Starting phenix.real_space_refine on Thu Mar 5 15:39:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wi1_21682/03_2026/6wi1_21682.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wi1_21682/03_2026/6wi1_21682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wi1_21682/03_2026/6wi1_21682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wi1_21682/03_2026/6wi1_21682.map" model { file = "/net/cci-nas-00/data/ceres_data/6wi1_21682/03_2026/6wi1_21682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wi1_21682/03_2026/6wi1_21682.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.032 sd= 0.873 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 130 5.16 5 C 14940 2.51 5 N 3856 2.21 5 O 4440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23366 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 5910 Classifications: {'peptide': 806} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 35, 'TRANS': 770} Chain breaks: 2 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 19, 'HIS:plan': 3, 'GLU:plan': 17, 'GLN:plan1': 8, 'ASN:plan1': 9, 'ASP:plan': 7, 'PHE:plan': 6, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 331 Chain: "B" Number of atoms: 5661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5661 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 28, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 563 Unresolved non-hydrogen angles: 691 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 16, 'GLU:plan': 18, 'HIS:plan': 6, 'PHE:plan': 8, 'ARG:plan': 12, 'GLN:plan1': 9, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 371 Chain: "C" Number of atoms: 5910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 5910 Classifications: {'peptide': 806} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 35, 'TRANS': 770} Chain breaks: 2 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 19, 'HIS:plan': 3, 'GLU:plan': 17, 'GLN:plan1': 8, 'ASN:plan1': 9, 'ASP:plan': 7, 'PHE:plan': 6, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 331 Chain: "D" Number of atoms: 5661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5661 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 28, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 563 Unresolved non-hydrogen angles: 691 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 16, 'GLU:plan': 18, 'HIS:plan': 6, 'PHE:plan': 8, 'ARG:plan': 12, 'GLN:plan1': 9, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 371 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: "F" 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: "G" 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: "H" 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: 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: "B" 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: "C" 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: "D" 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 Time building chain proxies: 5.41, per 1000 atoms: 0.23 Number of scatterers: 23366 At special positions: 0 Unit cell: (135.63, 149.33, 186.32, 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 130 16.00 O 4440 8.00 N 3856 7.00 C 14940 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 719 " - pdb=" SG CYS B 795 " distance=2.00 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.05 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.05 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 746 " - pdb=" SG CYS B 801 " distance=2.03 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 719 " - pdb=" SG CYS D 795 " distance=2.09 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.05 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.05 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 901 " - " ASN A 224 " " NAG A 902 " - " ASN A 297 " " NAG B 903 " - " ASN B 491 " " NAG B 904 " - " ASN B 341 " " NAG C 901 " - " ASN C 224 " " NAG C 902 " - " ASN C 297 " " NAG D 903 " - " ASN D 491 " " NAG D 904 " - " ASN D 341 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN B 348 " " NAG G 1 " - " ASN D 688 " " NAG H 1 " - " ASN D 348 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 982.1 milliseconds 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 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: 102 helices and 34 sheets defined 43.6% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 37 through 53 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 104 through 113 removed outlier: 4.275A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.551A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.811A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.570A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 Processing helix chain 'A' and resid 297 through 317 removed outlier: 3.920A pdb=" N HIS A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 520 through 529 removed outlier: 4.149A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 581 through 605 removed outlier: 4.242A pdb=" N VAL A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 647 through 679 removed outlier: 4.044A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 734 through 744 Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 787 through 803 removed outlier: 4.069A pdb=" N GLN A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 830 through 862 removed outlier: 4.449A pdb=" N GLY A 836 " --> pdb=" O GLU A 832 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL A 837 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.723A pdb=" N ASP B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 removed outlier: 3.948A pdb=" N ASP B 58 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N HIS B 60 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HIS B 61 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 62 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 93 removed outlier: 3.632A pdb=" N LYS B 93 " --> pdb=" O MET B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.603A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 3.593A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 222 Processing helix chain 'B' and resid 233 through 247 Processing helix chain 'B' and resid 288 through 312 removed outlier: 4.183A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 removed outlier: 3.928A pdb=" N ILE B 329 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 341 removed outlier: 4.243A pdb=" N ASN B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.687A 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 521 removed outlier: 3.766A pdb=" N SER B 520 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 578 Processing helix chain 'B' and resid 601 through 615 removed outlier: 3.823A pdb=" N ALA B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 654 removed outlier: 4.016A pdb=" N ILE B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 690 through 699 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 714 through 724 removed outlier: 3.572A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.116A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.481A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 795 removed outlier: 3.585A pdb=" N LEU B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 844 removed outlier: 3.857A pdb=" N TRP B 844 " --> pdb=" O