Starting phenix.real_space_refine on Sun Jul 5 01:41:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eoq_31227/07_2026/7eoq_31227_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eoq_31227/07_2026/7eoq_31227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eoq_31227/07_2026/7eoq_31227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eoq_31227/07_2026/7eoq_31227.map" model { file = "/net/cci-nas-00/data/ceres_data/7eoq_31227/07_2026/7eoq_31227_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eoq_31227/07_2026/7eoq_31227_trim.cif" } resolution = 4.1 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 152 5.16 5 C 15838 2.51 5 N 4160 2.21 5 O 4590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24742 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6111 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 31, 'TRANS': 751} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 6188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6188 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 6111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6111 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 31, 'TRANS': 751} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 6188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6188 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'7RC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'7RC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.24, per 1000 atoms: 0.17 Number of scatterers: 24742 At special positions: 0 Unit cell: (114.582, 145.002, 188.604, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 152 16.00 P 2 15.00 O 4590 8.00 N 4160 7.00 C 15838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, 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 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 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 276 " " NAG B 902 " - " ASN B 771 " " NAG B 903 " - " ASN B 471 " " NAG C 901 " - " ASN C 687 " " NAG D 901 " - " ASN D 276 " " NAG D 902 " - " ASN D 771 " " NAG D 903 " - " ASN D 471 " Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 882.7 milliseconds 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 32 sheets defined 41.7% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.712A pdb=" N GLN A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 removed outlier: 4.059A pdb=" N THR A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A 157 " --> pdb=" O GLN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 194 Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 232 through 247 removed outlier: 3.536A pdb=" N LEU A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 310 removed outlier: 3.667A pdb=" N LYS A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.857A pdb=" N ARG A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 517 through 522 removed outlier: 4.000A pdb=" N VAL A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 579 removed outlier: 3.907A pdb=" N LEU A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 612 removed outlier: 4.449A pdb=" N ILE A 605 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.827A pdb=" N MET A 630 " --> pdb=" O THR A 626 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 652 removed outlier: 4.145A pdb=" N PHE A 637 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.770A pdb=" N GLN A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 removed outlier: 3.530A 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 696 removed outlier: 4.087A pdb=" N ARG A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 706 removed outlier: 4.277A pdb=" N GLN A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR A 704 " --> pdb=" O TYR A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 771 through 786 removed outlier: 4.158A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 786 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 795 removed outlier: 3.601A pdb=" N CYS A 794 " --> pdb=" O GLU A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 837 removed outlier: 3.744A pdb=" N MET A 817 " --> pdb=" O ASP A 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 70 through 82 Processing helix chain 'B' and resid 83 through 86 removed outlier: 3.665A pdb=" N GLN B 86 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 86' Processing helix chain 'B' and resid 104 through 112 removed outlier: 3.686A pdb=" N SER B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 159 removed outlier: 4.197A pdb=" N SER B 148 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 149 " --> pdb=" O SER B 145 " (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 251 through 260 removed outlier: 3.757A pdb=" N ILE B 254 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER B 255 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN B 257 " --> pdb=" O ILE B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 299 removed outlier: 3.576A pdb=" N ILE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 327 removed outlier: 3.516A pdb=" N LYS B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 470 removed outlier: 4.041A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.758A pdb=" N TYR B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 583 removed outlier: 4.482A pdb=" N LEU B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 removed outlier: 3.874A pdb=" N LEU B 614 " --> pdb=" O SER B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 656 removed outlier: 3.885A pdb=" N MET B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 removed outlier: 3.629A pdb=" N ASN B 674 " --> pdb=" O PRO B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 696 removed outlier: 3.902A pdb=" N GLN B 696 " --> pdb=" O TYR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 707 Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 743 removed outlier: 3.659A pdb=" N PHE B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 782 removed outlier: 3.651A pdb=" N VAL B 772 " --> pdb=" O TRP B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 792 Processing helix chain 'B' and resid 810 through 843 Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.710A pdb=" N GLN C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS C 119 " --> pdb=" O PHE C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 166 removed outlier: 4.058A pdb=" N THR C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 194 Processing helix chain 'C' and resid 214 through 221 Processing helix chain 'C' and resid 