Starting phenix.real_space_refine on Sun Sep 13 13:03:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wi1_21682/09_2026/6wi1_21682.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wi1_21682/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6wi1_21682/09_2026/6wi1_21682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wi1_21682/09_2026/6wi1_21682.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6wi1_21682/09_2026/6wi1_21682.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wi1_21682/09_2026/6wi1_21682.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wi1_21682/09_2026/6wi1_21682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wi1_21682/09_2026/6wi1_21682.map" } 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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 5.65, per 1000 atoms: 0.24 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: 2.11 Conformation dependent library (CDL) restraints added in 932.7 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: 0.82 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: 5.15 Time building geometry restraints manager: 2.82 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: 12669 17.46 - 34.92: 1075 34.92 - 52.38: 166 52.38 - 69.83: 38 69.83 - 87.29: 18 Dihedral angle restraints: 13966 sinusoidal: 4768 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 13963 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: 0.05 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: 1.460 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: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 23.300 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 13.822 87.292 7972 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/Z covalent geometry : bond 0.00669 / 0.32 (23850) covalent geometry : angle 0.84480 / 0.47 (32582) SS BOND : bond 0.01797 / 1.35 ( 18) SS BOND : angle 2.50791 / 1.82 ( 36) hydrogen bonds : bond 0.16872 / 11.54 ( 1060) hydrogen bonds : angle 7.32779 / 5.20 ( 3102) link_BETA1-4 : bond 0.06393 / 3.20 ( 4) link_BETA1-4 : angle 26.45577 / 14.56 ( 12) link_NAG-ASN : bond 0.00480 / 0.33 ( 12) link_NAG-ASN : angle 3.63345 / 2.64 ( 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 : 1.078 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: 0.1354 time to fit residues: 62.1944 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 : 0.945 ------------------------------------------------------------------------------- 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... 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 86 GLN C 134 HIS C 314 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 730 HIS D 127 HIS D 649 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.092483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.068328 restraints weight = 83800.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.070311 restraints weight = 42867.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.071620 restraints weight = 28527.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.072496 restraints weight = 22231.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.072944 restraints weight = 18958.063| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23884 Z= 0.152 Angle : 0.735 10.985 32666 Z= 0.380 Chirality : 0.046 0.260 3928 Planarity : 0.005 0.055 4140 Dihedral : 6.502 60.431 3346 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.20 % Favored : 89.61 % Rotamer: Outliers : 2.48 % Allowed : 14.34 % Favored : 83.17 % 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: -2.91 (0.14), residues: 3158 helix: 0.06 (0.14), residues: 1286 sheet: -3.52 (0.22), residues: 412 loop : -3.40 (0.14), residues: 1460 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 0.029 0.002 PHE D 169 TRP 0.024 0.002 TRP A 813 HIS 0.004 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (23850) covalent geometry : angle 0.72413 / 0.38 (32582) SS BOND : bond 0.00707 / 0.52 ( 18) SS BOND : angle 2.03102 / 1.55 ( 36) hydrogen bonds : bond 0.04978 / 3.43 ( 1060) hydrogen bonds : angle 5.48348 / 3.91 ( 3102) link_BETA1-4 : bond 0.00601 / 0.30 ( 4) link_BETA1-4 : angle 0.69896 / 0.45 ( 12) link_NAG-ASN : bond 0.00257 / 0.17 ( 12) link_NAG-ASN : angle 3.44970 / 2.49 ( 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 286 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 229 time to evaluate : 0.911 Fit side-chains REVERT: A 230 MET cc_start: 0.8641 (mmm) cc_final: 0.8347 (mmm) REVERT: A 269 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8769 (pt) REVERT: A 377 LEU cc_start: 0.8866 (tp) cc_final: 0.8551 (tp) REVERT: A 758 GLU cc_start: 0.8608 (tp30) cc_final: 0.8239 (tm-30) REVERT: A 783 MET cc_start: 0.8102 (mtm) cc_final: 0.7853 (mtp) REVERT: A 789 TRP cc_start: 0.6871 (m-10) cc_final: 0.6669 (m100) REVERT: A 806 MET cc_start: 0.9281 (mmm) cc_final: 0.8508 (mmt) REVERT: B 354 ASP cc_start: 0.8865 (m-30) cc_final: 0.8577 (m-30) REVERT: B 706 MET cc_start: 0.7981 (mtm) cc_final: 0.7763 (mtm) REVERT: C 74 MET cc_start: 0.9039 (tmm) cc_final: 0.8813 (tmm) REVERT: C 230 MET cc_start: 0.8535 (mmm) cc_final: 0.8215 (mmm) REVERT: C 269 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8839 (pt) REVERT: C 347 MET cc_start: 0.9010 (ttp) cc_final: 0.8698 (ttm) REVERT: C 