HIS B 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 53 Processing helix chain 'C' and resid 70 through 84 Processing helix chain 'C' and resid 104 through 113 removed outlier: 4.274A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.552A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.811A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.570A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU C 234 " --> pdb=" O MET C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 260 Processing helix chain 'C' and resid 297 through 317 removed outlier: 3.921A pdb=" N HIS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 478 through 492 Processing helix chain 'C' and resid 520 through 529 removed outlier: 4.149A pdb=" N GLY C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 581 through 605 removed outlier: 4.242A pdb=" N VAL C 587 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY C 588 " --> pdb=" O TRP C 584 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 647 through 679 removed outlier: 4.046A pdb=" N ARG C 651 " --> pdb=" O SER C 647 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL C 677 " --> pdb=" O ALA C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 694 Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 717 through 719 No H-bonds generated for 'chain 'C' and resid 717 through 719' Processing helix chain 'C' and resid 720 through 729 Processing helix chain 'C' and resid 734 through 744 Processing helix chain 'C' and resid 754 through 764 Processing helix chain 'C' and resid 787 through 803 removed outlier: 4.070A pdb=" N GLN C 791 " --> pdb=" O SER C 787 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 830 through 862 removed outlier: 4.451A pdb=" N GLY C 836 " --> pdb=" O GLU C 832 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL C 837 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 removed outlier: 3.723A pdb=" N ASP D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 62 removed outlier: 3.949A pdb=" N ASP D 58 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N HIS D 60 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS D 61 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D 62 " --> pdb=" O PHE D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 removed outlier: 3.632A pdb=" N LYS D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 Processing helix chain 'D' and resid 150 through 164 removed outlier: 3.603A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 removed outlier: 3.593A pdb=" N VAL D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 222 Processing helix chain 'D' and resid 233 through 247 Processing helix chain 'D' and resid 288 through 312 removed outlier: 4.183A pdb=" N GLU D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 331 removed outlier: 3.928A pdb=" N ILE D 329 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 removed outlier: 4.243A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.687A 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 521 removed outlier: 3.767A pdb=" N SER D 520 " --> pdb=" O ASN D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 578 Processing helix chain 'D' and resid 601 through 615 removed outlier: 3.823A pdb=" N ALA D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 654 removed outlier: 4.016A pdb=" N ILE D 630 " --> pdb=" O THR D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 690 through 699 Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 714 through 724 removed outlier: 3.572A pdb=" N GLY D 724 " --> pdb=" O SER D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.117A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 786 removed outlier: 4.481A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 795 removed outlier: 3.585A pdb=" N LEU D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 844 removed outlier: 3.858A pdb=" N TRP D 844 " --> pdb=" O HIS D 840 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 61 removed outlier: 7.931A pdb=" N VAL A 87 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 211 through 216 removed outlier: 7.505A pdb=" N ILE A 163 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 215 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 165 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL A 239 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 243 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 269 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 242 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 292 removed outlier: 3.712A pdb=" N GLY A 386 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 431 through 434 removed outlier: 3.563A pdb=" N TYR A 477 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 456 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU A 499 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N THR A 458 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 510 Processing sheet with id=AA7, first strand: chain 'A' and resid 549 through 550 Processing sheet with id=AA8, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 703 removed outlier: 6.612A pdb=" N ALA A 703 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ASP A 753 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 561 " --> pdb=" O THR A 770 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 71 through 73 removed outlier: 7.768A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ALA B 100 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 204 removed outlier: 6.281A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 170 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 231 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 257 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 230 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB4, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AB5, first strand: chain 'B' and resid 418 through 420 removed outlier: 3.621A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB7, first strand: chain 'B' and resid 728 through 732 removed outlier: 3.543A pdb=" N LEU B 748 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 728 through 732 removed outlier: 5.017A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 6.282A 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 61 Processing sheet with id=AC1, first strand: chain 'C' and resid 59 through 61 removed outlier: 7.931A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 211 through 216 removed outlier: 7.505A pdb=" N ILE C 163 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 215 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 165 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL C 239 " --> pdb=" O HIS C 162 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 243 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 269 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 242 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 290 through 292 removed outlier: 3.711A pdb=" N GLY C 386 " --> pdb=" O ILE C 374 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 431 through 434 removed outlier: 3.563A pdb=" N TYR C 477 " --> pdb=" O TYR C 431 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 456 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU C 499 