Starting phenix.real_space_refine on Thu Mar 5 19:53:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9un3_64338/03_2026/9un3_64338.cif Found real_map, /net/cci-nas-00/data/ceres_data/9un3_64338/03_2026/9un3_64338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9un3_64338/03_2026/9un3_64338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9un3_64338/03_2026/9un3_64338.map" model { file = "/net/cci-nas-00/data/ceres_data/9un3_64338/03_2026/9un3_64338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9un3_64338/03_2026/9un3_64338.cif" } resolution = 3.37 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= 0.017 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 15587 2.51 5 N 4029 2.21 5 O 4454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24220 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6007 Classifications: {'peptide': 805} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 35, 'TRANS': 769} Chain breaks: 1 Unresolved non-hydrogen bonds: 358 Unresolved non-hydrogen angles: 431 Unresolved non-hydrogen dihedrals: 302 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 10, 'HIS:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 25, 'ASN:plan1': 9, 'ASP:plan': 9, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 248 Chain: "B" Number of atoms: 5944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 5944 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 30, 'TRANS': 767} Chain breaks: 1 Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 435 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 39, 'ASP:plan': 13, 'ARG:plan': 4, 'GLN:plan1': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 248 Chain: "C" Number of atoms: 5978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 5978 Classifications: {'peptide': 805} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 35, 'TRANS': 769} Chain breaks: 1 Unresolved non-hydrogen bonds: 385 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 322 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 30, 'HIS:plan': 3, 'ARG:plan': 13, 'ASP:plan': 9, 'ASN:plan1': 9, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 266 Chain: "D" Number of atoms: 5929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 5929 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 29, 'TRANS': 769} Chain breaks: 1 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 495 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 6, 'GLU:plan': 37, 'ARG:plan': 7, 'ASP:plan': 11, 'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 290 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 116 Unusual residues: {'NAG': 8} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 102 Unusual residues: {'NAG': 7} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 79 Unusual residues: {'NAG': 5} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.26, per 1000 atoms: 0.22 Number of scatterers: 24220 At special positions: 0 Unit cell: (110.775, 141.37, 185.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 4454 8.00 N 4029 7.00 C 15587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.04 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 61 " " NAG A 902 " - " ASN A 203 " " NAG A 903 " - " ASN A 239 " " NAG A 904 " - " ASN A 276 " " NAG A 905 " - " ASN A 350 " " NAG A 906 " - " ASN A 368 " " NAG A 907 " - " ASN A 471 " " NAG A 908 " - " ASN A 771 " " NAG B 901 " - " ASN B 341 " " NAG B 902 " - " ASN B 688 " " NAG B 903 " - " ASN B 74 " " NAG B 904 " - " ASN B 542 " " NAG C 901 " - " ASN C 61 " " NAG C 902 " - " ASN C 203 " " NAG C 903 " - " ASN C 239 " " NAG C 904 " - " ASN C 276 " " NAG C 905 " - " ASN C 350 " " NAG C 906 " - " ASN C 471 " " NAG C 907 " - " ASN C 771 " " NAG D 901 " - " ASN D 341 " " NAG D 902 " - " ASN D 348 " " NAG D 903 " - " ASN D 688 " " NAG D 904 " - " ASN D 74 " " NAG D 905 " - " ASN D 542 " Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 821.6 milliseconds 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5994 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 27 sheets defined 46.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.970A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.641A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.841A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.938A pdb=" N ASP A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.534A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.726A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 299 Processing helix chain 'A' and resid 316 through 328 removed outlier: 4.430A pdb=" N LEU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.149A pdb=" N GLU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 526 removed outlier: 4.016A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 556 removed outlier: 4.213A pdb=" N PHE A 554 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 583 Processing helix chain 'A' and resid 602 through 616 Processing helix chain 'A' and resid 626 through 657 removed outlier: 3.620A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 652 " --> pdb=" O THR A 648 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA A 653 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.606A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'A' and resid 813 through 841 removed outlier: 3.561A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 106 through 120 removed outlier: 3.825A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 288 through 312 Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.504A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 516 through 523 removed outlier: 3.850A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 552 removed outlier: 4.478A pdb=" N PHE B 550 " --> pdb=" O PRO B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 565 Processing helix chain 'B' and resid 565 through 580 