377 LEU cc_start: 0.8781 (tp) cc_final: 0.8423 (tp) REVERT: C 693 LEU cc_start: 0.8900 (tp) cc_final: 0.8487 (tp) REVERT: C 758 GLU cc_start: 0.8764 (tp30) cc_final: 0.8196 (tm-30) REVERT: C 783 MET cc_start: 0.8313 (mtm) cc_final: 0.8046 (mtp) REVERT: C 786 ASP cc_start: 0.6663 (t70) cc_final: 0.6394 (t0) REVERT: C 806 MET cc_start: 0.9204 (mmm) cc_final: 0.8483 (mmt) REVERT: D 132 MET cc_start: 0.8232 (mmm) cc_final: 0.8014 (mmm) REVERT: D 272 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: D 562 MET cc_start: 0.8353 (ttp) cc_final: 0.8091 (ttp) outliers start: 57 outliers final: 25 residues processed: 278 average time/residue: 0.1311 time to fit residues: 63.0753 Evaluate side-chains 227 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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: 10.0000 chunk 74 optimal weight: 0.9990 chunk 230 optimal weight: 9.9990 chunk 257 optimal weight: 7.9990 chunk 271 optimal weight: 20.0000 chunk 47 optimal weight: 0.0270 chunk 299 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 294 optimal weight: 40.0000 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** 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 = 0.3750 r_free = 0.3750 target = 0.092414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.068336 restraints weight = 83446.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.070350 restraints weight = 42555.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.071667 restraints weight = 28166.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072492 restraints weight = 21862.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.073023 restraints weight = 18708.396| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23884 Z= 0.158 Angle : 0.718 11.313 32666 Z= 0.369 Chirality : 0.045 0.250 3928 Planarity : 0.005 0.057 4140 Dihedral : 6.074 60.743 3342 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.13 % Favored : 89.68 % Rotamer: Outliers : 3.49 % Allowed : 15.00 % Favored : 81.52 % 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: -2.26 (0.15), residues: 3158 helix: 0.61 (0.14), residues: 1296 sheet: -3.06 (0.23), residues: 442 loop : -3.08 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 694 TYR 0.018 0.001 TYR B 167 PHE 0.022 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/Z covalent geometry : bond 0.00350 / 0.16 (23850) covalent geometry : angle 0.70487 / 0.36 (32582) SS BOND : bond 0.00641 / 0.45 ( 18) SS BOND : angle 2.90517 / 2.09 ( 36) hydrogen bonds : bond 0.04668 / 3.23 ( 1060) hydrogen bonds : angle 5.18891 / 3.70 ( 3102) link_BETA1-4 : bond 0.00189 / 0.09 ( 4) link_BETA1-4 : angle 1.26172 / 0.74 ( 12) link_NAG-ASN : bond 0.00278 / 0.20 ( 12) link_NAG-ASN : angle 3.08440 / 2.20 ( 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 294 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 214 time to evaluate : 1.026 Fit side-chains REVERT: A 230 MET cc_start: 0.8622 (mmm) cc_final: 0.8334 (mmm) REVERT: A 269 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8779 (pt) REVERT: A 347 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8669 (ttm) REVERT: A 377 LEU cc_start: 0.8946 (tp) cc_final: 0.8612 (tp) REVERT: A 757 LEU cc_start: 0.8705 (tp) cc_final: 0.8493 (tp) REVERT: A 758 GLU cc_start: 0.8585 (tp30) cc_final: 0.8263 (tm-30) REVERT: A 783 MET cc_start: 0.8129 (mtm) cc_final: 0.7918 (mtp) REVERT: A 806 MET cc_start: 0.9281 (mmm) cc_final: 0.8467 (mmt) REVERT: B 157 MET cc_start: 0.9088 (mtm) cc_final: 0.8618 (mtm) REVERT: B 354 ASP cc_start: 0.8853 (m-30) cc_final: 0.8546 (m-30) REVERT: C 74 MET cc_start: 0.9131 (tmm) cc_final: 0.8860 (tmm) REVERT: C 230 MET cc_start: 0.8539 (mmm) cc_final: 0.8210 (mmm) REVERT: C 269 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8834 (pt) REVERT: C 347 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8692 (ttm) REVERT: C 377 LEU cc_start: 0.8791 (tp) cc_final: 0.8405 (tp) REVERT: C 758 GLU cc_start: 0.8615 (tp30) cc_final: 0.8184 (tm-30) REVERT: C 783 MET cc_start: 0.8290 (mtm) cc_final: 0.8069 (mtp) REVERT: C 786 ASP cc_start: 0.6646 (t70) cc_final: 0.6404 (t0) REVERT: C 806 MET cc_start: 0.9213 (mmm) cc_final: 0.8556 (mmt) REVERT: D 132 MET cc_start: 0.8310 (mmm) cc_final: 0.8063 (mmm) REVERT: D 157 MET cc_start: 0.9013 (mtm) cc_final: 0.8408 (mtm) outliers start: 80 outliers final: 44 residues processed: 278 average time/residue: 0.1330 time to fit residues: 64.2550 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 : 0.891 ------------------------------------------------------------------------------- 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 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 B residue 68 VAL Chi-restraints excluded: chain B residue 123 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 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 179 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: 0.6980 chunk 201 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 242 optimal weight: 3.9990 chunk 311 optimal weight: 0.0570 chunk 300 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 overall best weight: 3.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 GLN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.092370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.068257 restraints weight = 83388.