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N THR C 458 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 508 through 510 Processing sheet with id=AC6, first strand: chain 'C' and resid 549 through 550 Processing sheet with id=AC7, first strand: chain 'C' and resid 556 through 557 Processing sheet with id=AC8, first strand: chain 'C' and resid 702 through 703 removed outlier: 6.613A pdb=" N ALA C 703 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ASP C 753 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 561 " --> pdb=" O THR C 770 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 71 through 73 removed outlier: 7.767A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 201 through 204 removed outlier: 6.281A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 170 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR D 231 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 257 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 230 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AD3, first strand: chain 'D' and resid 408 through 409 Processing sheet with id=AD4, first strand: chain 'D' and resid 418 through 420 removed outlier: 3.622A pdb=" N CYS D 456 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD6, first strand: chain 'D' and resid 728 through 732 removed outlier: 3.544A pdb=" N LEU D 748 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 728 through 732 removed outlier: 5.016A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 1074 hydrogen bonds defined for protein. 3102 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: 4.41 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7574 1.34 - 1.47: 5765 1.47 - 1.59: 10295 1.59 - 1.71: 0 1.71 - 1.83: 216 Bond restraints: 23850 Sorted by residual: bond pdb=" C ILE A 401 " pdb=" N TRP A 402 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.86e-02 2.89e+03 9.07e+00 bond pdb=" C ILE C 401 " pdb=" N TRP C 402 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.86e-02 2.89e+03 8.93e+00 bond pdb=" CB TRP D 166 " pdb=" CG TRP D 166 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.43e+00 bond pdb=" CB TRP B 166 " pdb=" CG TRP B 166 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.34e+00 bond pdb=" CA PRO D 674 " pdb=" CB PRO D 674 " ideal model delta sigma weight residual 1.532 1.517 0.015 7.10e-03 1.98e+04 4.19e+00 ... (remaining 23845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 32040 2.65 - 5.31: 484 5.31 - 7.96: 46 7.96 - 10.62: 8 10.62 - 13.27: 4 Bond angle restraints: 32582 Sorted by residual: angle pdb=" C ILE D 85 " pdb=" N CYS D 86 " pdb=" CA CYS D 86 " ideal model delta sigma weight residual 121.14 111.58 9.56 1.75e+00 3.27e-01 2.98e+01 angle pdb=" C ILE B 85 " pdb=" N CYS B 86 " pdb=" CA CYS B 86 " ideal model delta sigma weight residual 121.14 111.58 9.56 1.75e+00 3.27e-01 2.98e+01 angle pdb=" CA CYS C 765 " pdb=" CB CYS C 765 " pdb=" SG CYS C 765 " ideal model delta sigma weight residual 114.40 126.66 -12.26 2.30e+00 1.89e-01 2.84e+01 angle pdb=" CA CYS A 765 " pdb=" CB CYS A 765 " pdb=" SG CYS A 765 " ideal model delta sigma weight residual 114.40 126.64 -12.24 2.30e+00 1.89e-01 2.83e+01 angle pdb=" C PRO A 468 " pdb=" N ARG A 469 " pdb=" CA ARG A 469 " ideal model delta sigma weight residual 121.54 131.51 -9.97 1.91e+00 2.74e-01 2.73e+01 ... (remaining 32577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 12959 17.46 - 34.92: 1097 34.92 - 52.38: 178 52.38 - 69.83: 50 69.83 - 87.29: 18 Dihedral angle restraints: 14302 sinusoidal: 5104 harmonic: 9198 Sorted by residual: dihedral pdb=" CA LYS A 764 " pdb=" C LYS A 764 " pdb=" N CYS A 765 " pdb=" CA CYS A 765 " ideal model delta harmonic sigma weight residual 180.00 121.51 58.49 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA LYS C 764 " pdb=" C LYS C 764 " pdb=" N CYS C 765 " pdb=" CA CYS C 765 " ideal model delta harmonic sigma weight residual 180.00 121.56 58.44 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 321 " pdb=" CB CYS B 321 " ideal model delta sinusoidal sigma weight residual -86.00 -7.29 -78.71 1 1.00e+01 1.00e-02 7.72e+01 ... (remaining 14299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.743: 3926 0.743 - 1.486: 0 1.486 - 2.229: 0 2.229 - 2.972: 0 2.972 - 3.715: 2 Chirality restraints: 3928 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 1.31 -3.71 2.00e-02 2.50e+03 3.45e+04 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 1.31 -3.71 2.00e-02 2.50e+03 3.44e+04 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 -2.54 0.14 2.00e-02 2.50e+03 4.88e+01 ... (remaining 3925 not shown) Planarity restraints: 4152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 813 " 0.023 2.00e-02 2.50e+03 1.64e-02 6.72e+00 pdb=" CG TRP C 813 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 813 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 813 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 813 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 813 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 813 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 813 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 813 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 813 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 813 " -0.022 2.00e-02 2.50e+03 1.62e-02 6.60e+00 pdb=" CG TRP A 813 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 813 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 813 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 813 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 813 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 813 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 813 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 813 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 813 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 567 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO C 568 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 568 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 568 " -0.033 5.00e-02 4.00e+02 ... (remaining 4149 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 831 2.68 - 3.24: 25441 3.24 - 3.79: 35411 3.79 - 4.35: 43273 4.35 - 4.90: 70471 Nonbonded interactions: 175427 Sorted by model distance: nonbonded pdb=" O ASP A 324 " pdb=" NE1 TRP A 336 " model vdw 2.127 3.120 nonbonded pdb=" O ASP C 324 " pdb=" NE1 TRP C 336 " model vdw 2.127 3.120 nonbonded pdb=" OD1 ASP D 77 " pdb=" N SER D 80 " model vdw 2.152 3.120 nonbonded pdb=" OD1 ASP B 77 " pdb=" N SER B 80 " model vdw 2.153 3.120 nonbonded pdb=" OD1 ASP D 101 " pdb=" N ASP D 102 " model vdw 2.188 3.120 ... (remaining 175422 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.310 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.007 0.065 23884 Z= 0.319 Angle : 0.995 57.599 32666 Z= 0.503 Chirality : 0.097 3.715 3928 Planarity : 0.005 0.061 4140 Dihedral : 13.878 87.292 8308 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.47 % Favored : 85.09 % Rotamer: Outliers : 0.70 % Allowed : 8.72 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.12), residues: 3158 helix: -1.66 (0.12), residues: 1276 sheet: -4.13 (0.21), residues: 372 loop : -4.04 (0.12), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 693 TYR 0.019 0.002 TYR B 507 PHE 0.019 0.002 