Processing helix chain 'B' and resid 601 through 614 Processing helix chain 'B' and resid 625 through 649 removed outlier: 4.613A pdb=" N ASN B 649 " --> pdb=" O SER B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 674 through 677 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 743 through 746 removed outlier: 3.513A pdb=" N CYS B 746 " --> pdb=" O ASP B 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 743 through 746' Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.597A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 removed outlier: 3.604A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 804 removed outlier: 3.547A pdb=" N ASN B 803 " --> pdb=" O GLY B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 845 removed outlier: 4.125A pdb=" N TRP B 844 " --> pdb=" O HIS B 840 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.191A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.770A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.662A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.578A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 276 through 298 removed outlier: 3.601A pdb=" N LYS C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.805A pdb=" N LEU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.158A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 559 through 583 Processing helix chain 'C' and resid 602 through 616 Processing helix chain 'C' and resid 626 through 656 removed outlier: 4.027A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA C 652 " --> pdb=" O THR C 648 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ALA C 653 " --> pdb=" O ALA C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 710 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 813 through 841 removed outlier: 3.958A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 removed outlier: 3.749A pdb=" N ASP D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.521A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 removed outlier: 3.869A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.560A pdb=" N SER D 130 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 165 Processing helix chain 'D' and resid 178 through 193 Processing helix chain 'D' and resid 212 through 222 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 288 through 312 Processing helix chain 'D' and resid 328 through 341 Processing helix chain 'D' and resid 394 through 399 removed outlier: 3.797A pdb=" N GLU D 399 " --> pdb=" O CYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 555 through 564 Processing helix chain 'D' and resid 565 through 581 Processing helix chain 'D' and resid 601 through 614 Processing helix chain 'D' and resid 625 through 647 Processing helix chain 'D' and resid 649 through 656 Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 704 through 709 removed outlier: 3.895A pdb=" N LYS D 708 " --> pdb=" O ALA D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 732 through 743 Processing helix chain 'D' and resid 772 through 787 Processing helix chain 'D' and resid 787 through 798 removed outlier: 3.909A pdb=" N THR D 798 " --> pdb=" O ALA D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 844 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 6.300A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR A 63 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N TYR A 88 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ASN A 28 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 90 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY A 30 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL A 92 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 32 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.223A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 5.914A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.562A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 477 removed outlier: 3.682A pdb=" N ILE A 400 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 514 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N ILE A 513 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ARG A 763 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.948A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 73 removed outlier: 4.251A pdb=" N GLY B 96 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 204 removed outlier: 7.841A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 227 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 406 through 410 Processing sheet with id=AB2, first strand: chain 'B' and resid 418 through 420 removed outlier: 3.673A pdb=" N ILE B 453 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 524 through 525 removed outlier: 3.567A pdb=" N ASP B 524 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.809A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 63 through 66 removed outlier: 3.588A pdb=" N VAL C 65 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN C 28 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE C 90 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY C 30 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 193 through 197 removed outlier: 3.940A pdb=" N LYS C 193 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.533A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 473 through 478 removed outlier: 7.116A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 409 through 413 Processing sheet with id=AC1, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC2, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.962A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 71 removed outlier: 3.522A pdb=" N VAL D 39 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N GLY D 96 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE D 123 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 198 through 