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.070239 restraints weight = 42988.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071535 restraints weight = 28656.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.072350 restraints weight = 22334.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.072864 restraints weight = 19163.999| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23884 Z= 0.168 Angle : 0.702 11.785 32666 Z= 0.359 Chirality : 0.045 0.276 3928 Planarity : 0.005 0.057 4140 Dihedral : 5.745 62.148 3337 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.72 % Favored : 90.15 % Rotamer: Outliers : 3.27 % Allowed : 16.96 % Favored : 79.77 % 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: -1.92 (0.15), residues: 3158 helix: 0.94 (0.14), residues: 1284 sheet: -2.82 (0.23), residues: 480 loop : -2.92 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 694 TYR 0.014 0.001 TYR D 167 PHE 0.026 0.001 PHE B 169 TRP 0.016 0.001 TRP A 813 HIS 0.004 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (23850) covalent geometry : angle 0.69047 / 0.36 (32582) SS BOND : bond 0.00684 / 0.50 ( 18) SS BOND : angle 2.37318 / 1.77 ( 36) hydrogen bonds : bond 0.04443 / 3.08 ( 1060) hydrogen bonds : angle 4.99366 / 3.57 ( 3102) link_BETA1-4 : bond 0.00272 / 0.14 ( 4) link_BETA1-4 : angle 1.23194 / 0.80 ( 12) link_NAG-ASN : bond 0.00238 / 0.16 ( 12) link_NAG-ASN : angle 3.01018 / 2.20 ( 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 289 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 214 time to evaluate : 0.900 Fit side-chains REVERT: A 230 MET cc_start: 0.8599 (mmm) cc_final: 0.8320 (mmm) REVERT: A 269 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8821 (pt) REVERT: A 347 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8742 (ttm) REVERT: A 377 LEU cc_start: 0.8891 (tp) cc_final: 0.8563 (tp) REVERT: A 757 LEU cc_start: 0.8796 (tp) cc_final: 0.8494 (tp) REVERT: A 758 GLU cc_start: 0.8594 (tp30) cc_final: 0.8297 (tm-30) REVERT: A 806 MET cc_start: 0.9273 (mmm) cc_final: 0.8490 (mmt) REVERT: B 157 MET cc_start: 0.9042 (mtm) cc_final: 0.8593 (mtm) REVERT: B 354 ASP cc_start: 0.8853 (m-30) cc_final: 0.8527 (m-30) REVERT: C 74 MET cc_start: 0.9084 (tmm) cc_final: 0.8766 (tmm) REVERT: C 230 MET cc_start: 0.8525 (mmm) cc_final: 0.8190 (mmm) REVERT: C 269 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8801 (pt) REVERT: C 347 MET cc_start: 0.8989 (ttp) cc_final: 0.8679 (ttm) REVERT: C 375 MET cc_start: 0.8164 (mpp) cc_final: 0.7929 (mpp) REVERT: C 377 LEU cc_start: 0.8875 (tp) cc_final: 0.8485 (tp) REVERT: C 758 GLU cc_start: 0.8689 (tp30) cc_final: 0.8229 (tm-30) REVERT: C 783 MET cc_start: 0.8284 (mtm) cc_final: 0.8083 (mtp) REVERT: C 806 MET cc_start: 0.9207 (mmm) cc_final: 0.8533 (mmt) REVERT: D 101 ASP cc_start: 0.7843 (t0) cc_final: 0.7593 (t0) REVERT: D 132 MET cc_start: 0.8478 (mmm) cc_final: 0.8186 (mmm) outliers start: 75 outliers final: 48 residues processed: 281 average time/residue: 0.1298 time to fit residues: 63.3508 Evaluate side-chains 252 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 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 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 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 383 VAL Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 662 MET 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 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: 3.9990 chunk 159 optimal weight: 5.9990 chunk 291 optimal weight: 20.0000 chunk 126 optimal weight: 0.2980 chunk 171 optimal weight: 0.0980 chunk 284 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 200 optimal weight: 0.5980 chunk 249 optimal weight: 0.9990 chunk 242 optimal weight: 8.9990 chunk 38 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.756 > 50:) overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS D 649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.094393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.070631 restraints weight = 82906.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.072661 restraints weight = 42019.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.074011 restraints weight = 27683.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.074852 restraints weight = 21322.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.075382 restraints weight = 18168.381| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2422 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= 0.119 Angle : 0.682 12.351 32666 Z= 0.346 Chirality : 0.044 0.219 3928 Planarity : 0.005 0.055 4140 Dihedral : 5.455 62.298 3335 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.99 % Favored : 90.88 % Rotamer: Outliers : 3.31 % Allowed : 17.70 % Favored : 78.99 % 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: -1.56 (0.15), residues: 3158 helix: 1.18 (0.15), residues: 1286 sheet: -2.53 (0.24), residues: 482 loop : -2.71 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 692 TYR 0.016 0.001 TYR B 479 PHE 0.039 0.001 PHE B 169 TRP 0.042 0.001 TRP C 657 HIS 0.003 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (23850) covalent geometry : angle 0.66949 / 0.34 (32582) SS BOND : bond 0.00842 / 0.62 ( 18) SS BOND : angle 3.15155 / 2.29 ( 36) hydrogen bonds : bond 0.04074 / 2.85 ( 1060) hydrogen bonds : angle 4.77875 / 3.42 ( 3102) link_BETA1-4 : bond 0.00356 / 0.18 ( 4) link_BETA1-4 : angle 1.13675 / 0.71 ( 12) link_NAG-ASN : bond 0.00261 / 0.19 ( 12) link_NAG-ASN : angle 2.56943 / 1.85 ( 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 302 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 226 time to evaluate : 0.886 Fit side-chains REVERT: A 230 MET cc_start: 0.8568 (mmm) cc_final: 0.8292 (mmm) REVERT: A 261 MET cc_start: 0.8584 (tpp) cc_final: 0.8339 (tpp) REVERT: A 347 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8674 (ttm) REVERT: A 377 LEU cc_start: 0.8784 (tp) cc_final: 0.8476 (tp) REVERT: A 757 LEU cc_start: 0.8781 (tp) cc_final: 0.8534 (tp) REVERT: A 758 GLU cc_start: 0.8511 (tp30) cc_final: 0.8234 (tm-30) REVERT: A 786 ASP cc_start: 0.6688 (t0) cc_final: 0.6458 (t0) REVERT: A 806 MET cc_start: 0.9262 (mmm) cc_final: 0.8832 (mmt) REVERT: B 157 MET cc_start: 0.8978 (mtm) cc_final: 0.8533 (mtm) REVERT: B 354 ASP cc_start: 0.8817 (m-30) cc_final: 0.8478 (m-30) REVERT: B 688 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8333 (p0) REVERT: C 74 MET cc_start: 0.9029 (tmm) cc_final: 0.8725 (tmm) REVERT: C 230 MET cc_start: 0.8483 (mmm) cc_final: 0.8158 (mmm) REVERT: C 347 MET cc_start: 0.8929 (ttp) cc_final: 0.8650 (ttm) REVERT: C 377 LEU cc_start: 0.8760 (tp) cc_final: 0.8407 (tp) REVERT: C 758 GLU cc_start: 0.8674 (tp30) cc_final: 0.8234 (tm-30) REVERT: C 806 MET cc_start: 0.9188 (mmm) cc_final: 0.8470 (mmt) REVERT: D 101 ASP cc_start: 0.7693 (t0) cc_final: 0.7480 (t0) REVERT: D 132 MET cc_start: 0.8492 (mmm) cc_final: 0.8080 (mmm) REVERT: D 688 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8246 (p0) outliers start: 76 outliers final: 47 residues processed: 290 average time/residue: 0.1267 time to fit residues: 64.0900 Evaluate side-chains 248 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 534 ILE 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 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 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 C residue 127 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 534 ILE 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 186 ILE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 65 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 194 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 204 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS B 782 GLN D 782 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.091191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.068561 restraints weight = 84734.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.069854 restraints weight = 45839.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.070499 restraints weight = 31376.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.070714 restraints weight = 24480.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.070843 restraints weight = 22911.527| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 23884 Z= 0.252 Angle : 0.778 12.120 32666 Z= 0.398 Chirality : 0.047 0.213 3928 Planarity : 0.005 0.051 4140 Dihedral : 5.734 63.523 3334 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.29 % Favored : 89.52 % Rotamer: Outliers : 3.66 % Allowed : 18.61 % Favored : 77.72 % 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: -1.73 (0.15), residues: 3158 helix: 1.11 (0.14), residues: 1298 sheet: -2.68 (0.23), residues: 492 loop : -2.88 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 489 TYR 0.015 0.002 TYR D 282 PHE 0.024 0.002 PHE C 554 TRP 0.049 0.002 TRP C 657 HIS 0.006 0.002 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.25 (23850) covalent geometry : angle 0.76844 / 0.39 (32582) SS BOND : bond 0.00790 / 0.59 ( 18) SS BOND : angle 2.72814 / 1.99 ( 36) hydrogen bonds : bond 0.04772 / 3.29 ( 1060) hydrogen bonds : angle 5.00748 / 3.59 ( 3102) link_BETA1-4 : bond 0.00097 / 0.05 ( 4) link_BETA1-4 : angle 1.33011 / 0.79 ( 12) link_NAG-ASN : bond 0.00444 / 0.28 ( 12) link_NAG-ASN : angle 2.65061 / 1.89 ( 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 283 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 199 time to evaluate : 0.915 Fit side-chains REVERT: A 230 MET cc_start: 0.8597 (mmm) cc_final: 0.8253 (mmm) REVERT: A 347 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8747 (ttm) REVERT: A 377 LEU cc_start: 0.8959 (tp) cc_final: 0.8582 (tp) REVERT: A 702 TYR cc_start: 0.7754 (m-80) cc_final: 0.7453 (m-10) REVERT: A 723 MET cc_start: 0.8474 (tpt) cc_final: 0.8208 (tpp) REVERT: A 757 LEU cc_start: 0.8962 (tp) cc_final: 0.8622 (tp) REVERT: A 758 GLU cc_start: 0.8668 (tp30) cc_final: 0.8351 (tm-30) REVERT: A 806 MET cc_start: 0.9249 (mmm) cc_final: 0.8410 (mmt) REVERT: B 354 ASP cc_start: 0.8858 (m-30) cc_final: 0.8519 (m-30) REVERT: B 688 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8372 (p0) REVERT: C 74 MET cc_start: 0.9170 (tmm) cc_final: 0.8609 (tpp) REVERT: C 230 MET cc_start: 0.8535 (mmm) cc_final: 0.8221 (mmm) REVERT: C 347 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8708 (ttm) REVERT: C 377 LEU cc_start: 0.8929 (tp) cc_final: 0.8509 (tp) REVERT: C 758 GLU cc_start: 0.8661 (tp30) cc_final: 0.8275 (tm-30) REVERT: C 806 MET cc_start: 0.9195 (mmm) cc_final: 0.8413 (mmt) REVERT: D 101 ASP cc_start: 0.7986 (t0) cc_final: 0.7740 (t70) REVERT: D 132 MET cc_start: 0.8520 (mmm) cc_final: 0.8091 (mmm) REVERT: D 165 ASP cc_start: 0.5155 (OUTLIER) cc_final: 0.4938 (m-30) REVERT: D 688 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8284 (p0) outliers start: 84 outliers final: 60 residues processed: 270 average time/residue: 0.1281 time to fit residues: 60.2009 Evaluate side-chains 257 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 192 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 522 MET 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 686 THR 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 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 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 479 TYR 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 688 ASN Chi-restraints excluded: chain B residue 691 THR 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 347 MET Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 675 PHE 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 68 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 167 TYR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 126 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 187 optimal weight: 0.0980 chunk 197 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 274 optimal weight: 10.0000 chunk 315 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 GLN C 378 GLN D 616 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.094054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.070194 restraints weight = 83402.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.072189 restraints weight = 42946.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.073543 restraints weight = 28734.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.074390 restraints weight = 22250.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.074815 restraints weight = 18998.794| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23884 Z= 0.125 Angle : 0.693 11.542 32666 Z= 0.348 Chirality : 0.044 0.210 3928 Planarity : 0.004 0.049 4140 Dihedral : 5.432 63.748 3334 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.42 % Favored : 91.45 % Rotamer: Outliers : 2.70 % Allowed : 20.05 % Favored : 77.24 % 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: -1.39 (0.15), residues: 3158 helix: 1.33 (0.15), residues: 1300 sheet: -2.38 (0.24), residues: 476 loop : -2.68 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 694 TYR 0.012 0.001 TYR B 479 PHE 0.020 0.001 PHE B 642 TRP 0.041 0.002 TRP C 657 HIS 0.003 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (23850) covalent geometry : angle 0.68439 / 0.35 (32582) SS BOND : bond 0.00723 / 0.51 ( 18) SS BOND : angle 2.39502 / 1.82 ( 36) hydrogen bonds : bond 0.03975 / 2.77 ( 1060) hydrogen bonds : angle 4.67492 / 3.34 ( 3102) link_BETA1-4 : bond 0.00441 / 0.22 ( 4) link_BETA1-4 : angle 1.22279 / 0.76 ( 12) link_NAG-ASN : bond 0.00248 / 0.18 ( 12) link_NAG-ASN : angle 2.41402 / 1.75 ( 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 267 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 205 time to evaluate : 1.139 Fit side-chains REVERT: A 230 MET cc_start: 0.8525 (mmm) cc_final: 0.8257 (mmm) REVERT: A 261 MET cc_start: 0.8763 (tpp) cc_final: 0.8376 (tpp) REVERT: A 347 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8701 (ttm) REVERT: A 377 LEU cc_start: 0.8789 (tp) cc_final: 0.8390 (tp) REVERT: A 469 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6654 (mmp80) REVERT: A 757 LEU cc_start: 0.8841 (tp) cc_final: 0.8504 (tp) REVERT: A 758 GLU cc_start: 0.8562 (tp30) cc_final: 0.8281 (tm-30) REVERT: A 806 MET cc_start: 0.9270 (mmm) cc_final: 0.8846 (mmt) REVERT: B 354 ASP cc_start: 0.8827 (m-30) cc_final: 0.8467 (m-30) REVERT: B 688 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8324 (p0) REVERT: C 74 MET cc_start: 0.9055 (tmm) cc_final: 0.8694 (tmm) REVERT: C 169 ASP cc_start: 0.8538 (t0) cc_final: 0.7696 (m-30) REVERT: C 230 MET cc_start: 0.8474 (mmm) cc_final: 0.8165 (mmm) REVERT: C 261 MET cc_start: 0.8653 (tpp) cc_final: 0.8398 (tpp) REVERT: C 347 MET cc_start: 0.8938 (ttp) cc_final: 0.8670 (ttm) REVERT: C 377 LEU cc_start: 0.8874 (tp) cc_final: 0.8537 (tp) REVERT: C 469 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6625 (mmp80) REVERT: C 491 MET cc_start: 0.8174 (mmm) cc_final: 0.7697 (mtt) REVERT: C 758 GLU cc_start: 0.8618 (tp30) cc_final: 0.8236 (tm-30) REVERT: C 806 MET cc_start: 0.9212 (mmm) cc_final: 0.8494 (mmt) REVERT: D 101 ASP cc_start: 0.7798 (t0) cc_final: 0.7552 (t0) REVERT: D 132 MET cc_start: 0.8605 (mmm) cc_final: 0.8158 (mmm) REVERT: D 157 MET cc_start: 0.8749 (mtt) cc_final: 0.8454 (mtm) REVERT: D 688 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8284 (p0) REVERT: D 748 LEU cc_start: 0.8657 (tp) cc_final: 0.8369 (tp) outliers start: 62 outliers final: 48 residues processed: 251 average time/residue: 0.1367 time to fit residues: 58.8389 Evaluate side-chains 250 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 347 MET 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 793 VAL Chi-restraints excluded: chain A residue 819 CYS 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 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 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 534 ILE 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 160 ILE Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 186 ILE 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: 1.9990 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 chunk 140 optimal weight: 30.0000 chunk 31 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 42 optimal weight: 0.0060 chunk 179 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.095023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.071368 restraints weight = 83107.