Starting phenix.real_space_refine on Thu Mar 5 19:10:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eot_31230/03_2026/7eot_31230_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eot_31230/03_2026/7eot_31230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eot_31230/03_2026/7eot_31230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eot_31230/03_2026/7eot_31230.map" model { file = "/net/cci-nas-00/data/ceres_data/7eot_31230/03_2026/7eot_31230_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eot_31230/03_2026/7eot_31230_trim.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Br 2 7.06 5 P 2 5.49 5 S 150 5.16 5 C 15758 2.51 5 N 4120 2.21 5 O 4566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24598 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5980 Classifications: {'peptide': 757} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 728} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 6186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6186 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 32, 'TRANS': 754} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 5980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5980 Classifications: {'peptide': 757} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 728} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 6186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6186 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 32, 'TRANS': 754} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 119 Unusual residues: {'J86': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 119 Unusual residues: {'J86': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.04, per 1000 atoms: 0.20 Number of scatterers: 24598 At special positions: 0 Unit cell: (118.8, 143.64, 185.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 2 34.99 S 150 16.00 P 2 15.00 O 4566 8.00 N 4120 7.00 C 15758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS A 745 " - pdb=" SG CYS A 800 " distance=2.03 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS D 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 79 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS C 794 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 456 " distance=2.03 Simple disulfide: pdb=" SG CYS C 745 " - pdb=" SG CYS C 800 " distance=2.03 Simple disulfide: pdb=" SG CYS D 79 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 420 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 744 " - pdb=" SG CYS D 798 " 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 NAG-ASN " NAG A 901 " - " ASN A 687 " " NAG B 901 " - " ASN B 61 " " NAG B 902 " - " ASN B 203 " " NAG B 903 " - " ASN B 239 " " NAG B 904 " - " ASN B 276 " " NAG B 905 " - " ASN B 368 " " NAG B 906 " - " ASN B 471 " " NAG B 907 " - " ASN B 771 " " NAG C 901 " - " ASN C 687 " " NAG D 901 " - " ASN D 61 " " NAG D 902 " - " ASN D 203 " " NAG D 903 " - " ASN D 239 " " NAG D 904 " - " ASN D 276 " " NAG D 905 " - " ASN D 368 " " NAG D 906 " - " ASN D 471 " " NAG D 907 " - " ASN D 771 " Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 845.3 milliseconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 29 sheets defined 42.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.689A pdb=" N PHE A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 166 removed outlier: 3.848A pdb=" N THR A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL A 157 " --> pdb=" O GLN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 194 removed outlier: 3.668A pdb=" N PHE A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 220 removed outlier: 4.286A pdb=" N VAL A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 removed outlier: 3.606A pdb=" N LEU A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 310 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.806A pdb=" N VAL A 339 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.046A pdb=" N THR A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 560 through 579 removed outlier: 3.855A pdb=" N LEU A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 613 removed outlier: 3.944A pdb=" N PHE A 613 " --> pdb=" O TRP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 632 Processing helix chain 'A' and resid 634 through 652 Processing helix chain 'A' and resid 667 through 672 removed outlier: 4.261A pdb=" N GLN A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 removed outlier: 4.095A pdb=" N TYR A 676 " --> pdb=" O PRO A 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 676' Processing helix chain 'A' and resid 688 through 698 removed outlier: 4.222A pdb=" N ARG A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 706 removed outlier: 4.154A pdb=" N GLN A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR A 704 " --> pdb=" O TYR A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 removed outlier: 3.510A pdb=" N ALA A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 771 through 786 removed outlier: 3.817A pdb=" N ASP A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 786 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 removed outlier: 3.688A pdb=" N CYS A 794 " --> pdb=" O GLU A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 837 Processing helix chain 'B' and resid 35 through 51 removed outlier: 4.117A pdb=" N LYS B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 104 through 112 removed outlier: 3.834A pdb=" N SER B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.743A pdb=" N TYR B 128 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 159 removed outlier: 3.907A pdb=" N VAL B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 224 through 238 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 276 through 297 removed outlier: 4.130A pdb=" N GLY B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 327 removed outlier: 3.986A pdb=" N SER B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 520 through 527 removed outlier: 4.355A pdb=" N TYR B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 582 removed outlier: 4.410A pdb=" N LEU B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B 582 " --> pdb=" O TYR B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'B' and resid 627 through 657 removed outlier: 3.535A pdb=" N ILE B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 removed outlier: 3.527A pdb=" N ASN B 674 " --> pdb=" O PRO B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 696 removed outlier: 3.562A pdb=" N ARG B 695 " --> pdb=" O ILE B 691 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 696 " --> pdb=" O TYR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.708A pdb=" N HIS B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 707 " --> pdb=" O TYR B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 732 through 743 removed outlier: 4.251A pdb=" N PHE B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 782 Processing helix chain 'B' and resid 783 through 793 Processing helix chain 'B' and resid 810 through 843 removed outlier: 3.563A pdb=" N ALA B 814 " --> pdb=" O PHE B 810 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL B 820 " --> pdb=" O VAL B 816 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.599A pdb=" N PHE C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 166 removed outlier: 3.873A pdb=" N THR C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 194 removed outlier: 3.674A pdb=" N PHE C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 220 removed outlier: 4.264A pdb=" N VAL C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 removed outlier: 3.614A pdb=" N LEU C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 310 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.941A pdb=" N VAL C 339 " --> pdb=" O