PHE C 774 TRP 0.044 0.002 TRP C 813 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00669 (23850) covalent geometry : angle 0.84480 (32582) SS BOND : bond 0.01797 ( 18) SS BOND : angle 2.50791 ( 36) hydrogen bonds : bond 0.16872 ( 1060) hydrogen bonds : angle 7.32779 ( 3102) link_BETA1-4 : bond 0.06393 ( 4) link_BETA1-4 : angle 26.45577 ( 12) link_NAG-ASN : bond 0.00480 ( 12) link_NAG-ASN : angle 3.63345 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 253 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 230 MET cc_start: 0.8822 (mmm) cc_final: 0.8620 (mmm) REVERT: A 261 MET cc_start: 0.8444 (mmm) cc_final: 0.8207 (mmm) REVERT: A 287 ILE cc_start: 0.8699 (pt) cc_final: 0.8485 (mm) REVERT: A 375 MET cc_start: 0.8708 (mpp) cc_final: 0.8136 (mpp) REVERT: A 377 LEU cc_start: 0.8989 (tp) cc_final: 0.8760 (tp) REVERT: A 702 TYR cc_start: 0.8513 (m-80) cc_final: 0.8295 (m-80) REVERT: A 758 GLU cc_start: 0.8830 (tp30) cc_final: 0.8458 (tm-30) REVERT: A 783 MET cc_start: 0.8403 (mtm) cc_final: 0.8130 (mtp) REVERT: A 806 MET cc_start: 0.9258 (mmm) cc_final: 0.8887 (mmt) REVERT: B 89 MET cc_start: 0.9099 (ptp) cc_final: 0.8591 (ppp) REVERT: B 354 ASP cc_start: 0.9463 (m-30) cc_final: 0.9191 (m-30) REVERT: B 430 MET cc_start: 0.8400 (tmm) cc_final: 0.8055 (ttm) REVERT: B 789 MET cc_start: 0.8776 (mmm) cc_final: 0.8516 (mmt) REVERT: C 230 MET cc_start: 0.8825 (mmm) cc_final: 0.8591 (mmm) REVERT: C 261 MET cc_start: 0.8437 (mmm) cc_final: 0.8177 (mmm) REVERT: C 375 MET cc_start: 0.8619 (mpp) cc_final: 0.8289 (mpp) REVERT: C 758 GLU cc_start: 0.8902 (tp30) cc_final: 0.8514 (tm-30) REVERT: C 783 MET cc_start: 0.8521 (mtm) cc_final: 0.8294 (mtp) REVERT: C 806 MET cc_start: 0.9220 (mmm) cc_final: 0.8844 (mmt) REVERT: D 89 MET cc_start: 0.8973 (ptp) cc_final: 0.8503 (ppp) REVERT: D 430 MET cc_start: 0.8492 (tmm) cc_final: 0.8145 (ttm) REVERT: D 562 MET cc_start: 0.7598 (ttp) cc_final: 0.7303 (ttp) REVERT: D 789 MET cc_start: 0.8766 (mmm) cc_final: 0.8480 (mmt) outliers start: 16 outliers final: 10 residues processed: 269 average time/residue: 0.1199 time to fit residues: 55.1761 Evaluate side-chains 203 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 193 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain D residue 471 SER Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 769 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.0030 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 134 HIS A 314 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 HIS A 730 HIS B 127 HIS B 616 ASN C 134 HIS C 314 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 730 HIS D 127 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.092297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.068129 restraints weight = 83812.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.070104 restraints weight = 42930.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.071445 restraints weight = 28569.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.072289 restraints weight = 22174.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.072786 restraints weight = 18981.870| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23884 Z= 0.157 Angle : 0.740 11.096 32666 Z= 0.383 Chirality : 0.046 0.261 3928 Planarity : 0.005 0.055 4140 Dihedral : 7.381 60.240 3682 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.32 % Favored : 89.49 % Rotamer: Outliers : 2.35 % Allowed : 14.39 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.14), residues: 3158 helix: 0.01 (0.14), residues: 1286 sheet: -3.55 (0.22), residues: 416 loop : -3.44 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 124 TYR 0.016 0.001 TYR D 479 PHE 0.027 0.002 PHE D 169 TRP 0.024 0.002 TRP A 813 HIS 0.004 0.001 HIS C 748 Details of bonding type rmsd covalent geometry : bond 0.00345 (23850) covalent geometry : angle 0.72832 (32582) SS BOND : bond 0.00546 ( 18) SS BOND : angle 1.98581 ( 36) hydrogen bonds : bond 0.05141 ( 1060) hydrogen bonds : angle 5.53068 ( 3102) link_BETA1-4 : bond 0.00577 ( 4) link_BETA1-4 : angle 0.82623 ( 12) link_NAG-ASN : bond 0.00226 ( 12) link_NAG-ASN : angle 3.47571 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 0.661 Fit side-chains REVERT: A 230 MET cc_start: 0.8645 (mmm) cc_final: 0.8350 (mmm) REVERT: A 269 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8759 (pt) REVERT: A 377 LEU cc_start: 0.8876 (tp) cc_final: 0.8562 (tp) REVERT: A 758 GLU cc_start: 0.8607 (tp30) cc_final: 0.8239 (tm-30) REVERT: A 783 MET cc_start: 0.8117 (mtm) cc_final: 0.7861 (mtp) REVERT: A 789 TRP cc_start: 0.6890 (m-10) cc_final: 0.6667 (m100) REVERT: A 806 MET cc_start: 0.9247 (mmm) cc_final: 0.8585 (mmt) REVERT: B 89 MET cc_start: 0.8455 (ptp) cc_final: 0.8143 (ppp) REVERT: B 157 MET cc_start: 0.9138 (mtm) cc_final: 0.8790 (mtm) REVERT: B 354 ASP cc_start: 0.8866 (m-30) cc_final: 0.8581 (m-30) REVERT: B 706 MET cc_start: 0.7991 (mtm) cc_final: 0.7772 (mtm) REVERT: C 74 MET cc_start: 0.9028 (tmm) cc_final: 0.8772 (tmm) REVERT: C 230 MET cc_start: 0.8521 (mmm) cc_final: 0.8199 (mmm) REVERT: C 261 MET cc_start: 0.8405 (mmm) cc_final: 0.7975 (mmp) REVERT: C 269 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8847 (pt) REVERT: C 347 MET cc_start: 0.9011 (ttp) cc_final: 0.8730 (ttm) REVERT: C 377 LEU cc_start: 0.8786 (tp) cc_final: 0.8432 (tp) REVERT: C 693 LEU cc_start: 0.8948 (tp) cc_final: 0.8646 (tp) REVERT: C 758 GLU cc_start: 0.8765 (tp30) cc_final: 0.8200 (tm-30) REVERT: C 783 MET cc_start: 0.8314 (mtm) cc_final: 0.8048 (mtp) REVERT: C 806 MET cc_start: 0.9200 (mmm) cc_final: 0.8893 (mmm) REVERT: D 132 MET cc_start: 0.8226 (mmm) cc_final: 0.8012 (mmm) REVERT: D 272 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: D 562 MET cc_start: 0.8348 (ttp) cc_final: 0.8089 (ttp) outliers start: 54 outliers final: 25 residues processed: 273 average time/residue: 0.1164 time to fit residues: 55.0415 Evaluate side-chains 228 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 471 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 632 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 162 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 230 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 271 optimal weight: 10.0000 chunk 47 optimal weight: 0.0570 chunk 299 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 294 optimal weight: 40.0000 overall best weight: 2.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 HIS C 86 GLN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.092562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.068461 restraints weight = 83180.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.070507 restraints weight = 41790.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.071853 restraints weight = 27415.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.072719 restraints weight = 21105.