022 Dihedral : 6.344 59.332 3492 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.44 % Favored : 91.50 % Rotamer: Outliers : 5.55 % Allowed : 21.72 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 3152 helix: 1.59 (0.15), residues: 1296 sheet: -2.10 (0.26), residues: 322 loop : -2.29 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 285 HIS 0.008 0.001 HIS B 127 PHE 0.025 0.001 PHE D 351 TYR 0.017 0.001 TYR B 239 ARG 0.003 0.000 ARG B 742 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 4) link_NAG-ASN : angle 1.37261 ( 12) link_BETA1-4 : bond 0.00500 ( 2) link_BETA1-4 : angle 1.32441 ( 6) hydrogen bonds : bond 0.03678 ( 1010) hydrogen bonds : angle 4.36999 ( 2964) SS BOND : bond 0.00325 ( 18) SS BOND : angle 1.96651 ( 36) covalent geometry : bond 0.00336 (23280) covalent geometry : angle 0.62708 (31862) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 288 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 730 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7693 (p-80) REVERT: B 207 MET cc_start: 0.5914 (mmm) cc_final: 0.5436 (mmt) REVERT: B 664 SER cc_start: 0.7840 (t) cc_final: 0.7358 (p) REVERT: D 112 LEU cc_start: 0.8794 (tp) cc_final: 0.8528 (tp) REVERT: D 207 MET cc_start: 0.5675 (mmm) cc_final: 0.5243 (mmt) REVERT: D 702 MET cc_start: 0.8088 (tpp) cc_final: 0.7039 (mtp) REVERT: D 789 MET cc_start: 0.8390 (tpp) cc_final: 0.8084 (tpp) outliers start: 121 outliers final: 111 residues processed: 383 average time/residue: 0.2653 time to fit residues: 173.2550 Evaluate side-chains 394 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 282 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 321 CYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 561 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 709 PHE Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 279 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 266 optimal weight: 50.0000 chunk 261 optimal weight: 0.0270 chunk 194 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 288 optimal weight: 0.2980 chunk 184 optimal weight: 7.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 803 ASN B 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.225565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.203511 restraints weight = 28830.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.194572 restraints weight = 34215.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.193287 restraints weight = 45917.285| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23304 Z= 0.119 Angle : 0.618 9.303 31916 Z= 0.316 Chirality : 0.044 0.229 3884 Planarity : 0.004 0.067 4022 Dihedral : 6.267 58.665 3492 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.77 % Favored : 92.16 % Rotamer: Outliers : 4.77 % Allowed : 22.69 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3152 helix: 1.67 (0.15), residues: 1296 sheet: -2.04 (0.26), residues: 340 loop : -2.26 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 285 HIS 0.008 0.001 HIS B 127 PHE 0.025 0.001 PHE D 351 TYR 0.022 0.001 TYR D 239 ARG 0.010 0.000 ARG B 742 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 4) link_NAG-ASN : angle 1.38921 ( 12) link_BETA1-4 : bond 0.00455 ( 2) link_BETA1-4 : angle 1.32809 ( 6) hydrogen bonds : bond 0.03437 ( 1010) hydrogen bonds : angle 4.30174 ( 2964) SS BOND : bond 0.00370 ( 18) SS BOND : angle 1.74171 ( 36) covalent geometry : bond 0.00259 (23280) covalent geometry : angle 0.61450 (31862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6830.66 seconds wall clock time: 120 minutes 11.91 seconds (7211.91 seconds total)