204 removed outlier: 8.005A pdb=" N PHE D 169 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL D 202 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE D 171 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU D 204 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR D 173 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE D 168 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU D 229 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER D 170 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N TYR D 231 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 418 through 420 removed outlier: 3.808A pdb=" N ILE D 453 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU D 478 " --> pdb=" O PRO D 435 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 408 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 683 through 685 Processing sheet with id=AC8, first strand: chain 'D' and resid 683 through 685 removed outlier: 6.610A pdb=" N ILE D 530 " --> pdb=" O GLY D 761 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY D 761 " --> pdb=" O ILE D 530 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR D 532 " --> pdb=" O SER D 759 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER D 759 " --> pdb=" O THR D 532 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 544 through 545 removed outlier: 3.550A pdb=" N GLU D 658 " --> pdb=" O THR D 544 " (cutoff:3.500A) 1162 hydrogen bonds defined for protein. 3366 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: 4.99 Time building geometry restraints manager: 2.90 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: 7686 1.34 - 1.46: 4930 1.46 - 1.58: 11889 1.58 - 1.70: 1 1.70 - 1.82: 260 Bond restraints: 24766 Sorted by residual: bond pdb=" N ILE C 546 " pdb=" CA ILE C 546 " ideal model delta sigma weight residual 1.460 1.494 -0.033 7.30e-03 1.88e+04 2.07e+01 bond pdb=" N GLU D 449 " pdb=" CA GLU D 449 " ideal model delta sigma weight residual 1.458 1.488 -0.031 7.40e-03 1.83e+04 1.71e+01 bond pdb=" N ILE D 440 " pdb=" CA ILE D 440 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.10e+01 bond pdb=" N VAL C 542 " pdb=" CA VAL C 542 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.09e+01 bond pdb=" N MET C 555 " pdb=" CA MET C 555 " ideal model delta sigma weight residual 1.458 1.487 -0.029 9.00e-03 1.23e+04 1.03e+01 ... (remaining 24761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 32957 1.75 - 3.50: 718 3.50 - 5.25: 82 5.25 - 7.00: 13 7.00 - 8.75: 4 Bond angle restraints: 33774 Sorted by residual: angle pdb=" N ASN A 300 " pdb=" CA ASN A 300 " pdb=" C ASN A 300 " ideal model delta sigma weight residual 112.26 106.89 5.37 1.32e+00 5.74e-01 1.66e+01 angle pdb=" CA PRO C 670 " pdb=" N PRO C 670 " pdb=" CD PRO C 670 " ideal model delta sigma weight residual 112.00 106.42 5.58 1.40e+00 5.10e-01 1.59e+01 angle pdb=" N ARG A 306 " pdb=" CA ARG A 306 " pdb=" C ARG A 306 " ideal model delta sigma weight residual 113.28 108.59 4.69 1.22e+00 6.72e-01 1.48e+01 angle pdb=" CA MET B 394 " pdb=" CB MET B 394 " pdb=" CG MET B 394 " ideal model delta sigma weight residual 114.10 121.37 -7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" CA SER D 442 " pdb=" C SER D 442 " pdb=" O SER D 442 " ideal model delta sigma weight residual 122.64 118.13 4.51 1.25e+00 6.40e-01 1.30e+01 ... (remaining 33769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 13658 17.27 - 34.54: 963 34.54 - 51.81: 190 51.81 - 69.08: 61 69.08 - 86.35: 14 Dihedral angle restraints: 14886 sinusoidal: 5584 harmonic: 9302 Sorted by residual: dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 455 " pdb=" CB CYS A 455 " ideal model delta sinusoidal sigma weight residual 93.00 176.73 -83.73 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS A 744 " pdb=" SG CYS A 744 " pdb=" SG CYS A 798 " pdb=" CB CYS A 798 " ideal model delta sinusoidal sigma weight residual 93.00 24.41 68.59 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 308 " pdb=" CB CYS A 308 " ideal model delta sinusoidal sigma weight residual 93.00 123.26 -30.26 1 1.00e+01 1.00e-02 1.31e+01 ... (remaining 14883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3616 0.080 - 0.160: 374 0.160 - 0.240: 23 0.240 - 0.320: 3 0.320 - 0.400: 1 Chirality restraints: 4017 Sorted by residual: chirality pdb=" C1 NAG B 904 " pdb=" ND2 ASN B 542 " pdb=" C2 NAG B 904 " pdb=" O5 NAG B 904 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" C1 NAG C 901 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C 901 " pdb=" O5 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 341 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 4014 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 669 " 0.071 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO C 670 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO C 670 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 670 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 350 " -0.024 2.00e-02 2.50e+03 2.26e-02 6.40e+00 pdb=" CG ASN A 350 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 350 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 350 " 0.028 2.00e-02 2.50e+03 pdb=" C1 NAG A 905 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 323 " -0.205 9.50e-02 1.11e+02 9.20e-02 5.20e+00 pdb=" NE ARG A 323 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 323 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 323 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 323 " -0.007 2.00e-02 2.50e+03 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2988 2.75 - 3.29: 25166 3.29 - 3.83: 41438 3.83 - 4.36: 47053 4.36 - 4.90: 81763 Nonbonded interactions: 198408 Sorted by model distance: nonbonded pdb=" O MET C 125 " pdb=" NH2 ARG C 139 " model vdw 2.214 3.120 nonbonded pdb=" OH TYR D 287 " pdb=" OD2 ASP D 295 " model vdw 2.233 3.040 nonbonded pdb=" O THR B 760 " pdb=" OH TYR C 535 " model vdw 2.247 3.040 nonbonded pdb=" OG SER C 741 " pdb=" O TYR C 795 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR C 414 " pdb=" O THR C 419 " model vdw 2.281 3.040 ... (remaining 198403 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 43 or (resid 44 through 45 and (na \ me N or name CA or name C or name O or name CB )) or resid 46 through 224 or (re \ sid 225 and (name N or name CA or name C or name O or name CB )) or resid 226 th \ rough 250 or (resid 251 and (name N or name CA or name C or name O or name CB )) \ or resid 252 or (resid 253 and (name N or name CA or name C or name O or name C \ B )) or resid 254 through 282 or (resid 283 through 284 and (name N or name CA o \ r name C or name O or name CB )) or resid 285 through 299 or (resid 300 and (nam \ e N or name CA or name C or name O or name CB )) or resid 301 through 305 or (re \ sid 306 and (name N or name CA or name C or name O or name CB )) or resid 307 th \ rough 321 or (resid 322 through 323 and (name N or name CA or name C or name O o \ r name CB )) or resid 324 through 325 or (resid 326 and (name N or name CA or na \ me C or name O or name CB )) or resid 327 through 358 or (resid 359 through 360 \ and (name N or name CA or name C or name O or name CB )) or resid 361 through 37 \ 6 or (resid 377 through 378 and (name N or name CA or name C or name O or name C \ B )) or resid 379 through 464 or (resid 465 and (name N or name CA or name C or \ name O or name CB )) or resid 466 through 495 or (resid 496 through 497 and (nam \ e N or name CA or name C or name O or name CB )) or resid 498 through 501 or (re \ sid 502 and (name N or name CA or name C or name O or name CB )) or resid 503 th \ rough 676 or (resid 677 through 678 and (name N or name CA or name C or name O o \ r name CB )) or resid 679 through 715 or (resid 716 through 717 and (name N or n \ ame CA or name C or name O or name CB )) or resid 718 through 724 or (resid 725 \ and (name N or name CA or name C or name O or name CB )) or resid 726 through 79 \ 8 or (resid 799 through 801 and (name N or name CA or name C or name O or name C \ B )) or resid 802 through 907 or resid 909)) selection = (chain 'C' and (resid 25 through 35 or (resid 36 through 37 and (name N or name \ CA or name C or name O or name CB )) or resid 38 through 55 or (resid 56 through \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 or (res \ id 59 and (name N or name CA or name C or name O or name CB )) or resid 60 throu \ gh 98 or (resid 99 through 100 and (name N or name CA or name C or name O or nam \ e CB )) or resid 101 through 263 or (resid 264 and (name N or name CA or name C \ or name O or name CB )) or resid 265 through 563 or (resid 564 and (name N or na \ me CA or name C or name O or name CB )) or resid 565 through 736 or (resid 737 a \ nd (name N or name CA or name C or name O or name CB )) or resid 738 through 742 \ or (resid 743 and (name N or name CA or name C or name O or name CB )) or resid \ 744 through 763 or (resid 764 through 765 and (name N or name CA or name C or n \ ame O or name CB )) or resid 766 through 788 or (resid 789 and (name N or name C \ A or name C or name O or name CB )) or resid 790 through 795 or (resid 796 and ( \ name N or name CA or name C or name O or name CB )) or resid 797 through 908)) } ncs_group { reference = (chain 'B' and (resid 33 through 49 or (resid 50 through 51 and (name N or name \ CA or name C or name O or name CB )) or resid 52 through 53 or (resid 54 through \ 56 and (name N or name CA or name C or name O or name CB )) or resid 57 through \ 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or res \ id 62 through 75 or (resid 76 through 77 and (name N or name CA or name C or nam \ e O or name CB )) or resid 78 through 89 or (resid 90 and (name N or name CA or \ name C or name O or name CB )) or resid 91 through 164 or (resid 165 and (name N \ or name CA or name C or name O or name CB )) or resid 166 through 205 or (resid \ 206 through 211 and (name N or name CA or name C or name O or name CB )) or res \ id 212 through 223 or (resid 224 and (name N or name CA or name C or name O or n \ ame CB )) or resid 225 through 251 or (resid 252 and (name N or name CA or name \ C or name O or name CB )) or resid 253 through 309 or (resid 310 and (name N or \ name CA or name C or name O or name CB )) or resid 311 or (resid 312 and (name N \ or name CA or name C or name O or name CB )) or resid 313 through 317 or (resid \ 318 through 321 and (name N or name CA or name C or name O or name CB )) or res \ id 322 through 323 or (resid 324 through 327 and (name N or name CA or name C or \ name O or name CB )) or resid 328 through 370 or (resid 371 through 372 and (na \ me N or name CA or name C or name O or name CB )) or resid 373 through 437 or (r \ esid 438 and (name N or name CA or name C or name O or name CB )) or resid 439 t \ hrough 582 or resid 600 through 603 or (resid 604 through 605 and (name N or nam \ e CA or name C or name O or name CB )) or resid 606 through 675 or (resid 676 an \ d (name N or name CA or name C or name O or name CB )) or resid 677 through 691 \ or (resid 692 and (name N or name CA or name C or name O or name CB )) or resid \ 693 through 711 or (resid 712 and (name N or name CA or name C or name O or name \ CB )) or resid 713 through 741 or (resid 742 and (name N or name CA or name C o \ r name O or name CB )) or resid 743 through 785 or (resid 786 and (name N or nam \ e CA or name C or name O or name CB )) or resid 787 through 801 or (resid 802 th \ rough 805 and (name N or name CA or name C or name O or name CB )) or resid 806 \ through 808 or (resid 809 and (name N or name CA or name C or name O or name CB \ )) or resid 810 through 838 or (resid 839 through 841 and (name N or name CA or \ name C or name O or name CB )) or resid 842 or (resid 843 through 