232 through 247 removed outlier: 3.537A pdb=" N LEU C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 310 removed outlier: 3.667A pdb=" N LYS C 309 " --> pdb=" O SER C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 472 removed outlier: 3.856A pdb=" N ARG C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'C' and resid 517 through 522 removed outlier: 3.998A pdb=" N VAL C 521 " --> pdb=" O GLU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 579 removed outlier: 3.912A pdb=" N LEU C 566 " --> pdb=" O PHE C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 612 removed outlier: 4.449A pdb=" N ILE C 605 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 632 removed outlier: 3.832A pdb=" N MET C 630 " --> pdb=" O THR C 626 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 652 removed outlier: 4.142A pdb=" N PHE C 637 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.773A pdb=" N GLN C 671 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 676 removed outlier: 3.522A 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: 4.087A pdb=" N ARG C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 706 removed outlier: 4.277A pdb=" N GLN C 703 " --> pdb=" O PRO C 699 " (cutoff:3.500A) removed outlier: 4.114A 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: 4.157A pdb=" N LEU C 777 " --> pdb=" O ARG C 773 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 786 " --> pdb=" O PHE C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 795 removed outlier: 3.604A pdb=" N CYS C 794 " --> pdb=" O GLU C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 837 removed outlier: 3.745A pdb=" N MET C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 50 Processing helix chain 'D' and resid 70 through 82 Processing helix chain 'D' and resid 83 through 86 removed outlier: 3.667A pdb=" N GLN D 86 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 83 through 86' Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.683A pdb=" N SER D 108 " --> pdb=" O PRO D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 159 removed outlier: 4.197A pdb=" N SER D 148 " --> pdb=" O TYR D 144 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 149 " --> pdb=" O SER D 145 " (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 251 through 260 removed outlier: 3.756A pdb=" N ILE D 254 " --> pdb=" O GLU D 251 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER D 255 " --> pdb=" O ARG D 252 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN D 257 " --> pdb=" O ILE D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 299 removed outlier: 3.575A pdb=" N ILE D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER D 282 " --> pdb=" O SER D 278 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 327 removed outlier: 3.516A pdb=" N LYS D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 4.043A pdb=" N LEU D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.756A pdb=" N TYR D 526 " --> pdb=" O GLU D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 583 removed outlier: 4.481A pdb=" N LEU D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 615 removed outlier: 3.873A pdb=" N LEU D 614 " --> pdb=" O SER D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 656 removed outlier: 3.887A pdb=" N MET D 641 " --> pdb=" O ALA D 637 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE D 643 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 674 removed outlier: 3.631A pdb=" N ASN D 674 " --> pdb=" O PRO D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 696 removed outlier: 3.900A pdb=" N GLN D 696 " --> pdb=" O TYR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 707 Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 removed outlier: 3.658A pdb=" N PHE D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 782 removed outlier: 3.651A pdb=" N VAL D 772 " --> pdb=" O TRP D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 792 Processing helix chain 'D' and resid 810 through 843 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 73 removed outlier: 3.765A pdb=" N LEU A 72 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA A 37 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 174 removed outlier: 7.020A pdb=" N VAL A 173 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU A 228 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 256 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 229 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL A 279 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 280 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 365 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 373 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 409 removed outlier: 6.421A pdb=" N LEU A 406 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N TYR A 478 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE A 408 " --> pdb=" O TYR A 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 420 through 421 removed outlier: 3.941A pdb=" N VAL A 452 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 438 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AA7, first strand: chain 'A' and resid 727 through 731 removed outlier: 3.685A pdb=" N VAL A 748 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 61 through 62 removed outlier: 3.555A pdb=" N ILE B 29 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL B 65 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA B 31 " --> pdb=" O VAL B 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 62 removed outlier: 3.555A pdb=" N ILE B 29 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 90 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 197 removed outlier: 6.724A pdb=" N LEU B 165 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 197 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B 167 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 164 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 220 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 222 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER B 168 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TRP B 247 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N LEU B 269 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL B 249 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N LEU B 271 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ILE B 266 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 356 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY B 