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.073165 restraints weight = 17943.558| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23884 Z= 0.151 Angle : 0.714 11.188 32666 Z= 0.367 Chirality : 0.045 0.248 3928 Planarity : 0.005 0.054 4140 Dihedral : 6.903 60.817 3678 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.78 % Favored : 90.03 % Rotamer: Outliers : 3.27 % Allowed : 14.82 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.15), residues: 3158 helix: 0.61 (0.14), residues: 1296 sheet: -3.06 (0.23), residues: 442 loop : -3.09 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 694 TYR 0.017 0.001 TYR D 479 PHE 0.023 0.001 PHE B 169 TRP 0.017 0.001 TRP A 813 HIS 0.004 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00335 (23850) covalent geometry : angle 0.70036 (32582) SS BOND : bond 0.00818 ( 18) SS BOND : angle 2.95262 ( 36) hydrogen bonds : bond 0.04667 ( 1060) hydrogen bonds : angle 5.18041 ( 3102) link_BETA1-4 : bond 0.00176 ( 4) link_BETA1-4 : angle 1.28252 ( 12) link_NAG-ASN : bond 0.00297 ( 12) link_NAG-ASN : angle 3.10077 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 215 time to evaluate : 0.737 Fit side-chains REVERT: A 230 MET cc_start: 0.8609 (mmm) cc_final: 0.8329 (mmm) REVERT: A 240 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8374 (pt) REVERT: A 269 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8786 (pt) REVERT: A 347 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8720 (ttm) REVERT: A 377 LEU cc_start: 0.8936 (tp) cc_final: 0.8614 (tp) REVERT: A 757 LEU cc_start: 0.8664 (tp) cc_final: 0.8456 (tp) REVERT: A 758 GLU cc_start: 0.8578 (tp30) cc_final: 0.8262 (tm-30) REVERT: A 806 MET cc_start: 0.9278 (mmm) cc_final: 0.8460 (mmt) REVERT: B 89 MET cc_start: 0.8714 (ptp) cc_final: 0.8503 (ppp) REVERT: B 157 MET cc_start: 0.9170 (mtm) cc_final: 0.8922 (mtm) REVERT: B 354 ASP cc_start: 0.8830 (m-30) cc_final: 0.8533 (m-30) REVERT: C 74 MET cc_start: 0.9116 (tmm) cc_final: 0.8856 (tmm) REVERT: C 230 MET cc_start: 0.8535 (mmm) cc_final: 0.8207 (mmm) REVERT: C 269 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8839 (pt) REVERT: C 347 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8695 (ttm) REVERT: C 377 LEU cc_start: 0.8773 (tp) cc_final: 0.8400 (tp) REVERT: C 758 GLU cc_start: 0.8603 (tp30) cc_final: 0.8195 (tm-30) REVERT: C 783 MET cc_start: 0.8257 (mtm) cc_final: 0.8050 (mtp) REVERT: C 806 MET cc_start: 0.9206 (mmm) cc_final: 0.8546 (mmt) REVERT: D 132 MET cc_start: 0.8292 (mmm) cc_final: 0.8052 (mmm) REVERT: D 157 MET cc_start: 0.8988 (mtm) cc_final: 0.8714 (mtt) outliers start: 75 outliers final: 43 residues processed: 273 average time/residue: 0.1159 time to fit residues: 54.8842 Evaluate side-chains 246 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 632 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 158 optimal weight: 20.0000 chunk 244 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 220 optimal weight: 20.0000 chunk 242 optimal weight: 10.0000 chunk 311 optimal weight: 6.9990 chunk 300 optimal weight: 4.9990 chunk 115 optimal weight: 0.0670 chunk 28 optimal weight: 30.0000 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 147 GLN A 426 GLN B 782 GLN C 67 HIS C 147 GLN C 426 GLN D 782 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.090990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.066746 restraints weight = 83530.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.068708 restraints weight = 42932.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.069995 restraints weight = 28618.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.070811 restraints weight = 22276.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.071312 restraints weight = 19119.840| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23884 Z= 0.230 Angle : 0.753 12.179 32666 Z= 0.388 Chirality : 0.046 0.265 3928 Planarity : 0.005 0.053 4140 Dihedral : 6.738 62.668 3673 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.51 % Favored : 89.36 % Rotamer: Outliers : 4.01 % Allowed : 16.70 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.15), residues: 3158 helix: 0.86 (0.14), residues: 1278 sheet: -2.92 (0.23), residues: 456 loop : -3.00 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 694 TYR 0.016 0.002 TYR B 507 PHE 0.027 0.002 PHE D 169 TRP 0.018 0.002 TRP A 813 HIS 0.006 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00520 (23850) covalent geometry : angle 0.74274 (32582) SS BOND : bond 0.00726 ( 18) SS BOND : angle 2.34954 ( 36) hydrogen bonds : bond 0.04853 ( 1060) hydrogen bonds : angle 5.15480 ( 3102) link_BETA1-4 : bond 0.00362 ( 4) link_BETA1-4 : angle 1.32924 ( 12) link_NAG-ASN : bond 0.00375 ( 12) link_NAG-ASN : angle 2.96363 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 209 time to evaluate : 0.885 Fit side-chains REVERT: A 147 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: A 230 MET cc_start: 0.8589 (mmm) cc_final: 0.8309 (mmm) REVERT: A 347 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8781 (ttm) REVERT: A 377 LEU cc_start: 0.8940 (tp) cc_final: 0.8596 (tp) REVERT: A 702 TYR cc_start: 0.7849 (m-10) cc_final: 0.7644 (m-10) REVERT: A 727 MET cc_start: 0.9058 (ttm) cc_final: 0.8775 (ttm) REVERT: A 757 LEU cc_start: 0.8866 (tp) cc_final: 0.8565 (tp) REVERT: A 758 GLU cc_start: 0.8670 (tp30) cc_final: 0.8353 (tm-30) REVERT: A 806 MET cc_start: 0.9264 (mmm) cc_final: 0.8473 (mmt) REVERT: B 89 MET cc_start: 0.8545 (ptp) cc_final: 0.8344 (ppp) REVERT: B 354 ASP cc_start: 0.8876 (m-30) cc_final: 0.8562 (m-30) REVERT: B 688 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8378 (p0) REVERT: C 74 MET cc_start: 0.9112 (tmm) cc_final: 0.8784 (tmm) REVERT: C 147 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8453 (tt0) REVERT: C 230 MET cc_start: 0.8536 (mmm) cc_final: 0.8214 (mmm) REVERT: C 269 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8859 (pt) REVERT: C 347 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8724 (ttm) REVERT: C 375 MET cc_start: 0.8084 (mpp) cc_final: 0.7881 (mpp) REVERT: C 377 LEU cc_start: 0.8917 (tp) cc_final: 0.8534 (tp) REVERT: C 693 LEU cc_start: 0.9071 (tp) cc_final: 0.8836 (tp) REVERT: C 758 GLU cc_start: 0.8696 (tp30) cc_final: 0.8243 (tm-30) REVERT: C 783 MET cc_start: 0.8352 (mtm) cc_final: 0.8148 (mtp) REVERT: C 806 MET cc_start: 0.9204 (mmm) cc_final: 0.8301 (mmm) REVERT: D 101 ASP cc_start: 0.7882 (t0) cc_final: 0.7648 (t0) REVERT: D 132 MET cc_start: 0.8487 (mmm) cc_final: 0.8198 (mmm) REVERT: D 272 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7552 (mp0) outliers start: 92 outliers final: 51 residues processed: 291 average time/residue: 0.1121 time to fit residues: 56.8422 Evaluate side-chains 252 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 688 ASN Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 147 GLN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 691 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 262 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 291 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 284 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 200 optimal weight: 0.0570 chunk 249 optimal weight: 0.8980 chunk 242 optimal weight: 0.0060 chunk 38 optimal weight: 5.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.093964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.069995 restraints weight = 83257.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.072037 restraints weight = 42123.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.073391 restraints weight = 27713.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.074255 restraints weight = 21359.