845 and (name \ N or name CA or name C or name O or name CB )) or resid 901 through 905)) selection = (chain 'D' and (resid 33 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 55 or (resid 56 and (name N or nam \ e CA or name C or name O or name CB )) or resid 57 through 76 or (resid 77 and ( \ name N or name CA or name C or name O or name CB )) or resid 78 through 87 or (r \ esid 88 and (name N or name CA or name C or name O or name CB )) or resid 89 thr \ ough 92 or (resid 93 and (name N or name CA or name C or name O or name CB )) or \ resid 94 through 135 or (resid 136 and (name N or name CA or name C or name O o \ r name CB )) or resid 137 or (resid 138 through 139 and (name N or name CA or na \ me C or name O or name CB )) or resid 140 through 206 or (resid 207 through 211 \ and (name N or name CA or name C or name O or name CB )) or resid 212 through 26 \ 6 or (resid 267 and (name N or name CA or name C or name O or name CB )) or resi \ d 268 through 368 or (resid 369 through 372 and (name N or name CA or name C or \ name O or name CB )) or resid 373 through 398 or (resid 399 through 403 and (nam \ e N or name CA or name C or name O or name CB )) or resid 404 through 412 or (re \ sid 413 through 414 and (name N or name CA or name C or name O or name CB )) or \ resid 415 through 424 or (resid 425 and (name N or name CA or name C or name O o \ r name CB )) or resid 426 through 440 or (resid 441 and (name N or name CA or na \ me C or name O or name CB )) or resid 442 through 451 or (resid 452 and (name N \ or name CA or name C or name O or name CB )) or resid 453 through 474 or (resid \ 475 and (name N or name CA or name C or name O or name CB )) or resid 476 throug \ h 481 or (resid 482 through 483 and (name N or name CA or name C or name O or na \ me CB )) or resid 484 through 530 or (resid 531 and (name N or name CA or name C \ or name O or name CB )) or resid 532 through 668 or (resid 669 and (name N or n \ ame CA or name C or name O or name CB )) or resid 670 through 700 or (resid 701 \ and (name N or name CA or name C or name O or name CB )) or resid 702 through 71 \ 5 or (resid 716 through 717 and (name N or name CA or name C or name O or name C \ B )) or resid 718 through 769 or (resid 770 and (name N or name CA or name C or \ name O or name CB )) or resid 771 through 845 or resid 902 through 906)) } 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 individual isotropic 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: 4.380 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.840 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.004 0.090 24804 Z= 0.236 Angle : 0.604 10.321 33874 Z= 0.346 Chirality : 0.047 0.400 4017 Planarity : 0.004 0.105 4248 Dihedral : 12.878 86.349 8850 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.08 % Allowed : 0.50 % Favored : 99.42 % 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: 0.43 (0.15), residues: 3191 helix: 1.56 (0.14), residues: 1369 sheet: -0.68 (0.29), residues: 376 loop : -0.66 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 704 TYR 0.020 0.001 TYR A 351 PHE 0.016 0.001 PHE D 182 TRP 0.017 0.001 TRP C 56 HIS 0.004 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00403 (24766) covalent geometry : angle 0.58774 (33774) SS BOND : bond 0.00387 ( 14) SS BOND : angle 0.84816 ( 28) hydrogen bonds : bond 0.13952 ( 1156) hydrogen bonds : angle 6.10067 ( 3366) link_NAG-ASN : bond 0.00449 ( 24) link_NAG-ASN : angle 3.05359 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 702 MET cc_start: 0.8647 (mmm) cc_final: 0.8329 (tpp) REVERT: B 132 MET cc_start: 0.7946 (mpp) cc_final: 0.7482 (mpp) REVERT: B 782 GLN cc_start: 0.7994 (tp40) cc_final: 0.7584 (tp-100) REVERT: D 89 MET cc_start: 0.8135 (tpt) cc_final: 0.7786 (tmm) REVERT: D 430 MET cc_start: 0.7881 (pmm) cc_final: 0.7613 (pmm) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.1498 time to fit residues: 45.4537 Evaluate side-chains 157 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN C 556 GLN D 105 GLN D 118 GLN D 767 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.068429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.055984 restraints weight = 101291.670| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.40 r_work: 0.3124 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24804 Z= 0.148 Angle : 0.521 8.981 33874 Z= 0.268 Chirality : 0.044 0.335 4017 Planarity : 0.004 0.064 4248 Dihedral : 5.200 53.582 3915 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.21 % Allowed : 5.99 % Favored : 93.80 % 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: 0.50 (0.15), residues: 3191 helix: 1.61 (0.14), residues: 1393 sheet: -0.82 (0.28), residues: 373 loop : -0.59 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 704 TYR 0.012 0.001 TYR A 647 PHE 0.014 0.001 PHE D 114 TRP 0.013 0.001 TRP C 563 HIS 0.005 0.001 HIS C 571 Details of bonding type rmsd covalent geometry : bond 0.00339 (24766) covalent geometry : angle 0.50790 (33774) SS BOND : bond 0.00225 ( 14) SS BOND : angle 0.75547 ( 28) hydrogen bonds : bond 0.04026 ( 1156) hydrogen bonds : angle 4.89197 ( 3366) link_NAG-ASN : bond 0.00426 ( 24) link_NAG-ASN : angle 2.52516 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 166 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.8606 (mmm) cc_final: 0.8368 (mmm) REVERT: B 132 MET cc_start: 0.8480 (mpp) cc_final: 0.8040 (mpp) REVERT: B 782 GLN cc_start: 0.8757 (tp40) cc_final: 0.8209 (tp-100) REVERT: C 470 MET cc_start: 0.7930 (ptt) cc_final: 0.7695 (ptt) REVERT: C 568 LEU cc_start: 0.9224 (tt) cc_final: 0.9015 (tt) REVERT: D 334 MET cc_start: 0.8158 (tpp) cc_final: 0.7847 (tpp) REVERT: D 386 MET cc_start: 0.8475 (tpp) cc_final: 0.7546 (mmm) REVERT: D 430 MET cc_start: 0.8309 (pmm) cc_final: 0.7928 (pmm) outliers start: 5 outliers final: 2 residues processed: 167 average time/residue: 