Starting phenix.real_space_refine on Thu Jun 19 16:40:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arh_43782/06_2025/9arh_43782.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arh_43782/06_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_43782/06_2025/9arh_43782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arh_43782/06_2025/9arh_43782.map" model { file = "/net/cci-nas-00/data/ceres_data/9arh_43782/06_2025/9arh_43782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arh_43782/06_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-5710/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: 22.17, per 1000 atoms: 0.97 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: 5.62 Conformation dependent library (CDL) restraints added in 3.3 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: 3.58 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: 8.77 Time building geometry restraints manager: 6.69 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: 0.13 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 63.060 Find NCS groups from input model: 0.440 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: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.140 ------------------------------------------------------------------------------- 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 : 2.476 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: 0.3126 time to fit residues: 326.1597 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 : 2.361 ------------------------------------------------------------------------------- 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 = 0.221866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.192089 restraints weight = 26377.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.186058 restraints weight = 30689.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.186782 restraints weight = 35443.269| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 1.16920 ( 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 : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLN cc_start: 0.9205 (pp30) cc_final: 0.8993 (pp30) REVERT: A 675 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8522 (t80) REVERT: A 730 HIS cc_start: 0.8462 (OUTLIER) cc_final: 0.8104 (p-80) REVERT: A 743 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.8044 (mtm180) REVERT: A 801 HIS cc_start: 0.8811 (OUTLIER) cc_final: 0.7666 (t-90) REVERT: B 358 MET cc_start: 0.7871 (mmm) cc_final: 0.7631 (mmt) REVERT: B 563 PHE cc_start: 0.7880 (t80) cc_final: 0.7122 (m-10) REVERT: B 796 TRP cc_start: 0.8831 (m100) cc_final: 0.8569 (m100) REVERT: C 342 PHE cc_start: 0.7216 (t80) cc_final: 0.6678 (t80) REVERT: C 557 GLN cc_start: 0.9154 (pp30) cc_final: 0.8943 (pp30) REVERT: C 675 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8348 (t80) REVERT: C 723 MET cc_start: 0.7858 (tmm) cc_final: 0.7501 (tmm) REVERT: C 730 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8140 (p-80) REVERT: C 743 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7912 (mtm180) REVERT: D 207 MET cc_start: 0.5468 (mmm) cc_final: 0.4865 (mmt) REVERT: D 307 MET cc_start: 0.4006 (OUTLIER) cc_final: 0.3532 (mmm) REVERT: D 358 MET cc_start: 0.7646 (mmm) cc_final: 0.7246 (mmt) REVERT: D 563 PHE cc_start: 0.8053 (t80) cc_final: 0.7190 (m-10) outliers start: 156 outliers final: 96 residues processed: 457 average time/residue: 0.3101 time to fit residues: 239.5383 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 : 2.726 ------------------------------------------------------------------------------- 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: 0.0770 chunk 315 optimal weight: 3.9990 chunk 279 optimal weight: 7.9990 chunk 133 optimal weight: 0.6980 chunk 269 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 108 optimal weight: 40.0000 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 GLN ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.233950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.199110 restraints weight = 29405.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.190754 restraints weight = 29479.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.191647 restraints weight = 42317.310| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23304 Z= 0.142 Angle : 0.616 8.752 31916 Z= 0.325 Chirality : 0.045 0.195 3884 Planarity : 0.004 0.056 4022 Dihedral : 8.147 66.230 3561 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.93 % Favored : 92.01 % Rotamer: Outliers : 6.69 % Allowed : 17.37 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.63 (0.15), residues: 3152 helix: 0.95 (0.15), residues: 1314 sheet: -2.57 (0.25), residues: 322 loop : -2.70 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 391 HIS 0.005 0.001 HIS B 703 PHE 0.021 0.001 PHE B 351 TYR 0.016 0.001 TYR C 266 ARG 0.006 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 4) link_NAG-ASN : angle 1.28641 ( 12) link_BETA1-4 : bond 0.00748 ( 2) link_BETA1-4 : angle 1.26944 ( 6) hydrogen bonds : bond 0.04208 ( 1010) hydrogen bonds : angle 4.80386 ( 2964) SS BOND : bond 0.00442 ( 18) SS BOND : angle 1.52402 ( 36) covalent geometry : bond 0.00318 (23280) covalent geometry : angle 0.61356 (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 467 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 321 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLN cc_start: 0.9244 (pp30) cc_final: 0.8946 (pp30) REVERT: A 597 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.7001 (ttm) REVERT: A 730 HIS cc_start: 0.8460 (OUTLIER) cc_final: 0.8100 (p-80) REVERT: A 743 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8006 (mtm180) REVERT: B 358 MET cc_start: 0.8144 (mmm) cc_final: 0.7904 (mpp) REVERT: B 563 PHE cc_start: 0.7950 (t80) cc_final: 0.6894 (m-10) REVERT: B 664 SER cc_start: 0.7940 (t) cc_final: 0.7551 (p) REVERT: C 557 GLN cc_start: 0.9235 (pp30) cc_final: 0.8948 (pp30) REVERT: C 723 MET cc_start: 0.7844 (tmm) cc_final: 0.7567 (tmm) REVERT: C 743 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7946 (mtm180) REVERT: D 112 LEU cc_start: 0.8944 (mm) cc_final: 0.8532 (tp) REVERT: D 207 MET cc_start: 0.5466 (mmm) cc_final: 0.4917 (mmt) REVERT: D 307 MET cc_start: 0.4099 (OUTLIER) cc_final: 0.3546 (mmm) REVERT: D 563 PHE cc_start: 0.8166 (t80) cc_final: 0.7033 (m-10) REVERT: D 616 ASN cc_start: 0.5704 (OUTLIER) cc_final: 0.5500 (p0) REVERT: D 643 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8184 (tt) REVERT: D 664 SER cc_start: 0.7654 (t) cc_final: 0.7307 (p) REVERT: D 796 TRP cc_start: 0.8777 (m100) cc_final: 0.8463 (m100) outliers start: 146 outliers final: 104 residues processed: 441 average time/residue: 0.2871 time to fit residues: 212.2605 Evaluate side-chains 402 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 291 time to evaluate : 2.409 ------------------------------------------------------------------------------- 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 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 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 677 VAL 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 275 THR 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 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 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 749 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 784 PHE 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 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 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 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 616 ASN 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 749 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 786 ASP Chi-restraints excluded: chain D residue 793 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 306 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 282 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 303 optimal weight: 10.0000 chunk 313 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 ASN B 703 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4565 r_free = 0.4565 target = 0.223052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.201305 restraints weight = 29091.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.194366 restraints weight = 36668.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.193688 restraints weight = 37578.906| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23304 Z= 0.149 Angle : 0.617 8.440 31916 Z= 0.325 Chirality : 0.045 0.251 3884 Planarity : 0.004 0.054 4022 Dihedral : 7.711 60.693 3540 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.25 % Favored : 91.66 % Rotamer: Outliers : 7.10 % Allowed : 17.83 % Favored : 75.07 % 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: -1.40 (0.15), residues: 3152 helix: 1.15 (0.15), residues: 1306 sheet: -2.43 (0.25), residues: 322 loop : -2.57 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 391 HIS 0.006 0.001 HIS B 703 PHE 0.023 0.002 PHE A 554 TYR 0.016 0.001 TYR A 266 ARG 0.006 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 4) link_NAG-ASN : angle 1.30830 ( 12) link_BETA1-4 : bond 0.00576 ( 2) link_BETA1-4 : angle 1.06760 ( 6) hydrogen bonds : bond 0.04106 ( 1010) hydrogen bonds : angle 4.65049 ( 2964) SS BOND : bond 0.00288 ( 18) SS BOND : angle 1.25853 ( 36) covalent geometry : bond 0.00347 (23280) covalent geometry : angle 0.61507 (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 469 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 314 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 MET cc_start: 0.7979 (ptp) cc_final: 0.7775 (ptp) REVERT: A 730 HIS cc_start: 0.8271 (OUTLIER) cc_final: 0.7849 (p-80) REVERT: C 261 MET cc_start: 0.7132 (tpp) cc_final: 0.6825 (tpp) REVERT: C 342 PHE cc_start: 0.6438 (t80) cc_final: 0.6117 (t80) REVERT: C 723 MET cc_start: 0.7796 (tmm) cc_final: 0.7521 (tmm) REVERT: C 743 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7925 (mtm180) REVERT: D 207 MET cc_start: 0.5586 (mmm) cc_final: 0.5063 (mmt) REVERT: D 307 MET cc_start: 0.3941 (OUTLIER) cc_final: 0.3663 (mmm) REVERT: D 563 PHE cc_start: 0.8227 (t80) cc_final: 0.7111 (m-10) REVERT: D 796 TRP cc_start: 0.8871 (m100) cc_final: 0.8604 (m100) REVERT: D 818 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7630 (ptm) outliers start: 155 outliers final: 114 residues processed: 436 average time/residue: 0.2672 time to fit residues: 198.2987 Evaluate side-chains 404 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 286 time to evaluate : 2.666 ------------------------------------------------------------------------------- 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 166 LEU 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 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 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 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 422 VAL Chi-restraints excluded: chain B residue 425 LEU 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 510 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 567 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 575 PHE 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 784 PHE Chi-restraints excluded: chain B residue 800 ILE 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 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 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 589 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 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 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 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 602 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 756 VAL Chi-restraints excluded: chain D residue 776 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 Chi-restraints excluded: chain D residue 835 THR 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: 0.0870 chunk 274 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 4.9990 chunk 288 optimal weight: 0.9990 chunk 240 optimal weight: 8.9990 chunk 154 optimal weight: 0.3980 chunk 82 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- 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 B 491 ASN B 703 HIS C 426 GLN ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS D 491 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.234026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.196837 restraints weight = 29368.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.189161 restraints weight = 30850.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.190557 restraints weight = 41260.316| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2870 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= 0.125 Angle : 0.603 7.901 31916 Z= 0.317 Chirality : 0.044 0.198 3884 Planarity : 0.004 0.061 4022 Dihedral : 7.281 59.792 3522 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.96 % Favored : 91.94 % Rotamer: Outliers : 6.55 % Allowed : 19.07 % Favored : 74.38 % 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: 1.26 (0.15), residues: 1318 sheet: -2.32 (0.26), residues: 322 loop : -2.46 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 197 HIS 0.009 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 716 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 4) link_NAG-ASN : angle 1.32007 ( 12) link_BETA1-4 : bond 0.00569 ( 2) link_BETA1-4 : angle 1.26224 ( 6) hydrogen bonds : bond 0.03774 ( 1010) hydrogen bonds : angle 4.52761 ( 2964) SS BOND : bond 0.00593 ( 18) SS BOND : angle 1.85250 ( 36) covalent geometry : bond 0.00275 (23280) covalent geometry : angle 0.59954 (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 440 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 297 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 730 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.7874 (p-80) REVERT: B 157 MET cc_start: 0.8520 (mtm) cc_final: 0.8192 (mtt) REVERT: B 207 MET cc_start: 0.5756 (mmm) cc_final: 0.5173 (mmt) REVERT: B 563 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.7276 (t80) REVERT: C 723 MET cc_start: 0.7799 (tmm) cc_final: 0.7527 (tmm) REVERT: C 743 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7921 (mtm180) REVERT: D 112 LEU cc_start: 0.9002 (mm) cc_final: 0.8776 (tp) REVERT: D 207 MET cc_start: 0.5598 (mmm) cc_final: 0.5146 (mmt) REVERT: D 307 MET cc_start: 0.4000 (OUTLIER) cc_final: 0.3477 (mmm) REVERT: D 563 PHE cc_start: 0.8321 (t80) cc_final: 0.7087 (m-10) REVERT: D 631 MET cc_start: 0.7012 (tpt) cc_final: 0.6676 (tpt) REVERT: D 789 MET cc_start: 0.8314 (tpp) cc_final: 0.7940 (tpp) REVERT: D 796 TRP cc_start: 0.8766 (m100) cc_final: 0.8530 (m100) REVERT: D 818 MET cc_start: 0.8147 (ptm) cc_final: 0.7933 (ptm) outliers start: 143 outliers final: 111 residues processed: 407 average time/residue: 0.2754 time to fit residues: 191.7267 Evaluate side-chains 395 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 280 time to evaluate : 2.411 ------------------------------------------------------------------------------- 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 452 VAL Chi-restraints excluded: chain A residue 471 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 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 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 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 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 262 