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.074756 restraints weight = 18180.470| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23884 Z= 0.126 Angle : 0.702 12.153 32666 Z= 0.356 Chirality : 0.045 0.277 3928 Planarity : 0.005 0.051 4140 Dihedral : 6.349 62.302 3672 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.90 % Favored : 90.98 % Rotamer: Outliers : 3.01 % Allowed : 18.48 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.15), residues: 3158 helix: 1.19 (0.15), residues: 1272 sheet: -2.58 (0.23), residues: 478 loop : -2.76 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 694 TYR 0.015 0.001 TYR B 479 PHE 0.039 0.001 PHE D 169 TRP 0.048 0.002 TRP C 657 HIS 0.003 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00266 (23850) covalent geometry : angle 0.68727 (32582) SS BOND : bond 0.00608 ( 18) SS BOND : angle 3.13254 ( 36) hydrogen bonds : bond 0.04175 ( 1060) hydrogen bonds : angle 4.84186 ( 3102) link_BETA1-4 : bond 0.00413 ( 4) link_BETA1-4 : angle 1.45024 ( 12) link_NAG-ASN : bond 0.00430 ( 12) link_NAG-ASN : angle 2.98481 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 230 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 230 MET cc_start: 0.8557 (mmm) cc_final: 0.8284 (mmm) REVERT: A 261 MET cc_start: 0.8603 (tpp) cc_final: 0.8350 (tpp) REVERT: A 347 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8709 (ttm) REVERT: A 377 LEU cc_start: 0.8840 (tp) cc_final: 0.8557 (tp) REVERT: A 757 LEU cc_start: 0.8782 (tp) cc_final: 0.8528 (tp) REVERT: A 758 GLU cc_start: 0.8504 (tp30) cc_final: 0.8228 (tm-30) REVERT: A 806 MET cc_start: 0.9266 (mmm) cc_final: 0.8859 (mmt) REVERT: B 354 ASP cc_start: 0.8846 (m-30) cc_final: 0.8502 (m-30) REVERT: C 74 MET cc_start: 0.8999 (tmm) cc_final: 0.8673 (tmm) REVERT: C 230 MET cc_start: 0.8484 (mmm) cc_final: 0.8164 (mmm) REVERT: C 347 MET cc_start: 0.8947 (ttp) cc_final: 0.8645 (ttm) REVERT: C 377 LEU cc_start: 0.8770 (tp) cc_final: 0.8430 (tp) REVERT: C 758 GLU cc_start: 0.8633 (tp30) cc_final: 0.8233 (tm-30) REVERT: C 806 MET cc_start: 0.9203 (mmm) cc_final: 0.8494 (mmt) REVERT: D 101 ASP cc_start: 0.7769 (t0) cc_final: 0.7564 (t0) REVERT: D 132 MET cc_start: 0.8538 (mmm) cc_final: 0.8112 (mmm) outliers start: 69 outliers final: 44 residues processed: 288 average time/residue: 0.1155 time to fit residues: 58.5064 Evaluate side-chains 247 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 545 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 65 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 chunk 289 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 194 optimal weight: 0.5980 chunk 90 optimal weight: 9.9990 chunk 218 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.092309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068355 restraints weight = 84301.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.070329 restraints weight = 43367.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.071623 restraints weight = 28901.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.072426 restraints weight = 22496.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.072910 restraints weight = 19314.423| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23884 Z= 0.190 Angle : 0.731 11.978 32666 Z= 0.373 Chirality : 0.045 0.251 3928 Planarity : 0.005 0.050 4140 Dihedral : 6.321 62.780 3670 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.78 % Favored : 90.09 % Rotamer: Outliers : 3.36 % Allowed : 19.44 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.15), residues: 3158 helix: 1.17 (0.14), residues: 1296 sheet: -2.54 (0.24), residues: 464 loop : -2.84 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 694 TYR 0.015 0.001 TYR D 507 PHE 0.029 0.001 PHE D 169 TRP 0.046 0.002 TRP C 657 HIS 0.004 0.001 HIS C 392 Details of bonding type rmsd covalent geometry : bond 0.00433 (23850) covalent geometry : angle 0.72080 (32582) SS BOND : bond 0.00618 ( 18) SS BOND : angle 2.60790 ( 36) hydrogen bonds : bond 0.04448 ( 1060) hydrogen bonds : angle 4.89959 ( 3102) link_BETA1-4 : bond 0.00120 ( 4) link_BETA1-4 : angle 1.33561 ( 12) link_NAG-ASN : bond 0.00364 ( 12) link_NAG-ASN : angle 2.63635 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 205 time to evaluate : 0.805 Fit side-chains REVERT: A 230 MET cc_start: 0.8565 (mmm) cc_final: 0.8291 (mmm) REVERT: A 347 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8754 (ttm) REVERT: A 377 LEU cc_start: 0.8907 (tp) cc_final: 0.8547 (tp) REVERT: A 757 LEU cc_start: 0.8963 (tp) cc_final: 0.8637 (tp) REVERT: A 758 GLU cc_start: 0.8603 (tp30) cc_final: 0.8304 (tm-30) REVERT: A 806 MET cc_start: 0.9268 (mmm) cc_final: 0.8468 (mmt) REVERT: B 101 ASP cc_start: 0.7688 (t0) cc_final: 0.7466 (t0) REVERT: B 354 ASP cc_start: 0.8871 (m-30) cc_final: 0.8508 (m-30) REVERT: C 74 MET cc_start: 0.9061 (tmm) cc_final: 0.8717 (tmm) REVERT: C 230 MET cc_start: 0.8511 (mmm) cc_final: 0.8185 (mmm) REVERT: C 347 MET cc_start: 0.8974 (ttp) cc_final: 0.8671 (ttm) REVERT: C 377 LEU cc_start: 0.8921 (tp) cc_final: 0.8530 (tp) REVERT: C 693 LEU cc_start: 0.8998 (tp) cc_final: 0.8758 (tp) REVERT: C 758 GLU cc_start: 0.8697 (tp30) cc_final: 0.8253 (tm-30) REVERT: C 806 MET cc_start: 0.9206 (mmm) cc_final: 0.8510 (mmt) REVERT: D 101 ASP cc_start: 0.7972 (t0) cc_final: 0.7679 (t0) REVERT: D 132 MET cc_start: 0.8521 (mmm) cc_final: 0.8101 (mmm) REVERT: D 688 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8355 (p0) outliers start: 77 outliers final: 58 residues processed: 266 average time/residue: 0.1225 time to fit residues: 56.6945 Evaluate side-chains 257 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 197 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 688 ASN Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 126 optimal weight: 0.0870 chunk 255 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 chunk 187 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 71 optimal weight: 0.0770 chunk 274 optimal weight: 8.9990 chunk 315 optimal weight: 3.9990 overall best weight: 2.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.093465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.069427 restraints weight = 83468.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.071451 restraints weight = 42322.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.072790 restraints weight = 28035.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.073621 restraints weight = 21725.