PRO C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 472 removed outlier: 3.515A pdb=" N ARG C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'C' and resid 560 through 579 removed outlier: 3.872A pdb=" N LEU C 566 " --> pdb=" O PHE C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 613 removed outlier: 3.939A pdb=" N PHE C 613 " --> pdb=" O TRP C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 632 Processing helix chain 'C' and resid 634 through 652 Processing helix chain 'C' and resid 667 through 672 removed outlier: 4.297A pdb=" N GLN C 671 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 676 removed outlier: 4.088A pdb=" N TYR C 676 " --> pdb=" O PRO C 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 673 through 676' Processing helix chain 'C' and resid 688 through 696 removed outlier: 4.314A pdb=" N ARG C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 693 " --> pdb=" O SER C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 706 removed outlier: 4.144A pdb=" N GLN C 703 " --> pdb=" O PRO C 699 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR C 704 " --> pdb=" O TYR C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 723 Processing helix chain 'C' and resid 732 through 741 Processing helix chain 'C' and resid 771 through 786 removed outlier: 3.833A pdb=" N ASP C 776 " --> pdb=" O LYS C 772 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU C 777 " --> pdb=" O ARG C 773 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY C 786 " --> pdb=" O PHE C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 796 removed outlier: 3.711A pdb=" N CYS C 794 " --> pdb=" O GLU C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 837 Processing helix chain 'D' and resid 35 through 51 removed outlier: 4.094A pdb=" N LYS D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 82 Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.918A pdb=" N SER D 108 " --> pdb=" O PRO D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.764A pdb=" N TYR D 128 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 146 through 159 removed outlier: 3.885A pdb=" N VAL D 150 " --> pdb=" O HIS D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 224 through 238 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 276 through 297 removed outlier: 4.191A pdb=" N GLY D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 327 removed outlier: 3.941A pdb=" N SER D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 471 Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 520 through 527 removed outlier: 4.362A pdb=" N TYR D 526 " --> pdb=" O GLU D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 582 removed outlier: 4.445A pdb=" N LEU D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG D 582 " --> pdb=" O TYR D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 627 through 657 removed outlier: 3.564A pdb=" N ILE D 643 " --> pdb=" O PHE D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 674 removed outlier: 3.500A pdb=" N ASN D 674 " --> pdb=" O PRO D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 696 removed outlier: 3.596A pdb=" N ARG D 695 " --> pdb=" O ILE D 691 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN D 696 " --> pdb=" O TYR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.691A pdb=" N HIS D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU D 707 " --> pdb=" O TYR D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 removed outlier: 4.307A pdb=" N PHE D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 782 Processing helix chain 'D' and resid 783 through 793 Processing helix chain 'D' and resid 810 through 843 removed outlier: 3.570A pdb=" N ALA D 814 " --> pdb=" O PHE D 810 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL D 820 " --> pdb=" O VAL D 816 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE D 833 " --> pdb=" O PHE D 829 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 73 removed outlier: 3.747A pdb=" N LEU A 72 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 40 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN A 35 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL A 99 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA A 37 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 125 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA3, first strand: chain 'A' and resid 204 through 206 removed outlier: 6.623A pdb=" N LEU A 172 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU A 206 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N THR A 174 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 230 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 175 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 229 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 277 " --> pdb=" O TRP A 255 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 279 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU A 276 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 366 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 455 removed outlier: 4.005A pdb=" N MET A 450 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 440 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 452 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N LEU A 479 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG A 437 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 476 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER A 407 " --> pdb=" O MET A 507 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 728 through 731 removed outlier: 3.509A pdb=" N TYR A 730 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 537 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 748 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.762A pdb=" N LEU B 91 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 90 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 194 through 197 removed outlier: 6.930A pdb=" N LEU B 165 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N PHE B 197 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL B 167 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 164 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 220 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 168 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TRP B 247 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 269 through 271 removed outlier: 3.573A pdb=" N GLY B 365 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN B 355 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLN B 363 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN B 357 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU B 361 " --> pdb=" O GLN B 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 330 through 333 removed outlier: 4.101A pdb=" N TYR B 330 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASP B 332 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU B 339 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 399 through 402 removed outlier: 6.887A pdb=" N ILE B 400 " --> pdb=" O HIS B 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 412 through 413 removed outlier: 3.520A pdb=" N CYS B 455 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 434 " --> pdb=" O CYS B 455 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 513 through 515 removed outlier: 4.554A pdb=" N ALA B 515 " --> pdb=" O GLY B 759 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY B 759 " --> pdb=" O ALA B 515 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 681 through 682 removed outlier: 7.248A pdb=" N ALA B 682 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP B 731 " --> pdb=" O THR B 539 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 68 through 73 