0.1424 time to fit residues: 40.1915 Evaluate side-chains 161 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 62 optimal weight: 0.3980 chunk 209 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 258 optimal weight: 4.9990 chunk 273 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 150 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.068049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.055463 restraints weight = 101739.975| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.41 r_work: 0.3107 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24804 Z= 0.154 Angle : 0.506 9.090 33874 Z= 0.260 Chirality : 0.044 0.345 4017 Planarity : 0.003 0.050 4248 Dihedral : 4.715 52.470 3915 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.62 % Allowed : 8.70 % Favored : 90.68 % 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: 0.48 (0.15), residues: 3191 helix: 1.61 (0.14), residues: 1393 sheet: -0.85 (0.28), residues: 381 loop : -0.61 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 323 TYR 0.013 0.001 TYR D 705 PHE 0.014 0.001 PHE D 114 TRP 0.012 0.001 TRP C 56 HIS 0.005 0.001 HIS C 571 Details of bonding type rmsd covalent geometry : bond 0.00354 (24766) covalent geometry : angle 0.49305 (33774) SS BOND : bond 0.00227 ( 14) SS BOND : angle 0.68671 ( 28) hydrogen bonds : bond 0.03795 ( 1156) hydrogen bonds : angle 4.68202 ( 3366) link_NAG-ASN : bond 0.00424 ( 24) link_NAG-ASN : angle 2.47799 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.8008 (p) REVERT: A 706 MET cc_start: 0.8765 (mtm) cc_final: 0.8542 (mtm) REVERT: B 132 MET cc_start: 0.8517 (mpp) cc_final: 0.8084 (mpp) REVERT: B 782 GLN cc_start: 0.8757 (tp40) cc_final: 0.8208 (tp-100) REVERT: B 809 MET cc_start: 0.4891 (pmm) cc_final: 0.4263 (mpp) REVERT: C 551 LEU cc_start: 0.7918 (mp) cc_final: 0.7555 (mt) REVERT: D 89 MET cc_start: 0.8539 (tpp) cc_final: 0.7574 (mmm) REVERT: D 142 MET cc_start: 0.8779 (mmm) cc_final: 0.8386 (mtp) REVERT: D 307 MET cc_start: 0.8391 (ttm) cc_final: 0.8157 (ttt) REVERT: D 334 MET cc_start: 0.8088 (tpp) cc_final: 0.7814 (tpp) REVERT: D 430 MET cc_start: 0.8287 (pmm) cc_final: 0.7947 (pmm) REVERT: D 824 MET cc_start: 0.4340 (mmt) cc_final: 0.3236 (mmt) outliers start: 15 outliers final: 6 residues processed: 178 average time/residue: 0.1506 time to fit residues: 44.7332 Evaluate side-chains 166 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 92 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 63 optimal weight: 0.0570 chunk 272 optimal weight: 7.9990 chunk 273 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.068694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.056048 restraints weight = 101206.213| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.40 r_work: 0.3123 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24804 Z= 0.108 Angle : 0.484 9.123 33874 Z= 0.248 Chirality : 0.043 0.344 4017 Planarity : 0.003 0.050 4248 Dihedral : 4.411 48.543 3915 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.46 % Allowed : 10.36 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3191 helix: 1.68 (0.14), residues: 1394 sheet: -0.84 (0.28), residues: 382 loop : -0.62 (0.17), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 323 TYR 0.009 0.001 TYR C 128 PHE 0.012 0.001 PHE A 458 TRP 0.012 0.001 TRP C 56 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00244 (24766) covalent geometry : angle 0.47192 (33774) SS BOND : bond 0.00163 ( 14) SS BOND : angle 0.67156 ( 28) hydrogen bonds : bond 0.03462 ( 1156) hydrogen bonds : angle 4.52461 ( 3366) link_NAG-ASN : bond 0.00477 ( 24) link_NAG-ASN : angle 2.35885 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9010 (mmm) cc_final: 0.8753 (mmt) REVERT: B 132 MET cc_start: 0.8534 (mpp) cc_final: 0.8130 (mpp) REVERT: B 782 GLN cc_start: 0.8748 (tp40) cc_final: 0.8193 (tp-100) REVERT: B 809 MET cc_start: 0.4828 (pmm) cc_final: 0.4332 (mpp) REVERT: C 551 LEU cc_start: 0.7921 (mp) cc_final: 0.7543 (mt) REVERT: D 89 MET cc_start: 0.8575 (tpp) cc_final: 0.8193 (mmp) REVERT: D 334 MET cc_start: 0.8055 (tpp) cc_final: 0.7818 (tpp) REVERT: D 430 MET cc_start: 0.8290 (pmm) cc_final: 0.7941 (pmm) outliers start: 11 outliers final: 8 residues processed: 170 average time/residue: 0.1373 time to fit residues: 39.9293 Evaluate side-chains 165 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 125 optimal weight: 4.9990 chunk 305 optimal weight: 9.9990 chunk 301 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 89 optimal weight: 0.0770 chunk 76 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 129 optimal weight: 0.0980 chunk 234 optimal weight: 3.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.068545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.055826 restraints weight = 100136.348| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.38 r_work: 0.3125 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24804 Z= 0.110 Angle : 0.478 9.090 33874 Z= 0.245 Chirality : 0.043 0.343 4017 Planarity : 0.003 0.050 4248 Dihedral : 4.172 39.857 3915 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.87 % Allowed : 11.57 % Favored : 87.56 % 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: 0.55 (0.15), residues: 3191 helix: 1.72 (0.14), residues: 1396 sheet: -0.84 (0.28), residues: 382 loop : -0.63 (0.17), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 92 TYR 0.010 0.001 TYR B 389 PHE 0.012 0.001 PHE A 458 TRP 0.013 0.001 TRP C 56 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00248 (24766) covalent geometry : angle 0.46667 (33774) SS BOND : bond 0.00160 ( 14) SS BOND : angle 0.66599 ( 28) hydrogen bonds : bond 0.03387 ( 1156) hydrogen bonds : angle 4.43912 ( 3366) link_NAG-ASN : bond 0.00459 ( 24) link_NAG-ASN : angle 2.30874 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 MET cc_start: 0.8883 (mmm) cc_final: 0.8666 (mmm) REVERT: A 706 MET cc_start: 0.8793 (mtm) cc_final: 0.8525 (mtm) REVERT: A 813 MET cc_start: 0.7855 (pmm) cc_final: 0.7627 (pmm) REVERT: B 73 MET cc_start: 0.7245 (tpt) cc_final: 0.6062 (mtp) REVERT: B 132 MET cc_start: 0.8534 (mpp) cc_final: 0.8112 (mpp) REVERT: B 782 GLN cc_start: 0.8740 (tp40) cc_final: 0.8184 (tp-100) REVERT: B 809 MET cc_start: 0.4815 (pmm) cc_final: 0.4365 (mpp) REVERT: D 89 MET cc_start: 0.8549 (tpp) cc_final: 0.8114 (mmp) REVERT: D 334 MET cc_start: 0.8010 (tpp) cc_final: 0.7788 (tpp) REVERT: D 430 MET cc_start: 0.8272 (pmm) cc_final: 0.7964 (pmm) outliers start: 21 outliers final: 13 residues processed: 179 average time/residue: 0.1407 time to fit residues: 42.8552 Evaluate side-chains 172 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 95 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 221 optimal weight: 0.0770 chunk 273 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS B 802 HIS ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.067447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.054897 restraints weight = 100920.163| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.39 r_work: 0.3092 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24804 Z= 0.180 Angle : 0.530 11.951 33874 Z= 0.270 Chirality : 0.044 0.351 4017 Planarity : 0.003 0.050 4248 Dihedral : 4.198 32.084 3915 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.04 % Allowed : 12.36 % Favored : 86.60 % 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: 0.45 (0.15), residues: 3191 helix: 1.65 (0.14), residues: 1386 sheet: -0.93 (0.28), residues: 383 loop : -0.67 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 92 TYR 0.015 0.001 TYR A 647 PHE 0.013 0.001 PHE A 458 TRP 0.013 0.001 TRP D 635 HIS 0.006 0.001 HIS C 571 Details of bonding type rmsd covalent geometry : bond 0.00417 (24766) covalent geometry : angle 0.51765 (33774) SS BOND : bond 0.00228 ( 14) SS BOND : angle 0.71346 ( 28) hydrogen bonds : bond 0.03728 ( 1156) hydrogen bonds : angle 4.54106 ( 3366) link_NAG-ASN : bond 0.00408 ( 24) link_NAG-ASN : angle 2.47537 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.8103 (ppp) cc_final: 0.7809 (ppp) REVERT: A 702 MET cc_start: 0.8908 (mmm) cc_final: 0.8690 (mmm) REVERT: A 706 MET cc_start: 0.8838 (mtm) cc_final: 0.8596 (mtm) REVERT: B 73 MET cc_start: 0.7495 (tpt) cc_final: 0.6441 (ttm) REVERT: B 132 MET cc_start: 0.8546 (mpp) cc_final: 0.8024 (mpp) REVERT: B 782 GLN cc_start: 0.8734 (tp40) cc_final: 0.8204 (tp-100) REVERT: D 89 MET cc_start: 0.8555 (tpp) cc_final: 0.8132 (mmp) REVERT: D 142 MET cc_start: 0.8798 (mmm) cc_final: 0.8442 (mtp) REVERT: D 240 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8991 (mp) REVERT: D 334 MET cc_start: 0.8046 (tpp) cc_final: 0.7818 (tpp) REVERT: D 365 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8884 (mt) REVERT: D 430 MET cc_start: 0.8198 (pmm) cc_final: 0.7919 (pmm) outliers start: 25 outliers final: 17 residues processed: 172 average time/residue: 0.1286 time to fit residues: 38.2134 Evaluate side-chains 175 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 660 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.1980 chunk 252 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 254 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 63 optimal weight: 0.0870 chunk 60 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 672 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.068736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.055564 restraints weight = 100511.362| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.69 r_work: 0.3115 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24804 Z= 0.095 Angle : 0.491 11.845 33874 Z= 0.247 Chirality : 0.042 0.344 4017 Planarity : 0.003 0.050 4248 Dihedral : 3.949 29.794 3915 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.92 % Allowed : 12.90 % Favored : 86.18 % 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: 0.59 (0.16), residues: 3191 helix: 1.77 (0.14), residues: 1391 sheet: -0.83 (0.28), residues: 382 loop : -0.62 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 92 TYR 0.011 0.001 TYR B 389 PHE 0.012 0.001 PHE A 458 TRP 0.010 0.001 TRP C 768 HIS 0.004 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00209 (24766) covalent geometry : angle 0.47971 (33774) SS BOND : bond 0.00156 ( 14) SS BOND : angle 0.66296 ( 28) hydrogen bonds : bond 0.03274 ( 1156) hydrogen bonds : angle 4.40371 ( 3366) link_NAG-ASN : bond 0.00505 ( 24) link_NAG-ASN : angle 2.28365 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 MET cc_start: 0.8908 (mmm) cc_final: 0.8706 (mmm) REVERT: A 706 MET cc_start: 0.8838 (mtm) cc_final: 0.8617 (mtm) REVERT: A 813 MET cc_start: 0.7873 (pmm) cc_final: 0.7516 (pmm) REVERT: B 73 MET cc_start: 0.7379 (tpt) cc_final: 0.6455 (ttm) REVERT: B 132 MET cc_start: 0.8576 (mpp) cc_final: 0.8122 (mpp) REVERT: B 782 GLN cc_start: 0.8737 (tp40) cc_final: 0.8179 (tp-100) REVERT: C 634 MET cc_start: 0.8611 (tpp) cc_final: 0.8392 (tpp) REVERT: D 89 MET cc_start: 0.8551 (tpp) cc_final: 0.8108 (mmp) REVERT: D 240 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8969 (mp) REVERT: D 430 MET cc_start: 0.8291 (pmm) cc_final: 0.7966 (pmm) REVERT: D 702 MET cc_start: 0.8145 (mmm) cc_final: 0.7741 (tpp) outliers start: 22 outliers final: 15 residues processed: 176 average time/residue: 0.1278 time to fit residues: 38.8432 Evaluate side-chains 174 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 240 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 279 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 269 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 146 optimal weight: 0.0370 chunk 115 optimal weight: 5.9990 chunk 317 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 271 optimal weight: 4.