365 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN B 355 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLN B 363 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 330 through 333 removed outlier: 6.250A pdb=" N ALA B 331 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 338 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY B 333 " --> pdb=" O GLY B 336 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 399 through 402 Processing sheet with id=AB4, first strand: chain 'B' and resid 409 through 412 removed outlier: 3.519A pdb=" N CYS B 455 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL B 434 " --> pdb=" O CYS B 455 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 512 through 514 Processing sheet with id=AB6, first strand: chain 'B' and resid 535 through 536 removed outlier: 3.507A pdb=" N SER B 756 " --> pdb=" O GLN B 536 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 681 through 682 removed outlier: 7.274A pdb=" N ALA B 682 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 10.104A pdb=" N ASP B 732 " --> pdb=" O ALA B 682 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TRP B 731 " --> pdb=" O THR B 539 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 72 through 73 removed outlier: 3.767A pdb=" N LEU C 72 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA C 37 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 172 through 174 removed outlier: 7.017A pdb=" N VAL C 173 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU C 228 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 256 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 229 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL C 279 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 280 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C 365 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU C 373 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 342 through 343 Processing sheet with id=AC2, first strand: chain 'C' and resid 405 through 409 removed outlier: 6.419A pdb=" N LEU C 406 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N TYR C 478 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 408 " --> pdb=" O TYR C 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 420 through 421 removed outlier: 3.940A pdb=" N VAL C 452 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 438 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 530 through 531 Processing sheet with id=AC5, first strand: chain 'C' and resid 727 through 731 removed outlier: 3.686A pdb=" N VAL C 748 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 61 through 62 removed outlier: 3.554A pdb=" N ILE D 29 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL D 65 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ALA D 31 " --> pdb=" O VAL D 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 61 through 62 removed outlier: 3.554A pdb=" N ILE D 29 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE D 90 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 194 through 197 removed outlier: 6.725A pdb=" N LEU D 165 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE D 197 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL D 167 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE D 164 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 220 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 222 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER D 168 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TRP D 247 " --> pdb=" O LEU D 267 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N LEU D 269 " --> pdb=" O TRP D 247 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL D 249 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N LEU D 271 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE D 266 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 356 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY D 365 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN D 355 " --> pdb=" O GLN D 363 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLN D 363 " --> pdb=" O ASN D 355 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 330 through 333 removed outlier: 6.255A pdb=" N ALA D 331 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL D 338 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY D 333 " --> pdb=" O GLY D 336 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 399 through 402 Processing sheet with id=AD2, first strand: chain 'D' and resid 409 through 412 removed outlier: 3.518A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 512 through 514 Processing sheet with id=AD4, first strand: chain 'D' and resid 535 through 536 removed outlier: 3.506A pdb=" N SER D 756 " --> pdb=" O GLN D 536 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 681 through 682 removed outlier: 7.275A pdb=" N ALA D 682 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 10.105A pdb=" N ASP D 732 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP D 731 " --> pdb=" O THR D 539 " (cutoff:3.500A) 932 hydrogen bonds defined for protein. 2724 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: 4.09 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7937 1.34 - 1.46: 4653 1.46 - 1.58: 12446 1.58 - 1.70: 4 1.70 - 1.81: 262 Bond restraints: 25302 Sorted by residual: bond pdb=" C08 7RC C 902 " pdb=" O01 7RC C 902 " ideal model delta sigma weight residual 1.256 1.356 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C08 7RC A 902 " pdb=" O01 7RC A 902 " ideal model delta sigma weight residual 1.256 1.355 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" O02 7RC C 902 " pdb=" P01 7RC C 902 " ideal model delta sigma weight residual 1.537 1.610 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" O03 7RC A 902 " pdb=" P01 7RC A 902 " ideal model delta sigma weight residual 1.536 1.609 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O03 7RC C 902 " pdb=" P01 7RC C 902 " ideal model delta sigma weight residual 1.536 1.609 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 25297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 34023 1.97 - 3.94: 250 3.94 - 5.92: 37 5.92 - 7.89: 12 7.89 - 9.86: 6 Bond angle restraints: 34328 Sorted by residual: angle pdb=" C LEU A 512 " pdb=" CA LEU A 512 " pdb=" CB LEU A 512 " ideal model delta sigma weight residual 109.64 119.50 -9.86 1.77e+00 3.19e-01 3.10e+01 angle pdb=" C LEU C 512 " pdb=" CA LEU C 512 " pdb=" CB LEU C 512 " ideal model delta sigma weight residual 