removed outlier: 3.794A pdb=" N LEU C 72 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 40 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN C 35 " --> pdb=" O GLY C 97 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL C 99 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA C 37 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 125 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 100 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 204 through 206 removed outlier: 6.404A pdb=" N LEU C 172 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU C 206 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR C 174 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 175 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 229 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 279 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU C 276 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 366 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL C 363 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 365 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU C 373 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 342 through 343 Processing sheet with id=AB9, first strand: chain 'C' and resid 475 through 479 removed outlier: 5.856A pdb=" N LEU C 406 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TYR C 478 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE C 408 " --> pdb=" O TYR C 478 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER C 407 " --> pdb=" O MET C 507 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 434 through 439 removed outlier: 4.298A pdb=" N VAL C 434 " --> pdb=" O CYS C 456 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 452 " --> pdb=" O LYS C 438 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 523 through 524 removed outlier: 3.936A pdb=" N ASP C 523 " --> pdb=" O LEU C 765 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 727 through 731 removed outlier: 3.581A pdb=" N VAL C 537 " --> pdb=" O VAL C 748 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 66 removed outlier: 3.731A pdb=" N LEU D 91 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE D 90 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 194 through 197 removed outlier: 6.743A pdb=" N LEU D 165 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N PHE D 197 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL D 167 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 164 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE D 220 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER D 222 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER D 168 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU D 267 " --> pdb=" O TRP D 247 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D 249 " --> pdb=" O LEU D 267 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 269 through 271 removed outlier: 6.537A pdb=" N ASN D 355 " --> pdb=" O GLN D 363 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLN D 363 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN D 357 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU D 361 " --> pdb=" O GLN D 357 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 339 through 340 removed outlier: 4.616A pdb=" N GLU D 339 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 400 through 402 removed outlier: 6.805A pdb=" N ILE D 400 " --> pdb=" O HIS D 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 410 through 413 removed outlier: 3.678A pdb=" N GLY D 438 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 513 through 515 removed outlier: 4.506A pdb=" N ALA D 515 " --> pdb=" O GLY D 759 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY D 759 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 681 through 682 removed outlier: 7.062A pdb=" N ALA D 682 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N ASP D 732 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP D 731 " --> pdb=" O THR D 539 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7932 1.36 - 1.49: 6505 1.49 - 1.62: 10461 1.62 - 1.76: 0 1.76 - 1.89: 260 Bond restraints: 25158 Sorted by residual: bond pdb=" N PRO B 516 " pdb=" CD PRO B 516 " ideal model delta sigma weight residual 1.473 1.541 -0.068 1.40e-02 5.10e+03 2.33e+01 bond pdb=" C1 J86 B 908 " pdb=" P1 J86 B 908 " ideal model delta sigma weight residual 1.887 1.798 0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C1 J86 D 908 " pdb=" P1 J86 D 908 " ideal model delta sigma weight residual 1.887 1.798 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" O2 J86 B 908 " pdb=" P1 J86 B 908 " ideal model delta sigma weight residual 1.533 1.620 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" O2 J86 D 908 " pdb=" P1 J86 D 908 " ideal model delta sigma weight residual 1.533 1.620 -0.087 2.00e-02 2.50e+03 1.88e+01 ... (remaining 25153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 33910 2.53 - 5.05: 183 5.05 - 7.58: 19 7.58 - 10.10: 2 10.10 - 12.63: 4 Bond angle restraints: 34118 Sorted by residual: angle pdb=" N LEU D 517 " pdb=" CA LEU D 517 " pdb=" C LEU D 517 " ideal model delta sigma weight residual 108.96 117.80 -8.84 1.59e+00 3.96e-01 3.09e+01 angle pdb=" N LEU B 517 " pdb=" CA LEU B 517 " pdb=" C LEU B 517 " ideal model delta sigma weight residual 108.41 116.83 -8.42 1.61e+00 3.86e-01 2.74e+01 angle pdb=" C1 J86 D 908 " pdb=" P1 J86 D 908 " pdb=" O3 J86 D 908 " ideal model delta sigma weight residual 102.38 115.01 -12.63 3.00e+00 1.11e-01 1.77e+01 angle pdb=" C1 J86 B 908 " pdb=" P1 J86 B 908 " pdb=" O3 J86 B 908 " ideal model delta sigma weight residual 102.38 115.00 -12.62 3.00e+00 1.11e-01 1.77e+01 angle pdb=" O1 J86 D 908 " pdb=" P1 J86 D 908 " pdb=" O2 J86 D 908 " ideal model delta sigma weight residual 114.24 103.00 11.24 3.00e+00 1.11e-01 1.40e+01 ... (remaining 34113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 13935 11.99 - 23.97: 835 23.97 - 35.96: 294 35.96 - 47.94: 95 47.94 - 59.93: 21 Dihedral angle restraints: 15180 sinusoidal: 6232 harmonic: 8948 Sorted by residual: dihedral pdb=" N SER D 688 " pdb=" C SER D 688 " pdb=" CA SER D 688 " pdb=" CB SER D 688 " ideal model delta harmonic sigma weight residual 122.80 111.13 11.67 0 2.50e+00 1.60e-01 2.18e+01 dihedral pdb=" N SER B 688 " pdb=" C SER B 688 " pdb=" CA SER B 688 " pdb=" CB SER B 688 " ideal model delta harmonic sigma weight residual 122.80 111.29 11.51 0 2.50e+00 1.60e-01 2.12e+01 dihedral pdb=" CA ASN B 491 " pdb=" C ASN B 491 " pdb=" N ASN B 492 " pdb=" CA ASN B 492 " ideal model delta harmonic sigma weight residual 180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 15177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3557 0.078 - 0.156: 321 0.156 - 0.234: 4 0.234 - 0.312: 2 0.312 - 0.390: 2 Chirality restraints: 3886 Sorted by residual: chirality pdb=" CA SER D 688 " pdb=" N SER D 688 " pdb=" C SER D 688 " pdb=" CB SER D 688 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA SER B 688 " pdb=" N SER B 688 " pdb=" C SER B 688 " pdb=" CB SER B 688 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA PRO B 516 " pdb=" N PRO B 516 " pdb=" C PRO B 516 " pdb=" CB PRO B 516 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3883 not shown) Planarity restraints: 4306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 515 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.01e+00 pdb=" N PRO B 516 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 516 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 516 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 326 " 0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO A 327 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 326 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO C 327 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 327 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 327 " 0.016 5.00e-02 4.00e+02 ... (remaining 4303 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 333 2.64 - 3.20: 22730 3.20 - 3.77: 37924 3.77 - 4.33: 49478 4.33 - 4.90: 80452 Nonbonded interactions: 190917 Sorted by model distance: nonbonded pdb=" CB LYS D 685 " pdb=" OE1 GLN D 686 " model vdw 2.074 3.440 nonbonded pdb=" N GLN D 686 " pdb=" OE1 GLN D 686 " model vdw 2.077 3.120 nonbonded pdb=" N GLN B 686 " pdb=" OE1 GLN B 686 " model vdw 2.078 3.120 nonbonded pdb=" CB LYS B 685 " pdb=" OE1 GLN B 686 " model vdw 2.097 3.440 nonbonded pdb=" O THR A 793 " pdb=" OG1 THR A 797 " model vdw 2.196 3.040 ... (remaining 190912 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.980 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 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 : 0.003 0.089 25192 Z= 0.146 Angle : 0.525 12.630 34202 Z= 0.289 Chirality : 0.041 0.390 3886 Planarity : 0.003 0.035 4290 Dihedral : 9.380 59.930 9346 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.22 % Allowed : 6.06 % Favored : 91.72 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 3048 helix: 1.53 (0.16), residues: 1186 sheet: -1.12 (0.30), residues: 340 loop : -0.94 (0.17), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 489 TYR 0.005 0.001 TYR C 180 PHE 0.009 0.001 PHE B 753 TRP 0.007 0.001 TRP B 636 HIS 0.002 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00260 (25158) covalent geometry : angle 0.52332 (34118) SS BOND : bond 0.00137 ( 18) SS BOND : angle 0.42004 ( 36) hydrogen bonds : bond 0.16076 ( 953) hydrogen bonds : angle 6.44493 ( 2793) link_NAG-ASN : bond 0.00265 ( 16) link_NAG-ASN : angle 1.14674 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 590 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7007 (mmp) cc_final: 0.6230 (tmm) REVERT: A 100 PHE cc_start: 0.8076 (t80) cc_final: 0.7807 (t80) REVERT: A 135 MET cc_start: 0.2040 (pmm) cc_final: 0.1801 (mmm) REVERT: A 145 PHE cc_start: 0.7004 (m-80) cc_final: 0.6678 (m-80) REVERT: A 162 MET cc_start: 0.7998 (mmm) cc_final: 0.7645 (mmt) REVERT: A 306 MET cc_start: 0.4479 (tmm) cc_final: 0.3622 (ttt) REVERT: A 419 VAL cc_start: 0.5969 (p) cc_final: 0.5468 (p) REVERT: A 434 VAL cc_start: 0.4835 (m) cc_final: 0.4051 (m) REVERT: A 606 TRP cc_start: 0.6506 (m100) cc_final: 0.6305 (m100) REVERT: A 609 TRP cc_start: 0.6801 (m100) cc_final: 0.6563 (m100) REVERT: B 39 GLU cc_start: 0.6462 (mt-10) cc_final: 0.5931 (tt0) REVERT: B 153 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7839 (tp30) REVERT: B 163 ILE cc_start: 0.8036 (tp) cc_final: 0.7687 (tt) REVERT: B 249 VAL cc_start: 0.7900 (t) cc_final: 0.7436 (t) REVERT: B 298 LYS cc_start: 0.7538 (mmmm) cc_final: 0.7178 (mtmm) REVERT: B 520 ASN cc_start: 0.8229 (m-40) cc_final: 0.7993 (m110) REVERT: C 135 MET cc_start: 0.3917 (pmm) cc_final: 0.3378 (mmm) REVERT: C 145 PHE cc_start: 0.6687 (m-80) cc_final: 0.6024 (m-80) REVERT: C 162 MET cc_start: 0.8245 (mmm) cc_final: 0.7847 (mmt) REVERT: C 257 VAL cc_start: 0.7323 (t) cc_final: 0.6935 (m) REVERT: C 419 VAL cc_start: 0.6912 (OUTLIER) cc_final: 0.6675 (p) REVERT: C 475 TYR cc_start: 0.5901 (m-10) cc_final: 0.5481 (m-80) REVERT: C 606 TRP cc_start: 0.6808 (m100) cc_final: 0.6112 (m100) REVERT: C 649 LEU cc_start: 0.8182 (mm) cc_final: 0.7693 (mp) REVERT: D 41 MET cc_start: 0.8089 (ptp) cc_final: 0.6640 (ptt) REVERT: D 232 TYR cc_start: 0.5244 (t80) cc_final: 0.2541 (t80) REVERT: D 329 LYS cc_start: 0.7687 (tmtt) cc_final: 0.7333 (mmtp) REVERT: D 341 ASN cc_start: 0.8857 (t0) cc_final: 0.8603 (m-40) REVERT: D 607 MET cc_start: 0.5784 (mpp) cc_final: 0.5282 (ptt) REVERT: D 703 TYR cc_start: 0.6503 (OUTLIER) cc_final: 0.5426 (m-80) REVERT: D 762 MET cc_start: 0.5860 (mtm) cc_final: 0.5508 (mtm) outliers start: 59 outliers final: 13 residues processed: 640 average time/residue: 0.1653 time to fit residues: 161.3437 Evaluate side-chains 353 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 338 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 731 TRP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 731 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 0.0040 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 85 HIS A 128 HIS B 40 GLN B 48 GLN ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS B 780 HIS C 193 ASN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 449 HIS D 477 HIS D 487 GLN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.126279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.101100 restraints weight = 80970.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.102614 restraints weight = 49120.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.103014 restraints weight = 34737.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.103462 restraints weight = 30596.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.103653 restraints weight = 28169.343| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25192 Z= 0.184 Angle : 0.638 9.960 34202 Z= 0.324 Chirality : 0.044 0.228 3886 Planarity : 0.005 0.077 4290 Dihedral : 5.344 59.715 3690 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.05 % Allowed : 12.42 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.16), residues: 3048 helix: 1.28 (0.15), residues: 1206 sheet: -1.14 (0.27), residues: 368 loop : -1.14 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 704 TYR 0.016 0.002 TYR C 312 PHE 0.024 0.002 PHE A 183 TRP 0.021 0.001 TRP C 255 HIS 0.006 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00415 (25158) covalent geometry : angle 0.63613 (34118) SS BOND : bond 0.00911 ( 18) SS BOND : angle 1.15847 ( 36) hydrogen bonds : bond 0.03809 ( 953) hydrogen bonds : angle 5.21474 ( 2793) link_NAG-ASN : bond 0.00158 ( 16) link_NAG-ASN : angle 1.21784 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 332 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7252 (mmp) cc_final: 0.6581 (tmm) REVERT: A 47 THR cc_start: 0.6135 (OUTLIER) cc_final: 0.5782 (t) REVERT: A 135 MET cc_start: 0.2843 (pmm) cc_final: 0.2546 (mmm) REVERT: A 162 MET cc_start: 0.8322 (mmm) cc_final: 0.7905 (mmt) REVERT: A 177 PHE cc_start: 0.3147 (OUTLIER) cc_final: 0.2854 (m-10) REVERT: A 475 TYR cc_start: 0.7158 (p90) cc_final: 0.6278 (m-10) REVERT: A 701 MET cc_start: 0.8117 (tmm) cc_final: 0.7648 (tmm) REVERT: A 823 MET cc_start: 0.7681 (ptp) cc_final: 0.6569 (mmm) REVERT: B 343 ASP cc_start: 0.6973 (p0) cc_final: 0.6758 (p0) REVERT: B 354 MET cc_start: 0.7840 (tpp) cc_final: 0.7603 (tpp) REVERT: C 133 MET cc_start: 0.7500 (mpp) cc_final: 0.7268 (mpp) REVERT: C 135 MET cc_start: 0.4412 (pmm) cc_final: 0.3630 (ptm) REVERT: C 229 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8301 (tp) REVERT: C 523 ASP cc_start: 0.6718 (p0) cc_final: 0.6115 (p0) REVERT: C 606 TRP cc_start: 0.6452 (m100) cc_final: 0.6011 (m100) REVERT: C 609 TRP cc_start: 0.7083 (m100) cc_final: 0.6878 (m100) REVERT: C 823 MET cc_start: 0.5578 (ptp) cc_final: 0.4822 (mmm) REVERT: D 41 MET cc_start: 0.8040 (ptp) cc_final: 0.6979 (ptp) REVERT: D 323 ARG cc_start: 0.8878 (mmp80) cc_final: 0.8577 (mmt180) REVERT: D 329 LYS cc_start: 0.7936 (tmtt) cc_final: 0.7494 (mmtp) REVERT: D 571 HIS cc_start: 0.6903 (m90) cc_final: 0.6116 (t-90) REVERT: D 762 MET cc_start: 0.6528 (mtm) cc_final: 0.6107 (mtm) REVERT: D 785 MET cc_start: 0.8760 (mmt) cc_final: 0.8254 (mmt) outliers start: 81 outliers final: 38 residues processed: 396 average time/residue: 0.1529 time to fit residues: 95.5030 Evaluate side-chains 296 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 730 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 213 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 264 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 285 optimal weight: 20.0000 chunk 143 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 40 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 363 GLN B 375 ASN B 780 HIS ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 780 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.122126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.093385 restraints weight = 80621.