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.074168 restraints weight = 18580.509| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23884 Z= 0.134 Angle : 0.695 11.414 32666 Z= 0.351 Chirality : 0.045 0.247 3928 Planarity : 0.005 0.049 4140 Dihedral : 6.107 63.498 3670 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.87 % Favored : 91.01 % Rotamer: Outliers : 2.96 % Allowed : 20.05 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.15), residues: 3158 helix: 1.31 (0.15), residues: 1298 sheet: -2.45 (0.24), residues: 478 loop : -2.68 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 694 TYR 0.012 0.001 TYR D 479 PHE 0.034 0.001 PHE B 169 TRP 0.044 0.002 TRP C 657 HIS 0.003 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00300 (23850) covalent geometry : angle 0.68640 (32582) SS BOND : bond 0.00685 ( 18) SS BOND : angle 2.37884 ( 36) hydrogen bonds : bond 0.04070 ( 1060) hydrogen bonds : angle 4.71055 ( 3102) link_BETA1-4 : bond 0.00242 ( 4) link_BETA1-4 : angle 1.38993 ( 12) link_NAG-ASN : bond 0.00244 ( 12) link_NAG-ASN : angle 2.45604 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 209 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 230 MET cc_start: 0.8529 (mmm) cc_final: 0.8270 (mmm) REVERT: A 261 MET cc_start: 0.8723 (tpp) cc_final: 0.8324 (tpp) REVERT: A 347 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8725 (ttm) REVERT: A 377 LEU cc_start: 0.8802 (tp) cc_final: 0.8400 (tp) REVERT: A 469 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6652 (mmp80) REVERT: A 757 LEU cc_start: 0.8881 (tp) cc_final: 0.8539 (tp) REVERT: A 758 GLU cc_start: 0.8564 (tp30) cc_final: 0.8287 (tm-30) REVERT: A 806 MET cc_start: 0.9263 (mmm) cc_final: 0.8827 (mmt) REVERT: B 101 ASP cc_start: 0.7822 (t0) cc_final: 0.7568 (t0) REVERT: B 354 ASP cc_start: 0.8858 (m-30) cc_final: 0.8485 (m-30) REVERT: B 688 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8388 (p0) REVERT: C 74 MET cc_start: 0.9049 (tmm) cc_final: 0.8691 (tmm) REVERT: C 169 ASP cc_start: 0.8373 (t0) cc_final: 0.7660 (m-30) REVERT: C 230 MET cc_start: 0.8475 (mmm) cc_final: 0.8173 (mmm) REVERT: C 347 MET cc_start: 0.8936 (ttp) cc_final: 0.8635 (ttm) REVERT: C 377 LEU cc_start: 0.8883 (tp) cc_final: 0.8498 (tp) REVERT: C 469 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6546 (mmp80) REVERT: C 758 GLU cc_start: 0.8610 (tp30) cc_final: 0.8180 (tm-30) REVERT: C 806 MET cc_start: 0.9206 (mmm) cc_final: 0.8476 (mmt) REVERT: D 101 ASP cc_start: 0.7836 (t0) cc_final: 0.7570 (t0) REVERT: D 132 MET cc_start: 0.8602 (mmm) cc_final: 0.8160 (mmm) REVERT: D 157 MET cc_start: 0.8737 (mtt) cc_final: 0.8444 (mtm) REVERT: D 688 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8293 (p0) outliers start: 68 outliers final: 50 residues processed: 264 average time/residue: 0.1228 time to fit residues: 55.7081 Evaluate side-chains 253 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 688 ASN Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 507 TYR Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 688 ASN Chi-restraints excluded: chain D residue 691 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 39 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 140 optimal weight: 40.0000 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 179 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.091879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.067838 restraints weight = 84002.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.069814 restraints weight = 42967.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.071108 restraints weight = 28548.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.071933 restraints weight = 22185.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.072362 restraints weight = 19002.303| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23884 Z= 0.210 Angle : 0.747 11.684 32666 Z= 0.379 Chirality : 0.046 0.355 3928 Planarity : 0.005 0.050 4140 Dihedral : 6.200 64.026 3670 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.13 % Favored : 89.74 % Rotamer: Outliers : 3.01 % Allowed : 20.79 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.15), residues: 3158 helix: 1.23 (0.14), residues: 1308 sheet: -2.55 (0.24), residues: 452 loop : -2.81 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 694 TYR 0.012 0.001 TYR B 179 PHE 0.035 0.002 PHE B 169 TRP 0.042 0.002 TRP C 657 HIS 0.004 0.001 HIS C 392 Details of bonding type rmsd covalent geometry : bond 0.00478 (23850) covalent geometry : angle 0.73825 (32582) SS BOND : bond 0.00730 ( 18) SS BOND : angle 2.37282 ( 36) hydrogen bonds : bond 0.04472 ( 1060) hydrogen bonds : angle 4.83903 ( 3102) link_BETA1-4 : bond 0.00125 ( 4) link_BETA1-4 : angle 1.41610 ( 12) link_NAG-ASN : bond 0.00389 ( 12) link_NAG-ASN : angle 2.54618 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 201 time to evaluate : 0.860 Fit side-chains REVERT: A 230 MET cc_start: 0.8541 (mmm) cc_final: 0.8213 (mmm) REVERT: A 261 MET cc_start: 0.8807 (tpp) cc_final: 0.8363 (tpp) REVERT: A 347 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8838 (ttm) REVERT: A 377 LEU cc_start: 0.8855 (tp) cc_final: 0.8455 (tp) REVERT: A 469 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6570 (mmp80) REVERT: A 702 TYR cc_start: 0.7812 (m-10) cc_final: 0.7400 (m-10) REVERT: A 757 LEU cc_start: 0.8892 (tp) cc_final: 0.8520 (tp) REVERT: A 758 GLU cc_start: 0.8579 (tp30) cc_final: 0.8324 (tm-30) REVERT: A 806 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8479 (mmt) REVERT: B 101 ASP cc_start: 0.8086 (t0) cc_final: 0.7869 (t0) REVERT: B 354 ASP cc_start: 0.8833 (m-30) cc_final: 0.8473 (m-30) REVERT: C 74 MET cc_start: 0.9059 (tmm) cc_final: 0.8703 (tmm) REVERT: C 230 MET cc_start: 0.8481 (mmm) cc_final: 0.8179 (mmm) REVERT: C 347 MET cc_start: 0.8991 (ttp) cc_final: 0.8723 (ttm) REVERT: C 377 LEU cc_start: 0.8919 (tp) cc_final: 0.8526 (tp) REVERT: C 469 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.6467 (mmp80) REVERT: C 758 GLU cc_start: 0.8672 (tp30) cc_final: 0.8287 (tm-30) REVERT: C 806 MET cc_start: 0.9197 (mmm) cc_final: 0.8420 (mmt) REVERT: D 101 ASP cc_start: 0.8015 (t0) cc_final: 0.7700 (t70) REVERT: D 132 MET cc_start: 0.8516 (mmm) cc_final: 0.8080 (mmm) REVERT: D 157 MET cc_start: 0.8729 (mtt) cc_final: 0.8455 (mtm) REVERT: D 688 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8315 (p0) outliers start: 69 outliers final: 57 residues processed: 257 average time/residue: 0.1182 time to fit residues: 52.5543 Evaluate side-chains 256 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 194 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 507 TYR Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 688 ASN Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 61 optimal weight: 5.9990 chunk 301 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 314 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.093146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.069172 restraints weight = 84039.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.071189 restraints weight = 42703.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.072512 restraints weight = 28245.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.073345 restraints weight = 21877.