109.64 117.83 -8.19 1.77e+00 3.19e-01 2.14e+01 angle pdb=" N CYS B 698 " pdb=" CA CYS B 698 " pdb=" C CYS B 698 " ideal model delta sigma weight residual 114.56 109.06 5.50 1.27e+00 6.20e-01 1.88e+01 angle pdb=" N CYS D 698 " pdb=" CA CYS D 698 " pdb=" C CYS D 698 " ideal model delta sigma weight residual 114.56 109.07 5.49 1.27e+00 6.20e-01 1.87e+01 angle pdb=" N THR A 513 " pdb=" CA THR A 513 " pdb=" C THR A 513 " ideal model delta sigma weight residual 110.42 103.83 6.59 1.55e+00 4.16e-01 1.81e+01 ... (remaining 34323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 14381 17.62 - 35.24: 656 35.24 - 52.86: 121 52.86 - 70.48: 12 70.48 - 88.10: 4 Dihedral angle restraints: 15174 sinusoidal: 6068 harmonic: 9106 Sorted by residual: dihedral pdb=" CA MET B 576 " pdb=" CB MET B 576 " pdb=" CG MET B 576 " pdb=" SD MET B 576 " ideal model delta sinusoidal sigma weight residual -60.00 -115.58 55.58 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" CA MET D 576 " pdb=" CB MET D 576 " pdb=" CG MET D 576 " pdb=" SD MET D 576 " ideal model delta sinusoidal sigma weight residual -60.00 -114.80 54.80 3 1.50e+01 4.44e-03 9.31e+00 dihedral pdb=" N MET D 502 " pdb=" CA MET D 502 " pdb=" CB MET D 502 " pdb=" CG MET D 502 " ideal model delta sinusoidal sigma weight residual -180.00 -125.22 -54.78 3 1.50e+01 4.44e-03 9.31e+00 ... (remaining 15171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3066 0.046 - 0.092: 608 0.092 - 0.137: 223 0.137 - 0.183: 5 0.183 - 0.229: 2 Chirality restraints: 3904 Sorted by residual: chirality pdb=" C1 NAG D 902 " pdb=" ND2 ASN D 771 " pdb=" C2 NAG D 902 " pdb=" O5 NAG D 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C1 NAG B 902 " pdb=" ND2 ASN B 771 " pdb=" C2 NAG B 902 " pdb=" O5 NAG B 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1 NAG D 903 " pdb=" ND2 ASN D 471 " pdb=" C2 NAG D 903 " pdb=" O5 NAG D 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 3901 not shown) Planarity restraints: 4348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 94 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.75e+00 pdb=" N PRO B 95 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 94 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO D 95 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 55 " 0.008 2.00e-02 2.50e+03 6.19e-03 9.57e-01 pdb=" CG TRP A 55 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 55 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 55 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 55 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 55 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 55 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 55 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 55 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 55 " -0.000 2.00e-02 2.50e+03 ... (remaining 4345 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1548 2.74 - 3.28: 25648 3.28 - 3.82: 40446 3.82 - 4.36: 45325 4.36 - 4.90: 76838 Nonbonded interactions: 189805 Sorted by model distance: nonbonded pdb=" OG1 THR C 531 " pdb=" OD1 ASP C 731 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR A 531 " pdb=" OD1 ASP A 731 " model vdw 2.196 3.040 nonbonded pdb=" O LYS C 465 " pdb=" OG SER C 468 " model vdw 2.232 3.040 nonbonded pdb=" O LYS A 465 " pdb=" OG SER A 468 " model vdw 2.233 3.040 nonbonded pdb=" O ASN B 50 " pdb=" NE2 GLN B 59 " model vdw 2.254 3.120 ... (remaining 189800 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: 0.03 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: 1.050 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.560 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.002 0.100 25326 Z= 0.118 Angle : 0.470 9.860 34384 Z= 0.238 Chirality : 0.041 0.229 3904 Planarity : 0.003 0.060 4340 Dihedral : 9.821 88.103 9246 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.14 % Allowed : 8.06 % Favored : 89.80 % 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: 0.09 (0.16), residues: 3112 helix: 1.96 (0.16), residues: 1200 sheet: -0.84 (0.32), residues: 302 loop : -1.30 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.005 0.001 TYR C 737 PHE 0.006 0.001 PHE B 784 TRP 0.017 0.001 TRP A 55 HIS 0.002 0.000 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 (25302) covalent geometry : angle 0.46838 / 0.24 (34328) SS BOND : bond 0.00101 / 0.06 ( 16) SS BOND : angle 0.53940 / 0.37 ( 32) hydrogen bonds : bond 0.14663 / 9.74 ( 932) hydrogen bonds : angle 6.17821 / 4.30 ( 2724) link_NAG-ASN : bond 0.00351 / 0.15 ( 8) link_NAG-ASN : angle 1.69144 / 1.18 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 372 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8331 (tpp) cc_final: 0.8106 (tpp) REVERT: A 785 ASP cc_start: 0.7401 (m-30) cc_final: 0.7150 (m-30) REVERT: B 182 THR cc_start: 0.9039 (t) cc_final: 0.8717 (p) REVERT: B 249 VAL cc_start: 0.7873 (t) cc_final: 0.7475 (p) REVERT: B 520 ASN cc_start: 0.7910 (t0) cc_final: 0.7515 (t0) REVERT: B 607 MET cc_start: 0.8691 (ppp) cc_final: 0.8324 (ppp) REVERT: D 249 VAL cc_start: 0.7820 (t) cc_final: 0.7451 (p) REVERT: D 520 ASN cc_start: 0.8006 (t0) cc_final: 0.7633 (t0) REVERT: D 607 MET cc_start: 0.8701 (ppp) cc_final: 0.8331 (ppp) REVERT: D 615 LEU cc_start: 0.7300 (mt) cc_final: 0.7046 (mp) outliers start: 57 outliers final: 5 residues processed: 417 average time/residue: 0.1464 time to fit residues: 96.8392 Evaluate side-chains 238 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 233 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.0040 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 6.9990 overall best weight: 3.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 119 HIS A 153 GLN A 432 ASN A 674 HIS B 59 GLN ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS B 147 GLN B 477 HIS B 499 ASN ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 119 HIS ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 432 ASN C 674 HIS D 59 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS D 147 GLN D 477 HIS D 499 ASN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.066844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.055026 restraints weight = 164234.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.056192 restraints weight = 103025.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.057000 restraints weight = 75288.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.057570 restraints weight = 60654.