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.095933 restraints weight = 47076.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.097620 restraints weight = 33136.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.098763 restraints weight = 26393.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.099460 restraints weight = 22647.079| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25192 Z= 0.172 Angle : 0.611 10.429 34202 Z= 0.312 Chirality : 0.044 0.218 3886 Planarity : 0.004 0.059 4290 Dihedral : 4.767 55.053 3680 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.65 % Allowed : 14.04 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.16), residues: 3048 helix: 0.97 (0.15), residues: 1222 sheet: -1.58 (0.25), residues: 406 loop : -1.10 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 630 TYR 0.018 0.002 TYR D 703 PHE 0.035 0.002 PHE A 183 TRP 0.020 0.001 TRP A 606 HIS 0.041 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00387 (25158) covalent geometry : angle 0.60792 (34118) SS BOND : bond 0.00573 ( 18) SS BOND : angle 1.54662 ( 36) hydrogen bonds : bond 0.03658 ( 953) hydrogen bonds : angle 4.92301 ( 2793) link_NAG-ASN : bond 0.00146 ( 16) link_NAG-ASN : angle 1.33892 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 277 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7118 (mmp) cc_final: 0.6480 (tmm) REVERT: A 45 ASP cc_start: 0.8561 (t0) cc_final: 0.8251 (t0) REVERT: A 112 MET cc_start: 0.7776 (mmm) cc_final: 0.7568 (mmm) REVERT: A 135 MET cc_start: 0.3572 (pmm) cc_final: 0.3267 (mmm) REVERT: A 162 MET cc_start: 0.8506 (mmm) cc_final: 0.8039 (mmt) REVERT: A 306 MET cc_start: 0.5029 (tmm) cc_final: 0.4353 (tmm) REVERT: A 313 ILE cc_start: 0.5994 (OUTLIER) cc_final: 0.5745 (pt) REVERT: A 338 MET cc_start: 0.6994 (ptp) cc_final: 0.6740 (ptp) REVERT: A 524 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7303 (p90) REVERT: A 823 MET cc_start: 0.7703 (ptp) cc_final: 0.6712 (mmm) REVERT: B 470 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8587 (ttp) REVERT: B 502 MET cc_start: 0.8532 (mmt) cc_final: 0.8321 (mmt) REVERT: C 39 MET cc_start: 0.7687 (tmm) cc_final: 0.7357 (tmm) REVERT: C 145 PHE cc_start: 0.7213 (m-80) cc_final: 0.6938 (m-80) REVERT: C 606 TRP cc_start: 0.6780 (m100) cc_final: 0.6135 (m100) REVERT: C 609 TRP cc_start: 0.7731 (m100) cc_final: 0.7458 (m100) REVERT: C 790 GLU cc_start: 0.7774 (pm20) cc_final: 0.7520 (pt0) REVERT: C 823 MET cc_start: 0.5795 (ptp) cc_final: 0.5080 (mmm) REVERT: D 41 MET cc_start: 0.8159 (ptp) cc_final: 0.7950 (ptm) REVERT: D 163 ILE cc_start: 0.8636 (tp) cc_final: 0.8276 (tt) REVERT: D 470 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8594 (ttp) REVERT: D 571 HIS cc_start: 0.7164 (m90) cc_final: 0.6456 (t-90) REVERT: D 641 MET cc_start: 0.8927 (tpp) cc_final: 0.8644 (tpt) outliers start: 97 outliers final: 51 residues processed: 358 average time/residue: 0.1413 time to fit residues: 82.9263 Evaluate side-chains 299 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 780 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 672 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 218 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 297 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 274 optimal weight: 6.9990 chunk 280 optimal weight: 20.0000 chunk 237 optimal weight: 0.0270 chunk 275 optimal weight: 0.8980 overall best weight: 2.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 HIS B 780 HIS C 163 GLN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN D 782 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.119588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.090137 restraints weight = 79411.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.092755 restraints weight = 44901.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.094466 restraints weight = 31341.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.095515 restraints weight = 24905.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.096287 restraints weight = 21527.200| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25192 Z= 0.209 Angle : 0.637 8.377 34202 Z= 0.325 Chirality : 0.044 0.252 3886 Planarity : 0.004 0.054 4290 Dihedral : 4.727 45.755 3677 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.92 % Allowed : 14.57 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.16), residues: 3048 helix: 0.87 (0.15), residues: 1232 sheet: -1.84 (0.24), residues: 420 loop : -1.21 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 43 TYR 0.030 0.002 TYR A 251 PHE 0.039 0.002 PHE C 272 TRP 0.016 0.001 TRP C 255 HIS 0.036 0.001 HIS B 780 Details of bonding type rmsd covalent geometry : bond 0.00480 (25158) covalent geometry : angle 0.63254 (34118) SS BOND : bond 0.00481 ( 18) SS BOND : angle 1.55940 ( 36) hydrogen bonds : bond 0.03597 ( 953) hydrogen bonds : angle 4.95059 ( 2793) link_NAG-ASN : bond 0.00156 ( 16) link_NAG-ASN : angle 1.61687 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 258 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7239 (mmp) cc_final: 0.6558 (tmm) REVERT: A 74 MET cc_start: 0.7593 (tpp) cc_final: 0.7344 (tpp) REVERT: A 306 MET cc_start: 0.5059 (tmm) cc_final: 0.4370 (tmm) REVERT: A 313 ILE cc_start: 0.6131 (OUTLIER) cc_final: 0.5867 (pt) REVERT: A 475 TYR cc_start: 0.8209 (p90) cc_final: 0.7908 (p90) REVERT: A 823 MET cc_start: 0.7766 (ptp) cc_final: 0.6849 (mmm) REVERT: B 354 MET cc_start: 0.7782 (tpp) cc_final: 0.7405 (tpp) REVERT: B 470 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8485 (ttp) REVERT: B 502 MET cc_start: 0.8666 (mmt) cc_final: 0.8109 (mmt) REVERT: B 654 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8197 (t80) REVERT: C 39 MET cc_start: 0.7888 (tmm) cc_final: 0.7527 (tmm) REVERT: C 135 MET cc_start: 0.5484 (pmm) cc_final: 0.5271 (ptt) REVERT: C 605 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6395 (mt) REVERT: C 606 TRP cc_start: 0.6720 (m100) cc_final: 0.6043 (m100) REVERT: C 609 TRP cc_start: 0.7692 (m100) cc_final: 0.7489 (m100) REVERT: C 823 MET cc_start: 0.5821 (ptp) cc_final: 0.5111 (mmm) REVERT: D 41 MET cc_start: 0.8116 (ptp) cc_final: 0.7902 (ptm) REVERT: D 163 ILE cc_start: 0.8967 (tp) cc_final: 0.8709 (tt) REVERT: D 470 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8564 (ttp) REVERT: D 571 HIS cc_start: 0.7108 (m90) cc_final: 0.6311 (t-90) REVERT: D 641 MET cc_start: 0.8809 (tpp) cc_final: 0.8556 (tpt) outliers start: 104 outliers final: 76 residues processed: 342 average time/residue: 0.1281 time to fit residues: 73.6593 Evaluate side-chains 314 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 233 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 780 HIS Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain D residue 780 HIS Chi-restraints excluded: chain D residue 795 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 125 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 299 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 291 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 279 optimal weight: 0.6980 chunk 198 optimal weight: 9.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 GLN D 477 HIS D 487 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.118830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.090169 restraints weight = 79322.