VAL Chi-restraints excluded: chain B residue 266 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 563 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 726 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 756 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 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 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 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 583 LEU 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 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 61 HIS Chi-restraints excluded: chain D residue 127 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 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 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 756 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 240 optimal weight: 30.0000 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 30.0000 chunk 234 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 C 730 HIS D 145 GLN D 491 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.221042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.198798 restraints weight = 28773.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.191284 restraints weight = 34092.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.189987 restraints weight = 38029.054| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23304 Z= 0.171 Angle : 0.635 8.803 31916 Z= 0.334 Chirality : 0.045 0.222 3884 Planarity : 0.004 0.058 4022 Dihedral : 7.255 59.545 3519 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.41 % Favored : 91.50 % Rotamer: Outliers : 7.52 % Allowed : 19.75 % 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: -1.22 (0.15), residues: 3152 helix: 1.29 (0.15), residues: 1306 sheet: -2.38 (0.25), residues: 322 loop : -2.46 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 584 HIS 0.023 0.001 HIS D 127 PHE 0.029 0.002 PHE A 554 TYR 0.027 0.001 TYR C 266 ARG 0.004 0.000 ARG A 716 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 4) link_NAG-ASN : angle 1.35076 ( 12) link_BETA1-4 : bond 0.00516 ( 2) link_BETA1-4 : angle 1.26466 ( 6) hydrogen bonds : bond 0.04172 ( 1010) hydrogen bonds : angle 4.59227 ( 2964) SS BOND : bond 0.00565 ( 18) SS BOND : angle 1.64702 ( 36) covalent geometry : bond 0.00408 (23280) covalent geometry : angle 0.63211 (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 460 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 296 time to evaluate : 2.552 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 430 VAL cc_start: 0.8697 (OUTLIER) cc_final: 0.8488 (t) REVERT: A 730 HIS cc_start: 0.8276 (OUTLIER) cc_final: 0.7800 (p-80) REVERT: B 207 MET cc_start: 0.5612 (mmm) cc_final: 0.5013 (mmt) REVERT: B 778 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8341 (tt) REVERT: C 430 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8538 (t) REVERT: C 723 MET cc_start: 0.7820 (tmm) cc_final: 0.7521 (tmm) REVERT: C 743 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7944 (mtm180) REVERT: D 207 MET cc_start: 0.5514 (mmm) cc_final: 0.5048 (mmt) REVERT: D 307 MET cc_start: 0.3809 (OUTLIER) cc_final: 0.3535 (mmm) REVERT: D 631 MET cc_start: 0.6895 (tpt) cc_final: 0.6556 (tpt) outliers start: 164 outliers final: 134 residues processed: 424 average time/residue: 0.2783 time to fit residues: 202.0541 Evaluate side-chains 423 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 283 time to evaluate : 2.516 ------------------------------------------------------------------------------- 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 430 VAL 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 579 PHE 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 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 720 LEU 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 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 238 THR 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 418 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 422 VAL 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 513 LEU 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 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 756 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 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 335 ILE Chi-restraints excluded: chain C residue 430 VAL 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 579 PHE Chi-restraints excluded: chain C residue 583 LEU 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 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 261 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 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 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 756 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 Chi-restraints excluded: chain D residue 835 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 191 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 222 optimal weight: 0.7980 chunk 201 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS B 127 HIS D 127 HIS D 491 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.232019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.196582 restraints weight = 29353.