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.057917 restraints weight = 52125.077| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25326 Z= 0.198 Angle : 0.628 10.184 34384 Z= 0.326 Chirality : 0.045 0.391 3904 Planarity : 0.004 0.060 4340 Dihedral : 4.486 52.852 3564 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.65 % 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: -0.25 (0.16), residues: 3112 helix: 1.56 (0.16), residues: 1170 sheet: -0.92 (0.29), residues: 366 loop : -1.35 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 672 TYR 0.019 0.002 TYR C 502 PHE 0.016 0.002 PHE B 529 TRP 0.038 0.002 TRP A 55 HIS 0.008 0.001 HIS D 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (25302) covalent geometry : angle 0.61679 / 0.32 (34328) SS BOND : bond 0.00676 / 0.46 ( 16) SS BOND : angle 1.93128 / 1.05 ( 32) hydrogen bonds : bond 0.03474 / 2.36 ( 932) hydrogen bonds : angle 4.99729 / 3.52 ( 2724) link_NAG-ASN : bond 0.00799 / 0.35 ( 8) link_NAG-ASN : angle 3.92561 / 2.96 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.956 Fit side-chains REVERT: A 90 MET cc_start: 0.8281 (tpp) cc_final: 0.7995 (tpp) REVERT: A 220 LYS cc_start: 0.6484 (ttmm) cc_final: 0.6160 (ttmt) REVERT: A 338 MET cc_start: 0.7718 (ppp) cc_final: 0.7043 (ptp) REVERT: A 549 PHE cc_start: 0.5808 (m-80) cc_final: 0.4982 (m-80) REVERT: B 33 LEU cc_start: 0.7038 (mt) cc_final: 0.6644 (mt) REVERT: B 41 MET cc_start: 0.8063 (ppp) cc_final: 0.7813 (ppp) REVERT: B 74 MET cc_start: 0.6919 (ppp) cc_final: 0.6701 (ppp) REVERT: B 607 MET cc_start: 0.8693 (ppp) cc_final: 0.8443 (ppp) REVERT: B 700 SER cc_start: 0.8085 (m) cc_final: 0.7788 (t) REVERT: B 813 MET cc_start: 0.6424 (ppp) cc_final: 0.6097 (ppp) REVERT: C 338 MET cc_start: 0.7891 (ppp) cc_final: 0.7497 (ptm) REVERT: C 549 PHE cc_start: 0.5782 (m-80) cc_final: 0.4895 (m-80) REVERT: D 240 MET cc_start: 0.8594 (mmm) cc_final: 0.8069 (mmm) REVERT: D 520 ASN cc_start: 0.8212 (t0) cc_final: 0.7471 (t0) REVERT: D 607 MET cc_start: 0.8714 (ppp) cc_final: 0.8469 (ppp) REVERT: D 615 LEU cc_start: 0.7989 (mt) cc_final: 0.7674 (mp) REVERT: D 700 SER cc_start: 0.8079 (m) cc_final: 0.7746 (t) REVERT: D 813 MET cc_start: 0.6292 (ppp) cc_final: 0.5935 (ppp) outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.1381 time to fit residues: 61.3633 Evaluate side-chains 194 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 122 optimal weight: 5.9990 chunk 165 optimal weight: 30.0000 chunk 131 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 GLN A 154 GLN B 59 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 154 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.062021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.049789 restraints weight = 164722.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.050831 restraints weight = 106571.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.051524 restraints weight = 79977.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.051980 restraints weight = 66059.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.052294 restraints weight = 58176.454| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25326 Z= 0.248 Angle : 0.696 9.708 34384 Z= 0.361 Chirality : 0.047 0.323 3904 Planarity : 0.005 0.055 4340 Dihedral : 5.389 58.495 3564 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.26 % Allowed : 5.29 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3112 helix: 0.95 (0.15), residues: 1190 sheet: -1.32 (0.26), residues: 412 loop : -1.56 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 386 TYR 0.022 0.002 TYR C 180 PHE 0.039 0.003 PHE B 817 TRP 0.072 0.002 TRP C 55 HIS 0.008 0.002 HIS C 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.25 (25302) covalent geometry : angle 0.68600 / 0.36 (34328) SS BOND : bond 0.00965 / 0.51 ( 16) SS BOND : angle 2.24502 / 1.32 ( 32) hydrogen bonds : bond 0.04097 / 2.75 ( 932) hydrogen bonds : angle 5.23519 / 3.69 ( 2724) link_NAG-ASN : bond 0.00550 / 0.27 ( 8) link_NAG-ASN : angle 3.79753 / 2.83 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 227 time to evaluate : 0.780 Fit side-chains REVERT: A 90 MET cc_start: 0.8092 (tpp) cc_final: 0.7720 (tpp) REVERT: A 338 MET cc_start: 0.8031 (ppp) cc_final: 0.7650 (ptm) REVERT: A 496 MET cc_start: 0.8300 (mtp) cc_final: 0.8077 (mtt) REVERT: A 817 MET cc_start: 0.4004 (mpp) cc_final: 0.3800 (mpp) REVERT: B 33 LEU cc_start: 0.7475 (mt) cc_final: 0.7175 (mt) REVERT: B 163 ILE cc_start: 0.9533 (tp) cc_final: 0.9291 (pt) REVERT: B 470 MET cc_start: 0.8884 (mtp) cc_final: 0.8555 (mtm) REVERT: B 634 MET cc_start: 0.7994 (mmt) cc_final: 0.7565 (mpp) REVERT: B 700 SER cc_start: 0.8350 (m) cc_final: 0.8042 (t) REVERT: B 762 MET cc_start: 0.7448 (mtp) cc_final: 0.7218 (mtm) REVERT: C 90 MET cc_start: 0.8044 (tpt) cc_final: 0.7807 (tpp) REVERT: C 338 MET cc_start: 0.8239 (ppp) cc_final: 0.7888 (ptm) REVERT: D 41 MET cc_start: 0.8084 (ppp) cc_final: 0.7877 (ppp) REVERT: D 634 MET cc_start: 0.8137 (mtt) cc_final: 0.7909 (mpp) REVERT: D 700 SER cc_start: 0.8379 (m) cc_final: 0.8033 (t) outliers start: 7 outliers final: 4 residues processed: 234 average time/residue: 0.1350 time to fit residues: 52.8313 Evaluate side-chains 179 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 175 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 209 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 188 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN A 153 GLN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 GLN ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 780 HIS ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN D 59 GLN D 86 GLN D 134 HIS D 556 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 780 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.061878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.049815 restraints weight = 162234.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.050864 restraints weight = 105034.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.051577 restraints weight = 78452.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.052045 restraints weight = 64250.