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.093273 restraints weight = 47916.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.093467 restraints weight = 33501.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.094172 restraints weight = 28405.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.094447 restraints weight = 25447.569| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 25192 Z= 0.166 Angle : 0.594 10.612 34202 Z= 0.303 Chirality : 0.044 0.200 3886 Planarity : 0.004 0.051 4290 Dihedral : 4.565 38.182 3677 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.31 % Allowed : 16.42 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 3048 helix: 0.83 (0.15), residues: 1236 sheet: -1.91 (0.24), residues: 420 loop : -1.19 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 187 TYR 0.013 0.001 TYR D 410 PHE 0.022 0.002 PHE C 183 TRP 0.013 0.001 TRP C 284 HIS 0.021 0.001 HIS B 780 Details of bonding type rmsd covalent geometry : bond 0.00383 (25158) covalent geometry : angle 0.59044 (34118) SS BOND : bond 0.00361 ( 18) SS BOND : angle 1.33700 ( 36) hydrogen bonds : bond 0.03323 ( 953) hydrogen bonds : angle 4.84641 ( 2793) link_NAG-ASN : bond 0.00228 ( 16) link_NAG-ASN : angle 1.59643 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 254 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7004 (mmp) cc_final: 0.6433 (tmm) REVERT: A 45 ASP cc_start: 0.8783 (t0) cc_final: 0.8521 (t0) REVERT: A 74 MET cc_start: 0.7747 (tpp) cc_final: 0.7509 (tpp) REVERT: A 162 MET cc_start: 0.8493 (mmm) cc_final: 0.8285 (mmt) REVERT: A 306 MET cc_start: 0.4688 (tmm) cc_final: 0.4092 (tmm) REVERT: A 313 ILE cc_start: 0.6400 (OUTLIER) cc_final: 0.6106 (pt) REVERT: A 823 MET cc_start: 0.7700 (ptp) cc_final: 0.6625 (mmm) REVERT: B 354 MET cc_start: 0.7873 (tpp) cc_final: 0.7471 (tpp) REVERT: B 470 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8629 (ttp) REVERT: B 502 MET cc_start: 0.8636 (mmt) cc_final: 0.8405 (mmt) REVERT: B 636 TRP cc_start: 0.5647 (t-100) cc_final: 0.5346 (t-100) REVERT: B 654 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8241 (t80) REVERT: C 39 MET cc_start: 0.7521 (tmm) cc_final: 0.7111 (tmm) REVERT: C 145 PHE cc_start: 0.7330 (m-80) cc_final: 0.7108 (m-80) REVERT: C 475 TYR cc_start: 0.5429 (m-10) cc_final: 0.5201 (m-10) REVERT: C 605 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6742 (mt) REVERT: C 606 TRP cc_start: 0.6774 (m100) cc_final: 0.6115 (m100) REVERT: C 653 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7963 (tpp) REVERT: C 823 MET cc_start: 0.5895 (ptp) cc_final: 0.5180 (mmm) REVERT: D 41 MET cc_start: 0.8361 (ptp) cc_final: 0.8031 (ptm) REVERT: D 571 HIS cc_start: 0.7159 (m90) cc_final: 0.6501 (t-90) REVERT: D 641 MET cc_start: 0.8912 (tpp) cc_final: 0.8602 (tpt) outliers start: 88 outliers final: 59 residues processed: 320 average time/residue: 0.1330 time to fit residues: 71.5521 Evaluate side-chains 301 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 237 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 780 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 817 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain D residue 780 HIS Chi-restraints excluded: chain D residue 795 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 178 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 186 optimal weight: 2.9990 chunk 285 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 224 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN C 693 ASN C 766 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.120588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.091943 restraints weight = 79224.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.094607 restraints weight = 44804.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.096298 restraints weight = 31141.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.097439 restraints weight = 24705.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.098197 restraints weight = 21172.056| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25192 Z= 0.110 Angle : 0.575 10.276 34202 Z= 0.286 Chirality : 0.043 0.165 3886 Planarity : 0.004 0.051 4290 Dihedral : 4.270 35.100 3675 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.24 % Allowed : 16.68 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 3048 helix: 0.82 (0.15), residues: 1236 sheet: -1.67 (0.25), residues: 386 loop : -1.20 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 181 TYR 0.013 0.001 TYR A 180 PHE 0.023 0.001 PHE C 183 TRP 0.012 0.001 TRP A 55 HIS 0.005 0.001 HIS D 780 Details of bonding type rmsd covalent geometry : bond 0.00252 (25158) covalent geometry : angle 0.57142 (34118) SS BOND : bond 0.00274 ( 18) SS BOND : angle 1.17695 ( 36) hydrogen bonds : bond 0.03019 ( 953) hydrogen bonds : angle 4.70772 ( 2793) link_NAG-ASN : bond 0.00284 ( 16) link_NAG-ASN : angle 1.45183 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 256 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.6988 (mmp) cc_final: 0.6447 (tmm) REVERT: A 473 PHE cc_start: 0.5215 (OUTLIER) cc_final: 0.3604 (m-80) REVERT: A 823 MET cc_start: 0.7734 (ptp) cc_final: 0.6844 (mmm) REVERT: B 354 MET cc_start: 0.7839 (tpp) cc_final: 0.7396 (tpp) REVERT: B 409 VAL cc_start: 0.7947 (OUTLIER) cc_final: 0.7629 (t) REVERT: B 470 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8641 (ttp) REVERT: B 502 MET cc_start: 0.8517 (mmt) cc_final: 0.8307 (mmt) REVERT: B 546 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7514 (pt) REVERT: B 636 TRP cc_start: 0.5602 (t-100) cc_final: 0.5363 (t-100) REVERT: B 654 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8278 (t80) REVERT: C 39 MET cc_start: 0.7252 (tmm) cc_final: 0.6874 (tmm) REVERT: C 145 PHE cc_start: 0.7037 (m-80) cc_final: 0.6665 (m-80) REVERT: C 200 MET cc_start: 0.7689 (mmm) cc_final: 0.6623 (tpt) REVERT: C 605 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.6356 (mt) REVERT: C 606 TRP cc_start: 0.6875 (m100) cc_final: 0.6167 (m100) REVERT: C 653 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8312 (tpp) REVERT: C 823 MET cc_start: 0.5997 (ptp) cc_final: 0.5475 (mmm) REVERT: D 470 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8517 (ttp) REVERT: D 571 HIS cc_start: 0.7205 (m90) cc_final: 0.6549 (t-90) REVERT: D 641 MET cc_start: 0.8777 (tpp) cc_final: 0.8476 (tpt) outliers start: 86 outliers final: 56 residues processed: 320 average time/residue: 0.1290 time to fit residues: 69.7063 Evaluate side-chains 296 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 232 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 780 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 817 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain D residue 780 HIS Chi-restraints excluded: chain D residue 795 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 213 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 65 optimal weight: 0.0770 chunk 142 optimal weight: 0.0870 chunk 132 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 167 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 HIS ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.121030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.094071 restraints weight = 79308.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.095642 restraints weight = 48465.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.098310 restraints weight = 34865.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.098399 restraints weight = 27558.