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.187466 restraints weight = 30350.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.189107 restraints weight = 38736.003| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23304 Z= 0.132 Angle : 0.615 9.226 31916 Z= 0.319 Chirality : 0.044 0.204 3884 Planarity : 0.004 0.056 4022 Dihedral : 6.988 59.711 3514 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.03 % Favored : 91.88 % Rotamer: Outliers : 6.74 % Allowed : 21.04 % Favored : 72.23 % 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: -1.07 (0.15), residues: 3152 helix: 1.47 (0.15), residues: 1292 sheet: -2.26 (0.25), residues: 322 loop : -2.40 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 197 HIS 0.016 0.001 HIS B 127 PHE 0.025 0.001 PHE D 351 TYR 0.026 0.001 TYR A 266 ARG 0.004 0.000 ARG A 716 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 4) link_NAG-ASN : angle 1.35175 ( 12) link_BETA1-4 : bond 0.00557 ( 2) link_BETA1-4 : angle 1.31721 ( 6) hydrogen bonds : bond 0.03793 ( 1010) hydrogen bonds : angle 4.46044 ( 2964) SS BOND : bond 0.00331 ( 18) SS BOND : angle 1.19540 ( 36) covalent geometry : bond 0.00297 (23280) covalent geometry : angle 0.61327 (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 447 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 300 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 THR cc_start: 0.7539 (t) cc_final: 0.7302 (m) REVERT: A 730 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.7725 (p-80) REVERT: B 207 MET cc_start: 0.5717 (mmm) cc_final: 0.5217 (mmt) REVERT: B 563 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.6630 (m-10) REVERT: B 778 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8377 (tt) REVERT: C 723 MET cc_start: 0.7843 (tmm) cc_final: 0.7603 (tmm) REVERT: D 207 MET cc_start: 0.5593 (mmm) cc_final: 0.5169 (mmt) outliers start: 147 outliers final: 122 residues processed: 415 average time/residue: 0.2635 time to fit residues: 187.8176 Evaluate side-chains 416 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 291 time to evaluate : 2.672 ------------------------------------------------------------------------------- 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 105 THR 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 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 672 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 787 SER 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 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 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 563 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 756 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 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 335 ILE Chi-restraints excluded: chain C residue 430 VAL 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 672 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 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 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 422 VAL Chi-restraints excluded: chain D residue 433 THR 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 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 756 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 116 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 228 optimal weight: 0.6980 chunk 287 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 314 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 104 optimal weight: 0.0570 chunk 158 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS D 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.223156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.200662 restraints weight = 28772.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.193685 restraints weight = 35186.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.191966 restraints weight = 39203.112| |-----------------------------------------------------------------------------| r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23304 Z= 0.128 Angle : 0.614 8.619 31916 Z= 0.317 Chirality : 0.044 0.194 3884 Planarity : 0.004 0.063 4022 Dihedral : 6.699 59.756 3505 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.34 % Favored : 91.59 % Rotamer: Outliers : 6.23 % Allowed : 21.59 % Favored : 72.18 % 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: -0.99 (0.15), residues: 3152 helix: 1.52 (0.15), residues: 1294 sheet: -2.17 (0.26), residues: 322 loop : -2.35 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 197 HIS 0.004 0.001 HIS D 127 PHE 0.025 0.001 PHE D 351 TYR 0.028 0.001 TYR A 266 ARG 0.003 0.000 ARG A 716 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 4) link_NAG-ASN : angle 1.35020 ( 12) link_BETA1-4 : bond 0.00489 ( 2) link_BETA1-4 : angle 1.33133 ( 6) hydrogen bonds : bond 0.03700 ( 1010) hydrogen bonds : angle 4.41387 ( 2964) SS BOND : bond 0.00308 ( 18) SS BOND : angle 1.17769 ( 36) covalent geometry : bond 0.00290 (23280) covalent geometry : angle 0.61221 (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 425 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 