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.052281 restraints weight = 56446.689| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25326 Z= 0.216 Angle : 0.628 10.601 34384 Z= 0.325 Chirality : 0.045 0.353 3904 Planarity : 0.004 0.053 4340 Dihedral : 5.358 52.551 3564 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.83 (0.15), residues: 3112 helix: 0.97 (0.15), residues: 1194 sheet: -1.47 (0.25), residues: 456 loop : -1.53 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 386 TYR 0.037 0.002 TYR B 144 PHE 0.043 0.002 PHE D 817 TRP 0.047 0.002 TRP A 55 HIS 0.009 0.001 HIS D 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 (25302) covalent geometry : angle 0.61673 / 0.32 (34328) SS BOND : bond 0.01073 / 0.71 ( 16) SS BOND : angle 2.20938 / 1.38 ( 32) hydrogen bonds : bond 0.03586 / 2.41 ( 932) hydrogen bonds : angle 5.08849 / 3.58 ( 2724) link_NAG-ASN : bond 0.00583 / 0.27 ( 8) link_NAG-ASN : angle 3.88562 / 2.93 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.978 Fit side-chains REVERT: A 90 MET cc_start: 0.8262 (tpp) cc_final: 0.8038 (tpp) REVERT: A 817 MET cc_start: 0.4137 (mpp) cc_final: 0.3906 (mpp) REVERT: B 33 LEU cc_start: 0.7780 (mt) cc_final: 0.7293 (mt) REVERT: B 41 MET cc_start: 0.8166 (ppp) cc_final: 0.7923 (ppp) REVERT: B 634 MET cc_start: 0.8002 (mmt) cc_final: 0.7553 (mpp) REVERT: B 700 SER cc_start: 0.8373 (m) cc_final: 0.8089 (t) REVERT: B 762 MET cc_start: 0.7403 (mtp) cc_final: 0.6847 (mtp) REVERT: C 338 MET cc_start: 0.8278 (ppp) cc_final: 0.7965 (ptm) REVERT: C 496 MET cc_start: 0.8367 (mtp) cc_final: 0.8159 (mtt) REVERT: D 607 MET cc_start: 0.8652 (ppp) cc_final: 0.8431 (ppp) REVERT: D 634 MET cc_start: 0.8171 (mtt) cc_final: 0.7941 (mpp) REVERT: D 700 SER cc_start: 0.8437 (m) cc_final: 0.8093 (t) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.1300 time to fit residues: 49.2807 Evaluate side-chains 177 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 55 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 300 optimal weight: 0.9980 chunk 296 optimal weight: 6.9990 chunk 75 optimal weight: 40.0000 chunk 168 optimal weight: 0.5980 chunk 269 optimal weight: 10.0000 chunk 156 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 132 optimal weight: 0.0040 chunk 278 optimal weight: 5.9990 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 GLN A 323 GLN A 648 ASN C 153 GLN ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.062931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.050790 restraints weight = 159817.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.051928 restraints weight = 100600.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.052700 restraints weight = 73613.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.053213 restraints weight = 59492.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.053559 restraints weight = 51696.960| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25326 Z= 0.120 Angle : 0.557 10.536 34384 Z= 0.286 Chirality : 0.044 0.351 3904 Planarity : 0.004 0.067 4340 Dihedral : 4.972 53.200 3564 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.04 % Allowed : 2.48 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.63 (0.16), residues: 3112 helix: 1.11 (0.15), residues: 1198 sheet: -1.34 (0.26), residues: 434 loop : -1.42 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 386 TYR 0.016 0.001 TYR D 232 PHE 0.020 0.001 PHE C 549 TRP 0.051 0.001 TRP A 55 HIS 0.006 0.001 HIS D 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (25302) covalent geometry : angle 0.54654 / 0.28 (34328) SS BOND : bond 0.00419 / 0.25 ( 16) SS BOND : angle 1.50721 / 0.91 ( 32) hydrogen bonds : bond 0.03165 / 2.13 ( 932) hydrogen bonds : angle 4.85229 / 3.42 ( 2724) link_NAG-ASN : bond 0.00639 / 0.27 ( 8) link_NAG-ASN : angle 3.71815 / 2.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.729 Fit side-chains REVERT: A 323 GLN cc_start: 0.4139 (OUTLIER) cc_final: 0.3637 (pm20) REVERT: A 496 MET cc_start: 0.8241 (mtp) cc_final: 0.7995 (mtt) REVERT: B 615 LEU cc_start: 0.7662 (mp) cc_final: 0.7258 (mp) REVERT: B 634 MET cc_start: 0.7998 (mmt) cc_final: 0.7523 (mpp) REVERT: B 700 SER cc_start: 0.8338 (m) cc_final: 0.8012 (t) REVERT: B 762 MET cc_start: 0.7479 (mtp) cc_final: 0.6929 (mtp) REVERT: C 338 MET cc_start: 0.8340 (ppp) cc_final: 0.8068 (ptm) REVERT: D 634 MET cc_start: 0.8147 (mtt) cc_final: 0.7934 (mpp) REVERT: D 700 SER cc_start: 0.8444 (m) cc_final: 0.8094 (t) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1280 time to fit residues: 49.1922 Evaluate side-chains 180 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 179 optimal weight: 2.9990 chunk 302 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 238 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 75 optimal weight: 50.0000 chunk 288 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 244 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.062788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.050690 restraints weight = 158911.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.051840 restraints weight = 99260.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.052603 restraints weight = 72366.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053051 restraints weight = 58426.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.053434 restraints weight = 51129.740| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25326 Z= 0.126 Angle : 0.551 10.449 34384 Z= 0.282 Chirality : 0.044 0.347 3904 Planarity : 0.004 0.054 4340 Dihedral : 4.789 56.158 3564 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3112 helix: 1.18 (0.15), residues: 1184 sheet: -1.37 (0.27), residues: 404 loop : -1.45 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 386 TYR 0.015 0.001 TYR C 645 PHE 0.035 0.001 PHE B 817 TRP 0.060 0.001 TRP C 55 HIS 0.005 0.001 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (25302) covalent geometry : angle 0.54202 / 0.28 (34328) SS BOND : bond 0.00384 / 0.23 ( 16) SS BOND : angle 1.19553 / 0.78 ( 32) hydrogen bonds : bond 0.03153 / 2.14 ( 932) hydrogen bonds : angle 4.78839 / 3.38 ( 2724) link_NAG-ASN : bond 0.00529 / 0.23 ( 8) link_NAG-ASN : angle 3.68013 / 2.81 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.591 Fit side-chains REVERT: A 74 MET cc_start: 0.8349 (pmm) cc_final: 0.7809 (pmm) REVERT: A 338 MET cc_start: 0.8087 (ppp) cc_final: 0.7838 (ppp) REVERT: B 41 MET cc_start: 0.8161 (ppp) cc_final: 0.7912 (ppp) REVERT: B 607 MET cc_start: 0.8394 (ppp) cc_final: 0.8146 (ppp) REVERT: B 615 LEU cc_start: 0.7647 (mp) cc_final: 0.7224 (mp) REVERT: B 634 MET cc_start: 0.8008 (mmt) cc_final: 0.7533 (mpp) REVERT: B 700 SER cc_start: 0.8396 (m) cc_final: 0.8046 (t) REVERT: B 762 MET cc_start: 0.7475 (mtp) cc_final: 0.6926 (mtp) REVERT: C 338 MET cc_start: 0.8433 (ppp) cc_final: 0.8185 (ptm) REVERT: D 354 MET cc_start: 0.8465 (mmm) cc_final: 0.8249 (mmm) REVERT: D 607 MET cc_start: 0.8414 (ppp) cc_final: 0.8170 (ppp) REVERT: D 700 SER cc_start: 0.8550 (m) cc_final: 0.8209 (t) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1291 time to fit residues: 49.3731 Evaluate side-chains 179 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 104 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 279 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 294 optimal weight: 0.9980 chunk 270 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.062111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.050065 restraints weight = 161155.