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.073424 restraints weight = 42251.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.074774 restraints weight = 27896.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.075640 restraints weight = 21505.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.076167 restraints weight = 18266.234| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2991 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= 0.118 Angle : 0.675 11.795 32666 Z= 0.337 Chirality : 0.044 0.208 3928 Planarity : 0.004 0.064 4140 Dihedral : 5.195 63.242 3334 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.80 % Favored : 91.07 % Rotamer: Outliers : 2.57 % Allowed : 20.27 % Favored : 77.16 % 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: -1.22 (0.15), residues: 3158 helix: 1.40 (0.15), residues: 1304 sheet: -2.21 (0.25), residues: 442 loop : -2.58 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 694 TYR 0.012 0.001 TYR B 479 PHE 0.025 0.001 PHE B 642 TRP 0.038 0.002 TRP A 657 HIS 0.003 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (23850) covalent geometry : angle 0.66607 / 0.33 (32582) SS BOND : bond 0.00554 / 0.40 ( 18) SS BOND : angle 2.36098 / 1.78 ( 36) hydrogen bonds : bond 0.03772 / 2.64 ( 1060) hydrogen bonds : angle 4.59180 / 3.28 ( 3102) link_BETA1-4 : bond 0.00242 / 0.12 ( 4) link_BETA1-4 : angle 1.21708 / 0.75 ( 12) link_NAG-ASN : bond 0.00240 / 0.17 ( 12) link_NAG-ASN : angle 2.35855 / 1.71 ( 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 274 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 0.926 Fit side-chains REVERT: A 230 MET cc_start: 0.8514 (mmm) cc_final: 0.8247 (mmm) REVERT: A 347 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8667 (ttm) REVERT: A 377 LEU cc_start: 0.8692 (tp) cc_final: 0.8368 (tp) REVERT: A 469 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6548 (mmp80) REVERT: A 757 LEU cc_start: 0.8856 (tp) cc_final: 0.8532 (tp) REVERT: A 758 GLU cc_start: 0.8551 (tp30) cc_final: 0.8312 (tm-30) REVERT: A 806 MET cc_start: 0.9257 (mmm) cc_final: 0.8760 (mmt) REVERT: B 354 ASP cc_start: 0.8841 (m-30) cc_final: 0.8493 (m-30) REVERT: B 508 MET cc_start: 0.8918 (mtm) cc_final: 0.8696 (mtt) REVERT: B 688 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8311 (p0) REVERT: C 74 MET cc_start: 0.9020 (tmm) cc_final: 0.8674 (tmm) REVERT: C 169 ASP cc_start: 0.8555 (t0) cc_final: 0.7763 (m-30) REVERT: C 230 MET cc_start: 0.8462 (mmm) cc_final: 0.8159 (mmm) REVERT: C 347 MET cc_start: 0.8884 (ttp) cc_final: 0.8609 (ttm) REVERT: C 377 LEU cc_start: 0.8833 (tp) cc_final: 0.8569 (tp) REVERT: C 469 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6587 (mmp80) REVERT: C 491 MET cc_start: 0.8247 (mmm) cc_final: 0.7957 (mtt) REVERT: C 758 GLU cc_start: 0.8600 (tp30) cc_final: 0.8258 (tm-30) REVERT: C 806 MET cc_start: 0.9185 (mmm) cc_final: 0.8477 (mmt) REVERT: D 101 ASP cc_start: 0.7729 (t0) cc_final: 0.7412 (t0) REVERT: D 132 MET cc_start: 0.8564 (mmm) cc_final: 0.8300 (mmm) REVERT: D 334 MET cc_start: 0.7033 (mmm) cc_final: 0.6822 (mmm) REVERT: D 354 ASP cc_start: 0.8807 (m-30) cc_final: 0.8400 (m-30) REVERT: D 688 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8243 (p0) REVERT: D 748 LEU cc_start: 0.8484 (tp) cc_final: 0.8255 (tp) outliers start: 59 outliers final: 43 residues processed: 258 average time/residue: 0.1323 time to fit residues: 58.2536 Evaluate side-chains 249 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 201 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 793 VAL Chi-restraints excluded: chain A residue 819 CYS 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 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 475 THR Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 545 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 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 160 ILE Chi-restraints excluded: chain D residue 167 TYR 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 422 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 507 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 61 optimal weight: 8.9990 chunk 301 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 314 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.092984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.068802 restraints weight = 84320.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.070857 restraints weight = 42877.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.072183 restraints weight = 28401.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.073014 restraints weight = 22003.