289 time to evaluate : 2.515 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: 0.8155 (OUTLIER) cc_final: 0.7580 (p-80) REVERT: B 207 MET cc_start: 0.5724 (mmm) cc_final: 0.5220 (mmt) REVERT: B 563 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.6684 (m-10) REVERT: C 730 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.7287 (p90) REVERT: D 207 MET cc_start: 0.5557 (mmm) cc_final: 0.5164 (mmt) outliers start: 136 outliers final: 117 residues processed: 394 average time/residue: 0.2588 time to fit residues: 175.6769 Evaluate side-chains 400 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 280 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 105 THR 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 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 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 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 563 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 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 756 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 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 430 VAL 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 672 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 730 HIS Chi-restraints excluded: chain C residue 773 LEU 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 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 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 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 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 756 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 140 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 138 optimal weight: 0.5980 chunk 300 optimal weight: 0.6980 chunk 262 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 285 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS B 127 HIS D 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.231512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.202031 restraints weight = 29306.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.199714 restraints weight = 63468.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.201253 restraints weight = 54721.346| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 23304 Z= 0.143 Angle : 0.629 8.750 31916 Z= 0.324 Chirality : 0.044 0.259 3884 Planarity : 0.004 0.067 4022 Dihedral : 6.621 59.122 3501 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.50 % Favored : 91.43 % Rotamer: Outliers : 6.14 % Allowed : 21.86 % Favored : 72.00 % 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: -0.99 (0.15), residues: 3152 helix: 1.52 (0.15), residues: 1294 sheet: -2.15 (0.26), residues: 322 loop : -2.35 (0.15), residues: 1536 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 0.025 0.001 TYR A 266 ARG 0.003 0.000 ARG A 716 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 4) link_NAG-ASN : angle 1.37148 ( 12) link_BETA1-4 : bond 0.00534 ( 2) link_BETA1-4 : angle 1.32904 ( 6) hydrogen bonds : bond 0.03784 ( 1010) hydrogen bonds : angle 4.41893 ( 2964) SS BOND : bond 0.00368 ( 18) SS BOND : angle 1.79137 ( 36) covalent geometry : bond 0.00334 (23280) covalent geometry : angle 0.62622 (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 421 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 287 time to evaluate : 2.429 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: 0.8221 (OUTLIER) cc_final: 0.7672 (p-80) REVERT: B 207 MET cc_start: 0.5821 (mmm) cc_final: 0.5300 (mmt) REVERT: B 340 ILE cc_start: 0.7923 (pt) cc_final: 0.7693 (pt) REVERT: D 207 MET cc_start: 0.5634 (mmm) cc_final: 0.5224 (mmt) REVERT: D 702 MET cc_start: 0.7665 (tpp) cc_final: 0.6964 (mtp) outliers start: 134 outliers final: 127 residues processed: 390 average time/residue: 0.2727 time to fit residues: 182.3717 Evaluate side-chains 409 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 281 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 105 THR 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 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 596 VAL 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 787 SER 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 126 ILE Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 144 PHE 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 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 756 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 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 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 672 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 773 LEU 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 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 411 LEU 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 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 599 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 756 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: 3.9990 chunk 310 optimal weight: 0.8980 chunk 312 optimal weight: 0.0030 chunk 94 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 89 optimal weight: 0.0370 chunk 136 optimal weight: 0.8980 chunk 271 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.4868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS D 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.224732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.202704 restraints weight = 28855.