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.051150 restraints weight = 103378.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.051867 restraints weight = 76662.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.052351 restraints weight = 62738.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.052687 restraints weight = 54735.052| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25326 Z= 0.150 Angle : 0.582 9.787 34384 Z= 0.299 Chirality : 0.044 0.339 3904 Planarity : 0.004 0.065 4340 Dihedral : 4.892 59.321 3564 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.63 (0.16), residues: 3112 helix: 1.19 (0.15), residues: 1184 sheet: -1.25 (0.26), residues: 440 loop : -1.51 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 377 TYR 0.017 0.001 TYR B 692 PHE 0.027 0.002 PHE B 817 TRP 0.052 0.001 TRP C 55 HIS 0.008 0.001 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (25302) covalent geometry : angle 0.57140 / 0.30 (34328) SS BOND : bond 0.00587 / 0.36 ( 16) SS BOND : angle 2.00335 / 1.26 ( 32) hydrogen bonds : bond 0.03252 / 2.20 ( 932) hydrogen bonds : angle 4.85099 / 3.42 ( 2724) link_NAG-ASN : bond 0.00546 / 0.24 ( 8) link_NAG-ASN : angle 3.54050 / 2.68 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.781 Fit side-chains REVERT: A 74 MET cc_start: 0.8461 (pmm) cc_final: 0.8005 (pmm) REVERT: A 133 MET cc_start: 0.7956 (ptp) cc_final: 0.7722 (mtm) REVERT: A 338 MET cc_start: 0.8220 (ppp) cc_final: 0.7890 (ppp) REVERT: B 41 MET cc_start: 0.8265 (ppp) cc_final: 0.8045 (ppp) REVERT: B 74 MET cc_start: 0.7743 (ppp) cc_final: 0.7404 (ppp) REVERT: B 615 LEU cc_start: 0.7817 (mp) cc_final: 0.7409 (mp) REVERT: B 634 MET cc_start: 0.8012 (mmt) cc_final: 0.7525 (mpp) REVERT: B 700 SER cc_start: 0.8578 (m) cc_final: 0.8232 (t) REVERT: B 762 MET cc_start: 0.7507 (mtp) cc_final: 0.7100 (mtp) REVERT: C 74 MET cc_start: 0.8527 (pmm) cc_final: 0.8062 (pmm) REVERT: C 133 MET cc_start: 0.7976 (ptp) cc_final: 0.7767 (mtm) REVERT: C 338 MET cc_start: 0.8490 (ppp) cc_final: 0.8245 (ptm) REVERT: D 354 MET cc_start: 0.8329 (mmm) cc_final: 0.8118 (mmm) REVERT: D 700 SER cc_start: 0.8677 (m) cc_final: 0.8322 (t) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1285 time to fit residues: 48.0093 Evaluate side-chains 181 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 245 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 228 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN B 405 GLN ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.062257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.050254 restraints weight = 159823.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.051340 restraints weight = 101649.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.052077 restraints weight = 75125.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.052576 restraints weight = 61088.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.052898 restraints weight = 53267.356| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25326 Z= 0.133 Angle : 0.580 10.111 34384 Z= 0.297 Chirality : 0.045 0.349 3904 Planarity : 0.004 0.079 4340 Dihedral : 4.859 58.487 3564 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.04 % Allowed : 1.16 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3112 helix: 1.10 (0.15), residues: 1186 sheet: -1.39 (0.25), residues: 478 loop : -1.48 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 386 TYR 0.017 0.001 TYR D 692 PHE 0.026 0.002 PHE C 183 TRP 0.071 0.001 TRP A 55 HIS 0.007 0.001 HIS D 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (25302) covalent geometry : angle 0.57108 / 0.29 (34328) SS BOND : bond 0.00377 / 0.22 ( 16) SS BOND : angle 1.56757 / 1.00 ( 32) hydrogen bonds : bond 0.03233 / 2.16 ( 932) hydrogen bonds : angle 4.90949 / 3.46 ( 2724) link_NAG-ASN : bond 0.00552 / 0.24 ( 8) link_NAG-ASN : angle 3.56497 / 2.70 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.970 Fit side-chains REVERT: A 74 MET cc_start: 0.8434 (pmm) cc_final: 0.8001 (pmm) REVERT: A 133 MET cc_start: 0.7892 (ptp) cc_final: 0.7640 (mtm) REVERT: B 41 MET cc_start: 0.8327 (ppp) cc_final: 0.8116 (ppp) REVERT: B 74 MET cc_start: 0.7810 (ppp) cc_final: 0.7509 (ppp) REVERT: B 354 MET cc_start: 0.8254 (mmm) cc_final: 0.7874 (mmm) REVERT: B 405 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8584 (tp40) REVERT: B 615 LEU cc_start: 0.7761 (mp) cc_final: 0.7350 (mp) REVERT: B 634 MET cc_start: 0.8041 (mmt) cc_final: 0.7489 (mpp) REVERT: B 700 SER cc_start: 0.8580 (m) cc_final: 0.8241 (t) REVERT: B 762 MET cc_start: 0.7495 (mtp) cc_final: 0.7009 (mtp) REVERT: C 74 MET cc_start: 0.8579 (pmm) cc_final: 0.8116 (pmm) REVERT: C 338 MET cc_start: 0.8424 (ppp) cc_final: 0.8204 (ptm) REVERT: D 41 MET cc_start: 0.8245 (ppp) cc_final: 0.8041 (ppp) REVERT: D 354 MET cc_start: 0.8255 (mmm) cc_final: 0.7776 (mmm) REVERT: D 528 GLU cc_start: 0.8267 (pp20) cc_final: 0.7727 (pp20) REVERT: D 700 SER cc_start: 0.8724 (m) cc_final: 0.8351 (t) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.1359 time to fit residues: 50.3491 Evaluate side-chains 176 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 183 optimal weight: 30.0000 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 195 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 274 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 278 optimal weight: 0.9980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN D 59 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.062404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.050313 restraints weight = 160900.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.051359 restraints weight = 104131.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.052102 restraints weight = 77847.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.052606 restraints weight = 63619.