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.098387 restraints weight = 23454.439| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25192 Z= 0.103 Angle : 0.554 11.085 34202 Z= 0.279 Chirality : 0.043 0.171 3886 Planarity : 0.004 0.052 4290 Dihedral : 4.130 31.464 3674 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.35 % Allowed : 17.02 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.16), residues: 3048 helix: 0.81 (0.15), residues: 1242 sheet: -1.55 (0.26), residues: 362 loop : -1.15 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 36 TYR 0.011 0.001 TYR A 180 PHE 0.053 0.001 PHE D 42 TRP 0.012 0.001 TRP A 55 HIS 0.004 0.001 HIS D 477 Details of bonding type rmsd covalent geometry : bond 0.00231 (25158) covalent geometry : angle 0.55130 (34118) SS BOND : bond 0.00251 ( 18) SS BOND : angle 1.00871 ( 36) hydrogen bonds : bond 0.02880 ( 953) hydrogen bonds : angle 4.59350 ( 2793) link_NAG-ASN : bond 0.00286 ( 16) link_NAG-ASN : angle 1.37803 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 253 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.6855 (mmp) cc_final: 0.6225 (tmm) REVERT: A 45 ASP cc_start: 0.8486 (t0) cc_final: 0.8217 (t0) REVERT: A 473 PHE cc_start: 0.5199 (OUTLIER) cc_final: 0.3593 (m-80) REVERT: A 823 MET cc_start: 0.7663 (ptp) cc_final: 0.6608 (mmm) REVERT: B 354 MET cc_start: 0.7800 (tpp) cc_final: 0.7413 (tpp) REVERT: B 409 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7560 (t) REVERT: B 470 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8566 (ttp) REVERT: B 502 MET cc_start: 0.8521 (mmt) cc_final: 0.8262 (mmt) REVERT: B 546 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7616 (pt) REVERT: B 636 TRP cc_start: 0.5630 (t-100) cc_final: 0.5302 (t-100) REVERT: B 654 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8325 (t80) REVERT: B 818 MET cc_start: 0.5647 (ppp) cc_final: 0.5344 (ppp) REVERT: C 39 MET cc_start: 0.6972 (tmm) cc_final: 0.6517 (tmm) REVERT: C 200 MET cc_start: 0.7664 (mmm) cc_final: 0.6613 (tpt) REVERT: C 229 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8442 (tp) REVERT: C 576 PHE cc_start: 0.4386 (t80) cc_final: 0.3857 (t80) REVERT: C 605 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6694 (mt) REVERT: C 606 TRP cc_start: 0.6735 (m100) cc_final: 0.6058 (m100) REVERT: C 653 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7904 (tpp) REVERT: C 823 MET cc_start: 0.5911 (ptp) cc_final: 0.5355 (mmm) REVERT: D 470 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8521 (ttp) REVERT: D 527 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8429 (mp) REVERT: D 571 HIS cc_start: 0.7189 (m90) cc_final: 0.6476 (t-90) REVERT: D 641 MET cc_start: 0.8920 (tpp) cc_final: 0.8615 (tpt) REVERT: D 703 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.6271 (t80) outliers start: 89 outliers final: 59 residues processed: 323 average time/residue: 0.1302 time to fit residues: 70.3860 Evaluate side-chains 305 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 235 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 780 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 817 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain D residue 780 HIS Chi-restraints excluded: chain D residue 795 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 303 optimal weight: 20.0000 chunk 300 optimal weight: 0.4980 chunk 2 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 164 optimal weight: 0.5980 chunk 241 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 ASN D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.119446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.090495 restraints weight = 79269.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.093126 restraints weight = 44833.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.094864 restraints weight = 31202.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.095965 restraints weight = 24707.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.096653 restraints weight = 21226.625| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25192 Z= 0.133 Angle : 0.595 11.612 34202 Z= 0.298 Chirality : 0.043 0.186 3886 Planarity : 0.004 0.052 4290 Dihedral : 4.225 32.476 3674 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.20 % Allowed : 17.58 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.16), residues: 3048 helix: 0.77 (0.15), residues: 1242 sheet: -1.67 (0.24), residues: 410 loop : -1.14 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 36 TYR 0.011 0.001 TYR C 475 PHE 0.038 0.001 PHE D 42 TRP 0.012 0.001 TRP D 381 HIS 0.006 0.001 HIS D 780 Details of bonding type rmsd covalent geometry : bond 0.00307 (25158) covalent geometry : angle 0.59037 (34118) SS BOND : bond 0.00353 ( 18) SS BOND : angle 1.88153 ( 36) hydrogen bonds : bond 0.02983 ( 953) hydrogen bonds : angle 4.62800 ( 2793) link_NAG-ASN : bond 0.00230 ( 16) link_NAG-ASN : angle 1.43557 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 234 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.6966 (mmp) cc_final: 0.6514 (tmm) REVERT: A 45 ASP cc_start: 0.8329 (t0) cc_final: 0.8073 (t0) REVERT: A 823 MET cc_start: 0.7763 (ptp) cc_final: 0.6824 (mmm) REVERT: B 354 MET cc_start: 0.7694 (tpp) cc_final: 0.7276 (tpp) REVERT: B 409 VAL cc_start: 0.8004 (OUTLIER) cc_final: 0.7675 (t) REVERT: B 470 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8604 (ttp) REVERT: B 502 MET cc_start: 0.8558 (mmt) cc_final: 0.8285 (mmt) REVERT: B 546 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7606 (pt) REVERT: B 636 TRP cc_start: 0.5597 (t-100) cc_final: 0.5250 (t-100) REVERT: B 654 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8281 (t80) REVERT: C 39 MET cc_start: 0.7137 (tmm) cc_final: 0.6665 (tmm) REVERT: C 145 PHE cc_start: 0.7476 (m-80) cc_final: 0.6576 (m-80) REVERT: C 200 MET cc_start: 0.7680 (mmm) cc_final: 0.6670 (tpt) REVERT: C 605 ILE cc_start: 0.6671 (OUTLIER) cc_final: 0.6389 (mt) REVERT: C 606 TRP cc_start: 0.6770 (m100) cc_final: 0.6092 (m100) REVERT: C 653 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8240 (tpt) REVERT: C 823 MET cc_start: 0.6001 (ptp) cc_final: 0.5497 (mmm) REVERT: D 470 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8539 (ttp) REVERT: D 571 HIS cc_start: 0.7103 (m90) cc_final: 0.6494 (t-90) outliers start: 85 outliers final: 62 residues processed: 299 average time/residue: 0.1256 time to fit residues: 63.7616 Evaluate side-chains 300 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 231 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 780 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 817 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain D residue 780 HIS Chi-restraints excluded: chain D residue 795 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 186 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 245 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 696 GLN D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.115404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.087299 restraints weight = 79268.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.089224 restraints weight = 47437.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.089120 restraints weight = 34073.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.089770 restraints weight = 33437.