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.073782 restraints weight = 18720.938| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23884 Z= 0.150 Angle : 0.716 13.072 32666 Z= 0.359 Chirality : 0.045 0.345 3928 Planarity : 0.005 0.046 4140 Dihedral : 6.077 64.545 3670 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.18 % Favored : 90.69 % Rotamer: Outliers : 2.92 % Allowed : 21.05 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.15), residues: 3158 helix: 1.40 (0.15), residues: 1298 sheet: -2.51 (0.24), residues: 480 loop : -2.65 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 694 TYR 0.012 0.001 TYR B 179 PHE 0.035 0.001 PHE B 169 TRP 0.046 0.002 TRP C 657 HIS 0.003 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00341 (23850) covalent geometry : angle 0.70566 (32582) SS BOND : bond 0.00669 ( 18) SS BOND : angle 2.24117 ( 36) hydrogen bonds : bond 0.04127 ( 1060) hydrogen bonds : angle 4.73087 ( 3102) link_BETA1-4 : bond 0.00336 ( 4) link_BETA1-4 : angle 1.59262 ( 12) link_NAG-ASN : bond 0.00358 ( 12) link_NAG-ASN : angle 2.84147 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 202 time to evaluate : 0.891 Fit side-chains REVERT: A 230 MET cc_start: 0.8513 (mmm) cc_final: 0.8190 (mmm) REVERT: A 261 MET cc_start: 0.8816 (tpp) cc_final: 0.8243 (tpp) REVERT: A 347 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8818 (ttm) REVERT: A 377 LEU cc_start: 0.8778 (tp) cc_final: 0.8480 (tp) REVERT: A 469 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6561 (mmp80) REVERT: A 702 TYR cc_start: 0.7655 (m-10) cc_final: 0.7413 (m-10) REVERT: A 757 LEU cc_start: 0.8901 (tp) cc_final: 0.8576 (tp) REVERT: A 758 GLU cc_start: 0.8566 (tp30) cc_final: 0.8298 (tm-30) REVERT: A 806 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8472 (mmt) REVERT: B 354 ASP cc_start: 0.8801 (m-30) cc_final: 0.8442 (m-30) REVERT: C 74 MET cc_start: 0.9048 (tmm) cc_final: 0.8681 (tmm) REVERT: C 230 MET cc_start: 0.8467 (mmm) cc_final: 0.8164 (mmm) REVERT: C 347 MET cc_start: 0.8964 (ttp) cc_final: 0.8691 (ttm) REVERT: C 377 LEU cc_start: 0.8885 (tp) cc_final: 0.8509 (tp) REVERT: C 469 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6457 (mmp80) REVERT: C 758 GLU cc_start: 0.8603 (tp30) cc_final: 0.8198 (tm-30) REVERT: C 806 MET cc_start: 0.9205 (mmm) cc_final: 0.8486 (mmt) REVERT: D 101 ASP cc_start: 0.7887 (t0) cc_final: 0.7583 (t70) REVERT: D 132 MET cc_start: 0.8596 (mmm) cc_final: 0.8170 (mmm) REVERT: D 157 MET cc_start: 0.8853 (mtt) cc_final: 0.8614 (mtm) outliers start: 67 outliers final: 57 residues processed: 255 average time/residue: 0.1201 time to fit residues: 52.5379 Evaluate side-chains 257 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 507 TYR Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 315 optimal weight: 9.9990 chunk 103 optimal weight: 0.0050 chunk 42 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 288 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 241 optimal weight: 10.0000 overall best weight: 5.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.091164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.067653 restraints weight = 84115.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.070165 restraints weight = 46856.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.070784 restraints weight = 26376.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.071131 restraints weight = 21566.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.071174 restraints weight = 20913.845| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 23884 Z= 0.259 Angle : 0.813 13.493 32666 Z= 0.410 Chirality : 0.048 0.358 3928 Planarity : 0.005 0.051 4140 Dihedral : 6.373 64.925 3670 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.64 % Favored : 89.23 % Rotamer: Outliers : 2.75 % Allowed : 21.36 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 3158 helix: 1.20 (0.15), residues: 1286 sheet: -2.68 (0.24), residues: 448 loop : -2.77 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 694 TYR 0.013 0.002 TYR B 179 PHE 0.044 0.002 PHE B 169 TRP 0.053 0.002 TRP C 657 HIS 0.005 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00590 (23850) covalent geometry : angle 0.80007 (32582) SS BOND : bond 0.00790 ( 18) SS BOND : angle 2.35031 ( 36) hydrogen bonds : bond 0.04747 ( 1060) hydrogen bonds : angle 4.97047 ( 3102) link_BETA1-4 : bond 0.00329 ( 4) link_BETA1-4 : angle 2.06029 ( 12) link_NAG-ASN : bond 0.00559 ( 12) link_NAG-ASN : angle 3.58077 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6316 Ramachandran restraints generated. 3158 Oldfield, 0 Emsley, 3158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 196 time to evaluate : 0.786 Fit side-chains REVERT: A 230 MET cc_start: 0.8543 (mmm) cc_final: 0.8201 (mmm) REVERT: A 261 MET cc_start: 0.8845 (tpp) cc_final: 0.8246 (tpp) REVERT: A 347 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8900 (ttm) REVERT: A 377 LEU cc_start: 0.8937 (tp) cc_final: 0.8590 (tp) REVERT: A 469 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6606 (mmp-170) REVERT: A 757 LEU cc_start: 0.8886 (tp) cc_final: 0.8517 (tp) REVERT: A 758 GLU cc_start: 0.8637 (tp30) cc_final: 0.8361 (tm-30) REVERT: A 806 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8458 (mmt) REVERT: A 834 MET cc_start: 0.2448 (ptt) cc_final: 0.2148 (mtm) REVERT: B 354 ASP cc_start: 0.8846 (m-30) cc_final: 0.8498 (m-30) REVERT: C 74 MET cc_start: 0.9136 (tmm) cc_final: 0.8741 (tmm) REVERT: C 230 MET cc_start: 0.8428 (mmm) cc_final: 0.8100 (mmm) REVERT: C 347 MET cc_start: 0.9039 (ttp) cc_final: 0.8788 (ttm) REVERT: C 377 LEU cc_start: 0.8927 (tp) cc_final: 0.8522 (tp) REVERT: C 469 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6680 (mmp-170) REVERT: C 758 GLU cc_start: 0.8677 (tp30) cc_final: 0.8294 (tm-30) REVERT: C 806 MET cc_start: 0.9187 (mmm) cc_final: 0.8428 (mmt) REVERT: D 101 ASP cc_start: 0.7830 (t0) cc_final: 0.7553 (t70) REVERT: D 132 MET cc_start: 0.8578 (mmm) cc_final: 0.8150 (mmm) outliers start: 63 outliers final: 57 residues processed: 248 average time/residue: 0.1186 time to fit residues: 50.5916 Evaluate side-chains 254 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 507 TYR Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 83 optimal weight: 0.0070 chunk 310 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 261 optimal weight: 0.0020 chunk 307 optimal weight: 0.5980 chunk 243 optimal weight: 0.0070 chunk 168 optimal weight: 0.1980 chunk 165 optimal weight: 6.9990 overall best weight: 0.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN B 649 ASN C 378 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.095147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.071280 restraints weight = 82965.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.073365 restraints weight = 41843.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.074736 restraints weight = 27584.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.075577 restraints weight = 21230.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.076035 restraints weight = 18123.499| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23884 Z= 0.125 Angle : 0.736 17.550 32666 Z= 0.365 Chirality : 0.045 0.319 3928 Planarity : 0.005 0.047 4140 Dihedral : 5.971 64.789 3670 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.26 % Favored : 91.61 % Rotamer: Outliers : 2.22 % Allowed : 21.97 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.15), residues: 3158 helix: 1.43 (0.15), residues: 1306 sheet: -2.43 (0.24), residues: 480 loop : -2.58 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 544 TYR 0.015 0.001 TYR B 479 PHE 0.022 0.001 PHE D 642 TRP 0.041 0.002 TRP A 657 HIS 0.004 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00269 (23850) covalent geometry : angle 0.72184 (32582) SS BOND : bond 0.00820 ( 18) SS BOND : angle 2.89170 ( 36) hydrogen bonds : bond 0.03771 ( 1060) hydrogen bonds : angle 4.66649 ( 3102) link_BETA1-4 : bond 0.00425 ( 4) link_BETA1-4 : angle 1.86710 ( 12) link_NAG-ASN : bond 0.00396 ( 12) link_NAG-ASN : angle 3.19861 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3868.45 seconds wall clock time: 67 minutes 22.61 seconds (4042.61 seconds total)