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.193899 restraints weight = 33547.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.191694 restraints weight = 44688.372| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23304 Z= 0.118 Angle : 0.616 8.414 31916 Z= 0.317 Chirality : 0.044 0.264 3884 Planarity : 0.004 0.068 4022 Dihedral : 6.526 59.554 3501 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.93 % Favored : 92.01 % Rotamer: Outliers : 5.09 % Allowed : 22.91 % Favored : 72.00 % 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: -0.87 (0.15), residues: 3152 helix: 1.64 (0.15), residues: 1280 sheet: -2.08 (0.26), residues: 340 loop : -2.27 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 285 HIS 0.008 0.001 HIS D 127 PHE 0.024 0.001 PHE D 351 TYR 0.023 0.001 TYR A 266 ARG 0.004 0.000 ARG B 742 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 4) link_NAG-ASN : angle 1.36697 ( 12) link_BETA1-4 : bond 0.00445 ( 2) link_BETA1-4 : angle 1.28736 ( 6) hydrogen bonds : bond 0.03516 ( 1010) hydrogen bonds : angle 4.35057 ( 2964) SS BOND : bond 0.00287 ( 18) SS BOND : angle 1.39763 ( 36) covalent geometry : bond 0.00257 (23280) covalent geometry : angle 0.61412 (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 400 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 289 time to evaluate : 2.324 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: 0.8144 (OUTLIER) cc_final: 0.7527 (p-80) REVERT: B 207 MET cc_start: 0.5693 (mmm) cc_final: 0.5168 (mmt) REVERT: B 340 ILE cc_start: 0.7963 (pt) cc_final: 0.7730 (pt) REVERT: B 563 PHE cc_start: 0.7507 (t80) cc_final: 0.6680 (m-10) REVERT: C 730 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7243 (p90) REVERT: D 207 MET cc_start: 0.5565 (mmm) cc_final: 0.5207 (mmt) REVERT: D 702 MET cc_start: 0.7586 (tpp) cc_final: 0.6935 (mtp) outliers start: 111 outliers final: 104 residues processed: 375 average time/residue: 0.2739 time to fit residues: 173.6936 Evaluate side-chains 388 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 282 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 105 THR 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 316 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 547 TYR 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 B residue 61 HIS Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 144 PHE 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 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 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 756 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 316 LEU 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 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 730 HIS 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 321 CYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 411 LEU 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 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 756 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: 0.0170 chunk 63 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 255 optimal weight: 0.7980 chunk 266 optimal weight: 40.0000 chunk 261 optimal weight: 0.0000 chunk 194 optimal weight: 0.0020 chunk 55 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 overall best weight: 0.2030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS C 689 ASN D 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.235892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.198907 restraints weight = 29382.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190975 restraints weight = 34075.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.193069 restraints weight = 41801.851| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 23304 Z= 0.112 Angle : 0.612 8.546 31916 Z= 0.312 Chirality : 0.043 0.251 3884 Planarity : 0.004 0.068 4022 Dihedral : 6.365 57.904 3499 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.77 % Favored : 92.13 % Rotamer: Outliers : 4.90 % Allowed : 23.33 % Favored : 71.77 % 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: -0.78 (0.15), residues: 3152 helix: 1.72 (0.15), residues: 1290 sheet: -1.99 (0.26), residues: 340 loop : -2.28 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 285 HIS 0.018 0.001 HIS D 127 PHE 0.024 0.001 PHE D 351 TYR 0.021 0.001 TYR D 239 ARG 0.010 0.000 ARG B 742 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 4) link_NAG-ASN : angle 1.37566 ( 12) link_BETA1-4 : bond 0.00504 ( 2) link_BETA1-4 : angle 1.34083 ( 6) hydrogen bonds : bond 0.03292 ( 1010) hydrogen bonds : angle 4.26864 ( 2964) SS BOND : bond 0.00260 ( 18) SS BOND : angle 1.09928 ( 36) covalent geometry : bond 0.00232 (23280) covalent geometry : angle 0.61018 (31862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7333.51 seconds wall clock time: 127 minutes 16.23 seconds (7636.23 seconds total)