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.089813 restraints weight = 29288.590| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25192 Z= 0.212 Angle : 0.677 12.106 34202 Z= 0.343 Chirality : 0.046 0.292 3886 Planarity : 0.004 0.060 4290 Dihedral : 4.782 39.159 3674 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.70 % Rotamer: Outliers : 3.54 % Allowed : 17.43 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.15), residues: 3048 helix: 0.69 (0.15), residues: 1234 sheet: -1.87 (0.24), residues: 380 loop : -1.27 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 187 TYR 0.018 0.002 TYR D 410 PHE 0.041 0.002 PHE D 42 TRP 0.022 0.001 TRP C 284 HIS 0.007 0.001 HIS D 780 Details of bonding type rmsd covalent geometry : bond 0.00489 (25158) covalent geometry : angle 0.67205 (34118) SS BOND : bond 0.00490 ( 18) SS BOND : angle 1.83776 ( 36) hydrogen bonds : bond 0.03444 ( 953) hydrogen bonds : angle 4.86041 ( 2793) link_NAG-ASN : bond 0.00263 ( 16) link_NAG-ASN : angle 1.71358 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 223 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.6808 (mmp) cc_final: 0.6292 (tmm) REVERT: A 45 ASP cc_start: 0.8749 (t0) cc_final: 0.8503 (t0) REVERT: B 354 MET cc_start: 0.7814 (tpp) cc_final: 0.7401 (tpp) REVERT: B 409 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8214 (t) REVERT: B 470 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8625 (ttp) REVERT: B 636 TRP cc_start: 0.5715 (t-100) cc_final: 0.5454 (t-100) REVERT: B 654 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8302 (t80) REVERT: B 690 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.7908 (t0) REVERT: B 703 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.6723 (m-80) REVERT: C 39 MET cc_start: 0.6794 (tmm) cc_final: 0.5925 (tmm) REVERT: C 145 PHE cc_start: 0.7688 (m-80) cc_final: 0.7132 (m-80) REVERT: C 475 TYR cc_start: 0.8286 (p90) cc_final: 0.7965 (p90) REVERT: C 606 TRP cc_start: 0.6676 (m100) cc_final: 0.6017 (m100) REVERT: C 653 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8109 (tpt) REVERT: C 823 MET cc_start: 0.6143 (ptp) cc_final: 0.5529 (mmm) REVERT: D 470 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8554 (ttp) REVERT: D 527 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8613 (mp) REVERT: D 571 HIS cc_start: 0.7164 (m90) cc_final: 0.6499 (t-90) outliers start: 94 outliers final: 67 residues processed: 298 average time/residue: 0.1321 time to fit residues: 66.3972 Evaluate side-chains 286 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 211 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 703 TYR Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 780 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 817 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain D residue 780 HIS Chi-restraints excluded: chain D residue 795 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 184 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 288 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 222 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 201 optimal weight: 0.0370 chunk 60 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 151 optimal weight: 5.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.118940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.090252 restraints weight = 79186.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.094323 restraints weight = 45468.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.094511 restraints weight = 28573.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.095140 restraints weight = 24476.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.095343 restraints weight = 22442.075| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 25192 Z= 0.114 Angle : 0.625 12.855 34202 Z= 0.311 Chirality : 0.044 0.258 3886 Planarity : 0.004 0.055 4290 Dihedral : 4.483 34.937 3674 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.82 % Allowed : 18.34 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.15), residues: 3048 helix: 0.70 (0.15), residues: 1238 sheet: -1.62 (0.25), residues: 358 loop : -1.24 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 36 TYR 0.018 0.001 TYR D 392 PHE 0.023 0.001 PHE C 473 TRP 0.021 0.001 TRP C 609 HIS 0.007 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00259 (25158) covalent geometry : angle 0.62074 (34118) SS BOND : bond 0.00382 ( 18) SS BOND : angle 1.67840 ( 36) hydrogen bonds : bond 0.03005 ( 953) hydrogen bonds : angle 4.71812 ( 2793) link_NAG-ASN : bond 0.00347 ( 16) link_NAG-ASN : angle 1.39148 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 231 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.6781 (mmp) cc_final: 0.6064 (tmm) REVERT: A 45 ASP cc_start: 0.8566 (t0) cc_final: 0.8298 (t0) REVERT: B 125 MET cc_start: 0.8481 (mmm) cc_final: 0.8201 (mmm) REVERT: B 354 MET cc_start: 0.7717 (tpp) cc_final: 0.7327 (tpp) REVERT: B 409 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7844 (t) REVERT: B 470 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8477 (ttm) REVERT: B 636 TRP cc_start: 0.5729 (t-100) cc_final: 0.5387 (t-100) REVERT: B 654 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8326 (t80) REVERT: C 39 MET cc_start: 0.6900 (tmm) cc_final: 0.6000 (tmm) REVERT: C 135 MET cc_start: 0.5609 (pmm) cc_final: 0.5126 (mtp) REVERT: C 145 PHE cc_start: 0.7299 (m-80) cc_final: 0.6860 (m-80) REVERT: C 200 MET cc_start: 0.7571 (mmm) cc_final: 0.6742 (tpt) REVERT: C 385 LEU cc_start: 0.8120 (pt) cc_final: 0.7898 (pt) REVERT: C 475 TYR cc_start: 0.8139 (p90) cc_final: 0.7879 (p90) REVERT: C 606 TRP cc_start: 0.6588 (m100) cc_final: 0.5941 (m100) REVERT: C 653 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7956 (tpt) REVERT: C 823 MET cc_start: 0.6246 (ptp) cc_final: 0.5674 (mmm) REVERT: D 42 PHE cc_start: 0.7619 (p90) cc_final: 0.7218 (p90) REVERT: D 362 VAL cc_start: 0.8270 (t) cc_final: 0.8070 (p) REVERT: D 473 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8228 (p) REVERT: D 527 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8397 (mp) REVERT: D 571 HIS cc_start: 0.7131 (m90) cc_final: 0.6479 (t-90) outliers start: 75 outliers final: 58 residues processed: 286 average time/residue: 0.1303 time to fit residues: 62.9395 Evaluate side-chains 289 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 225 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 780 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 817 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain D residue 780 HIS Chi-restraints excluded: chain D residue 795 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 292 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 176 optimal weight: 0.0470 chunk 4 optimal weight: 8.9990 overall best weight: 2.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.116101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.086527 restraints weight = 79582.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.089009 restraints weight = 45594.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.090702 restraints weight = 32188.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.091778 restraints weight = 25577.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.092350 restraints weight = 22081.516| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25192 Z= 0.186 Angle : 0.648 12.551 34202 Z= 0.326 Chirality : 0.045 0.230 3886 Planarity : 0.004 0.060 4290 Dihedral : 4.655 36.666 3674 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.97 % Favored : 94.00 % Rotamer: Outliers : 2.79 % Allowed : 18.60 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.15), residues: 3048 helix: 0.71 (0.15), residues: 1234 sheet: -1.90 (0.24), residues: 388 loop : -1.22 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 36 TYR 0.014 0.002 TYR B 410 PHE 0.022 0.002 PHE C 183 TRP 0.018 0.001 TRP C 284 HIS 0.006 0.001 HIS D 162 Details of bonding type rmsd covalent geometry : bond 0.00431 (25158) covalent geometry : angle 0.64399 (34118) SS BOND : bond 0.00437 ( 18) SS BOND : angle 1.70975 ( 36) hydrogen bonds : bond 0.03210 ( 953) hydrogen bonds : angle 4.78873 ( 2793) link_NAG-ASN : bond 0.00209 ( 16) link_NAG-ASN : angle 1.57699 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4048.46 seconds wall clock time: 70 minutes 44.99 seconds (4244.99 seconds total)