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.052924 restraints weight = 55411.332| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25326 Z= 0.130 Angle : 0.587 10.282 34384 Z= 0.301 Chirality : 0.044 0.357 3904 Planarity : 0.004 0.058 4340 Dihedral : 4.834 54.728 3564 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.04 % Allowed : 0.75 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.66 (0.16), residues: 3112 helix: 1.05 (0.15), residues: 1194 sheet: -1.30 (0.26), residues: 424 loop : -1.41 (0.17), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 386 TYR 0.014 0.001 TYR D 232 PHE 0.022 0.001 PHE A 636 TRP 0.065 0.001 TRP A 55 HIS 0.006 0.001 HIS D 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (25302) covalent geometry : angle 0.57725 / 0.30 (34328) SS BOND : bond 0.00359 / 0.21 ( 16) SS BOND : angle 1.63810 / 0.98 ( 32) hydrogen bonds : bond 0.03239 / 2.16 ( 932) hydrogen bonds : angle 4.89239 / 3.45 ( 2724) link_NAG-ASN : bond 0.00512 / 0.22 ( 8) link_NAG-ASN : angle 3.60203 / 2.74 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8432 (pmm) cc_final: 0.7982 (pmm) REVERT: A 338 MET cc_start: 0.8259 (ppp) cc_final: 0.7931 (ppp) REVERT: B 74 MET cc_start: 0.7808 (ppp) cc_final: 0.7525 (ppp) REVERT: B 181 GLU cc_start: 0.9195 (mp0) cc_final: 0.8977 (mp0) REVERT: B 354 MET cc_start: 0.8330 (mmm) cc_final: 0.7946 (mmm) REVERT: B 470 MET cc_start: 0.8799 (mtp) cc_final: 0.8557 (tpp) REVERT: B 502 MET cc_start: 0.8732 (mmm) cc_final: 0.8485 (tpp) REVERT: B 615 LEU cc_start: 0.7773 (mp) cc_final: 0.7362 (mp) REVERT: B 634 MET cc_start: 0.8048 (mmt) cc_final: 0.7504 (mpp) REVERT: B 700 SER cc_start: 0.8593 (m) cc_final: 0.8249 (t) REVERT: B 762 MET cc_start: 0.7413 (mtp) cc_final: 0.7041 (mtp) REVERT: C 74 MET cc_start: 0.8609 (pmm) cc_final: 0.8200 (pmm) REVERT: C 338 MET cc_start: 0.8469 (ppp) cc_final: 0.8213 (ppp) REVERT: D 181 GLU cc_start: 0.9191 (mp0) cc_final: 0.8987 (mp0) REVERT: D 354 MET cc_start: 0.8239 (mmm) cc_final: 0.7781 (mmm) REVERT: D 405 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8543 (tp40) REVERT: D 634 MET cc_start: 0.7962 (mpp) cc_final: 0.7652 (mpp) REVERT: D 700 SER cc_start: 0.8749 (m) cc_final: 0.8373 (t) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.1286 time to fit residues: 47.5755 Evaluate side-chains 182 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.061396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.049309 restraints weight = 161872.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.050364 restraints weight = 103887.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.051085 restraints weight = 77377.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.051549 restraints weight = 63214.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.051876 restraints weight = 55525.263| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25326 Z= 0.167 Angle : 0.608 10.064 34384 Z= 0.313 Chirality : 0.045 0.348 3904 Planarity : 0.004 0.063 4340 Dihedral : 5.019 48.583 3564 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.66 (0.16), residues: 3112 helix: 1.14 (0.15), residues: 1168 sheet: -1.53 (0.25), residues: 480 loop : -1.35 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 386 TYR 0.018 0.002 TYR D 232 PHE 0.022 0.002 PHE A 636 TRP 0.062 0.002 TRP A 55 HIS 0.009 0.001 HIS D 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (25302) covalent geometry : angle 0.59867 / 0.31 (34328) SS BOND : bond 0.00382 / 0.22 ( 16) SS BOND : angle 1.61008 / 0.99 ( 32) hydrogen bonds : bond 0.03384 / 2.27 ( 932) hydrogen bonds : angle 4.97891 / 3.51 ( 2724) link_NAG-ASN : bond 0.00533 / 0.24 ( 8) link_NAG-ASN : angle 3.60099 / 2.72 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8683 (pmm) cc_final: 0.8322 (pmm) REVERT: A 200 MET cc_start: 0.8225 (mmp) cc_final: 0.7448 (tpt) REVERT: B 41 MET cc_start: 0.8260 (ppp) cc_final: 0.8026 (ppp) REVERT: B 74 MET cc_start: 0.8006 (ppp) cc_final: 0.7745 (ppp) REVERT: B 354 MET cc_start: 0.8297 (mmm) cc_final: 0.7913 (mmm) REVERT: B 470 MET cc_start: 0.8796 (mtp) cc_final: 0.8595 (tpp) REVERT: B 615 LEU cc_start: 0.8005 (mp) cc_final: 0.7622 (mp) REVERT: B 634 MET cc_start: 0.8037 (mmt) cc_final: 0.7500 (mpp) REVERT: B 700 SER cc_start: 0.8703 (m) cc_final: 0.8359 (t) REVERT: B 762 MET cc_start: 0.7537 (mtp) cc_final: 0.7172 (mtp) REVERT: C 74 MET cc_start: 0.8608 (pmm) cc_final: 0.8157 (pmm) REVERT: C 200 MET cc_start: 0.8245 (mmp) cc_final: 0.7480 (tpt) REVERT: C 338 MET cc_start: 0.8510 (ppp) cc_final: 0.8297 (ppp) REVERT: D 354 MET cc_start: 0.8241 (mmm) cc_final: 0.7737 (mmm) REVERT: D 700 SER cc_start: 0.8858 (m) cc_final: 0.8466 (t) REVERT: D 762 MET cc_start: 0.7668 (ptm) cc_final: 0.6141 (ptt) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1275 time to fit residues: 44.9569 Evaluate side-chains 173 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 6.9990 chunk 267 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 263 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 139 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 chunk 177 optimal weight: 0.0670 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN D 59 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.062167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.050011 restraints weight = 159973.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.051140 restraints weight = 100068.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.051915 restraints weight = 73314.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.052421 restraints weight = 59323.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.052772 restraints weight = 51519.017| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25326 Z= 0.120 Angle : 0.588 10.042 34384 Z= 0.300 Chirality : 0.045 0.362 3904 Planarity : 0.004 0.061 4340 Dihedral : 4.902 44.564 3564 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.69 (0.16), residues: 3112 helix: 0.98 (0.15), residues: 1202 sheet: -1.34 (0.26), residues: 418 loop : -1.38 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 386 TYR 0.021 0.001 TYR D 692 PHE 0.021 0.001 PHE C 636 TRP 0.062 0.001 TRP C 55 HIS 0.007 0.001 HIS D 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (25302) covalent geometry : angle 0.57882 / 0.30 (34328) SS BOND : bond 0.00348 / 0.20 ( 16) SS BOND : angle 1.37406 / 0.84 ( 32) hydrogen bonds : bond 0.03171 / 2.11 ( 932) hydrogen bonds : angle 4.89921 / 3.46 ( 2724) link_NAG-ASN : bond 0.00598 / 0.26 ( 8) link_NAG-ASN : angle 3.59138 / 2.71 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3301.86 seconds wall clock time: 58 minutes 29.82 seconds (3509.82 seconds total)