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.073518 restraints weight = 18816.657| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23884 Z= 0.182 Angle : 0.723 12.916 32666 Z= 0.364 Chirality : 0.045 0.208 3928 Planarity : 0.005 0.049 4140 Dihedral : 5.327 64.038 3334 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.56 % Favored : 90.31 % Rotamer: Outliers : 2.35 % Allowed : 20.92 % Favored : 76.72 % 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: -1.26 (0.15), residues: 3158 helix: 1.41 (0.15), residues: 1298 sheet: -2.23 (0.25), residues: 446 loop : -2.63 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 725 TYR 0.011 0.001 TYR B 179 PHE 0.019 0.001 PHE D 169 TRP 0.043 0.002 TRP A 657 HIS 0.004 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (23850) covalent geometry : angle 0.71489 / 0.36 (32582) SS BOND : bond 0.00622 / 0.46 ( 18) SS BOND : angle 2.27260 / 1.71 ( 36) hydrogen bonds : bond 0.04201 / 2.92 ( 1060) hydrogen bonds : angle 4.71491 / 3.37 ( 3102) link_BETA1-4 : bond 0.00102 / 0.05 ( 4) link_BETA1-4 : angle 1.32781 / 0.81 ( 12) link_NAG-ASN : bond 0.00289 / 0.18 ( 12) link_NAG-ASN : angle 2.40367 / 1.72 ( 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 254 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 0.847 Fit side-chains REVERT: A 230 MET cc_start: 0.8534 (mmm) cc_final: 0.8205 (mmm) REVERT: A 347 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8718 (ttm) REVERT: A 377 LEU cc_start: 0.8859 (tp) cc_final: 0.8505 (tp) REVERT: A 469 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6589 (mmp80) REVERT: A 723 MET cc_start: 0.8865 (tpp) cc_final: 0.8641 (tpp) REVERT: A 757 LEU cc_start: 0.8872 (tp) cc_final: 0.8509 (tp) REVERT: A 758 GLU cc_start: 0.8708 (tp30) cc_final: 0.8403 (tm-30) REVERT: A 806 MET cc_start: 0.9230 (mmm) cc_final: 0.8500 (mmt) REVERT: A 834 MET cc_start: 0.2382 (ptt) cc_final: 0.2117 (mtm) REVERT: B 175 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6503 (p90) REVERT: B 354 ASP cc_start: 0.8903 (m-30) cc_final: 0.8554 (m-30) REVERT: B 688 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8307 (p0) REVERT: C 74 MET cc_start: 0.9052 (tmm) cc_final: 0.8697 (tmm) REVERT: C 169 ASP cc_start: 0.8678 (t0) cc_final: 0.7810 (m-30) REVERT: C 230 MET cc_start: 0.8489 (mmm) cc_final: 0.8185 (mmm) REVERT: C 347 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8653 (ttm) REVERT: C 377 LEU cc_start: 0.8903 (tp) cc_final: 0.8539 (tp) REVERT: C 469 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6542 (mmp80) REVERT: C 491 MET cc_start: 0.8293 (mmm) cc_final: 0.7888 (mtt) REVERT: C 758 GLU cc_start: 0.8641 (tp30) cc_final: 0.8303 (tm-30) REVERT: C 806 MET cc_start: 0.9189 (mmm) cc_final: 0.8421 (mmt) REVERT: D 101 ASP cc_start: 0.7873 (t0) cc_final: 0.7542 (t70) REVERT: D 132 MET cc_start: 0.8598 (mmm) cc_final: 0.8254 (mmm) REVERT: D 157 MET cc_start: 0.8867 (mtt) cc_final: 0.8566 (mtm) REVERT: D 334 MET cc_start: 0.7064 (mmm) cc_final: 0.6845 (mmm) REVERT: D 688 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8276 (p0) REVERT: D 748 LEU cc_start: 0.8559 (tp) cc_final: 0.8328 (tp) outliers start: 54 outliers final: 43 residues processed: 243 average time/residue: 0.1369 time to fit residues: 56.8340 Evaluate side-chains 245 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 793 VAL Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 179 TYR 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 507 TYR Chi-restraints excluded: chain B residue 545 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 269 LEU Chi-restraints excluded: chain C residue 347 MET 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 819 CYS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 167 TYR 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 422 VAL Chi-restraints excluded: chain D residue 440 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 315 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 288 optimal weight: 30.0000 chunk 83 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.093499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.069328 restraints weight = 83789.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.071384 restraints weight = 42528.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.072743 restraints weight = 28150.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.073576 restraints weight = 21778.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.074081 restraints weight = 18652.329| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23884 Z= 0.152 Angle : 0.708 13.893 32666 Z= 0.355 Chirality : 0.044 0.208 3928 Planarity : 0.004 0.048 4140 Dihedral : 5.304 64.434 3334 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.37 % Favored : 90.50 % Rotamer: Outliers : 2.53 % Allowed : 20.97 % Favored : 76.50 % 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: -1.23 (0.16), residues: 3158 helix: 1.44 (0.15), residues: 1300 sheet: -2.43 (0.24), residues: 470 loop : -2.53 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 694 TYR 0.011 0.001 TYR B 179 PHE 0.026 0.001 PHE D 614 TRP 0.050 0.002 TRP C 657 HIS 0.003 0.001 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (23850) covalent geometry : angle 0.70019 / 0.35 (32582) SS BOND : bond 0.00619 / 0.45 ( 18) SS BOND : angle 2.22789 / 1.69 ( 36) hydrogen bonds : bond 0.04018 / 2.80 ( 1060) hydrogen bonds : angle 4.65220 / 3.32 ( 3102) link_BETA1-4 : bond 0.00187 / 0.09 ( 4) link_BETA1-4 : angle 1.31997 / 0.81 ( 12) link_NAG-ASN : bond 0.00214 / 0.14 ( 12) link_NAG-ASN : angle 2.32478 / 1.67 ( 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 261 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 0.909 Fit side-chains REVERT: A 230 MET cc_start: 0.8516 (mmm) cc_final: 0.8193 (mmm) REVERT: A 347 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8711 (ttm) REVERT: A 377 LEU cc_start: 0.8831 (tp) cc_final: 0.8498 (tp) REVERT: A 469 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6582 (mmp80) REVERT: A 657 TRP cc_start: 0.8504 (t60) cc_final: 0.8284 (t60) REVERT: A 702 TYR cc_start: 0.7549 (m-10) cc_final: 0.7262 (m-10) REVERT: A 723 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8612 (tpp) REVERT: A 757 LEU cc_start: 0.8810 (tp) cc_final: 0.8448 (tp) REVERT: A 758 GLU cc_start: 0.8651 (tp30) cc_final: 0.8357 (tm-30) REVERT: A 806 MET cc_start: 0.9236 (mmm) cc_final: 0.8464 (mmt) REVERT: A 834 MET cc_start: 0.2365 (ptt) cc_final: 0.2080 (mtm) REVERT: B 354 ASP cc_start: 0.8840 (m-30) cc_final: 0.8502 (m-30) REVERT: B 508 MET cc_start: 0.8950 (mtm) cc_final: 0.8662 (mtt) REVERT: B 688 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8303 (p0) REVERT: C 74 MET cc_start: 0.9035 (tmm) cc_final: 0.8680 (tmm) REVERT: C 169 ASP cc_start: 0.8653 (t0) cc_final: 0.7799 (m-30) REVERT: C 230 MET cc_start: 0.8467 (mmm) cc_final: 0.8169 (mmm) REVERT: C 347 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8666 (ttm) REVERT: C 377 LEU cc_start: 0.8886 (tp) cc_final: 0.8482 (tp) REVERT: C 469 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6545 (mmp80) REVERT: C 491 MET cc_start: 0.8245 (mmm) cc_final: 0.7883 (mtt) REVERT: C 758 GLU cc_start: 0.8649 (tp30) cc_final: 0.8263 (tm-30) REVERT: C 806 MET cc_start: 0.9191 (mmm) cc_final: 0.8418 (mmt) REVERT: D 101 ASP cc_start: 0.7807 (t0) cc_final: 0.7522 (t70) REVERT: D 132 MET cc_start: 0.8575 (mmm) cc_final: 0.8132 (mmm) REVERT: D 334 MET cc_start: 0.7065 (mmm) cc_final: 0.6826 (mmm) REVERT: D 688 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8260 (p0) REVERT: D 748 LEU cc_start: 0.8545 (tp) cc_final: 0.8316 (tp) outliers start: 58 outliers final: 51 residues processed: 248 average time/residue: 0.1343 time to fit residues: 57.1219 Evaluate side-chains 257 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 199 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 288 ILE 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 693 LEU Chi-restraints excluded: chain A residue 723 MET Chi-restraints excluded: chain A residue 783 MET 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 167 TYR Chi-restraints excluded: chain B residue 173 THR 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 507 TYR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 688 ASN Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 780 ILE 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 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 793 VAL Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 167 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 422 VAL Chi-restraints excluded: chain D residue 440 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 83 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 261 optimal weight: 0.6980 chunk 307 optimal weight: 9.9990 chunk 243 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.093721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.069604 restraints weight = 82484.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.071671 restraints weight = 41741.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.073020 restraints weight = 27558.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.073856 restraints weight = 21279.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.074356 restraints weight = 18176.656| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3163 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= 0.133 Angle : 0.693 13.860 32666 Z= 0.346 Chirality : 0.044 0.207 3928 Planarity : 0.004 0.047 4140 Dihedral : 5.207 64.320 3334 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.12 % Favored : 90.75 % Rotamer: Outliers : 2.62 % Allowed : 21.05 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.14 (0.16), residues: 3158 helix: 1.52 (0.15), residues: 1300 sheet: -2.32 (0.24), residues: 472 loop : -2.49 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 694 TYR 0.011 0.001 TYR B 479 PHE 0.020 0.001 PHE D 642 TRP 0.044 0.002 TRP C 657 HIS 0.003 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (23850) covalent geometry : angle 0.68522 / 0.34 (32582) SS BOND : bond 0.00576 / 0.41 ( 18) SS BOND : angle 2.19312 / 1.68 ( 36) hydrogen bonds : bond 0.03861 / 2.70 ( 1060) hydrogen bonds : angle 4.60826 / 3.28 ( 3102) link_BETA1-4 : bond 0.00202 / 0.10 ( 4) link_BETA1-4 : angle 1.30985 / 0.81 ( 12) link_NAG-ASN : bond 0.00214 / 0.15 ( 12) link_NAG-ASN : angle 2.28190 / 1.65 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4290.72 seconds wall clock time: 74 minutes 47.15 seconds (4487.15 seconds total)