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 672 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.068670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.055847 restraints weight = 100749.807| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.53 r_work: 0.3126 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24804 Z= 0.103 Angle : 0.496 11.834 33874 Z= 0.248 Chirality : 0.042 0.340 4017 Planarity : 0.003 0.050 4248 Dihedral : 3.814 29.835 3915 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.92 % Allowed : 13.15 % Favored : 85.93 % 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: 0.64 (0.16), residues: 3191 helix: 1.82 (0.14), residues: 1390 sheet: -0.81 (0.28), residues: 382 loop : -0.60 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 92 TYR 0.009 0.001 TYR B 389 PHE 0.012 0.001 PHE A 458 TRP 0.012 0.001 TRP C 56 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00234 (24766) covalent geometry : angle 0.48531 (33774) SS BOND : bond 0.00145 ( 14) SS BOND : angle 0.65434 ( 28) hydrogen bonds : bond 0.03216 ( 1156) hydrogen bonds : angle 4.34825 ( 3366) link_NAG-ASN : bond 0.00464 ( 24) link_NAG-ASN : angle 2.22826 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 813 MET cc_start: 0.7781 (pmm) cc_final: 0.7437 (pmm) REVERT: B 73 MET cc_start: 0.7557 (tpt) cc_final: 0.6857 (ttm) REVERT: B 132 MET cc_start: 0.8585 (mpp) cc_final: 0.8097 (mpp) REVERT: B 394 MET cc_start: 0.6270 (ppp) cc_final: 0.5647 (tpp) REVERT: B 782 GLN cc_start: 0.8703 (tp40) cc_final: 0.8153 (tp-100) REVERT: C 634 MET cc_start: 0.8590 (tpp) cc_final: 0.8345 (tpp) REVERT: D 89 MET cc_start: 0.8663 (tpp) cc_final: 0.8211 (mmp) REVERT: D 240 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8986 (mp) REVERT: D 430 MET cc_start: 0.8308 (pmm) cc_final: 0.7983 (pmm) REVERT: D 470 LYS cc_start: 0.9329 (tppt) cc_final: 0.9113 (pttp) REVERT: D 702 MET cc_start: 0.8263 (mmm) cc_final: 0.7898 (tpp) outliers start: 22 outliers final: 20 residues processed: 168 average time/residue: 0.1332 time to fit residues: 38.4767 Evaluate side-chains 176 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 678 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 181 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 175 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.068039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.055624 restraints weight = 101046.239| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.41 r_work: 0.3101 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24804 Z= 0.142 Angle : 0.517 12.964 33874 Z= 0.259 Chirality : 0.043 0.345 4017 Planarity : 0.003 0.050 4248 Dihedral : 3.865 30.550 3915 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.00 % Allowed : 13.11 % Favored : 85.89 % 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: 0.57 (0.15), residues: 3191 helix: 1.77 (0.14), residues: 1388 sheet: -0.89 (0.27), residues: 382 loop : -0.63 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 92 TYR 0.013 0.001 TYR A 647 PHE 0.015 0.001 PHE A 829 TRP 0.011 0.001 TRP D 635 HIS 0.005 0.001 HIS C 571 Details of bonding type rmsd covalent geometry : bond 0.00330 (24766) covalent geometry : angle 0.50581 (33774) SS BOND : bond 0.00187 ( 14) SS BOND : angle 0.67667 ( 28) hydrogen bonds : bond 0.03428 ( 1156) hydrogen bonds : angle 4.39921 ( 3366) link_NAG-ASN : bond 0.00421 ( 24) link_NAG-ASN : angle 2.31189 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 706 MET cc_start: 0.8823 (mtm) cc_final: 0.8594 (mtm) REVERT: A 813 MET cc_start: 0.7896 (pmm) cc_final: 0.7549 (pmm) REVERT: B 73 MET cc_start: 0.7723 (tpt) cc_final: 0.7142 (ttp) REVERT: B 132 MET cc_start: 0.8554 (mpp) cc_final: 0.8071 (mpp) REVERT: B 782 GLN cc_start: 0.8698 (tp40) cc_final: 0.8170 (tp-100) REVERT: D 89 MET cc_start: 0.8661 (tpp) cc_final: 0.8240 (mmp) REVERT: D 142 MET cc_start: 0.8765 (mmm) cc_final: 0.8402 (mtp) REVERT: D 240 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.9001 (mp) REVERT: D 358 MET cc_start: 0.8703 (mmm) cc_final: 0.8445 (mmt) REVERT: D 430 MET cc_start: 0.8207 (pmm) cc_final: 0.7913 (pmm) REVERT: D 470 LYS cc_start: 0.9324 (tppt) cc_final: 0.9086 (pttp) outliers start: 24 outliers final: 19 residues processed: 167 average time/residue: 0.1387 time to fit residues: 40.1509 Evaluate side-chains 173 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 678 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 56 optimal weight: 0.3980 chunk 202 optimal weight: 1.9990 chunk 301 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 275 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 672 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.068923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.056442 restraints weight = 101375.167| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.51 r_work: 0.3136 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24804 Z= 0.097 Angle : 0.503 12.937 33874 Z= 0.249 Chirality : 0.042 0.341 4017 Planarity : 0.003 0.050 4248 Dihedral : 3.717 29.019 3915 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.87 % Allowed : 13.40 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.65 (0.16), residues: 3191 helix: 1.84 (0.14), residues: 1390 sheet: -0.83 (0.27), residues: 382 loop : -0.60 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 92 TYR 0.010 0.001 TYR B 389 PHE 0.012 0.001 PHE A 458 TRP 0.011 0.001 TRP C 768 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00216 (24766) covalent geometry : angle 0.49308 (33774) SS BOND : bond 0.00140 ( 14) SS BOND : angle 0.64588 ( 28) hydrogen bonds : bond 0.03136 ( 1156) hydrogen bonds : angle 4.30763 ( 3366) link_NAG-ASN : bond 0.00494 ( 24) link_NAG-ASN : angle 2.17949 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 702 MET cc_start: 0.8894 (mmm) cc_final: 0.8549 (tpp) REVERT: A 813 MET cc_start: 0.7782 (pmm) cc_final: 0.7433 (pmm) REVERT: B 73 MET cc_start: 0.7694 (tpt) cc_final: 0.7173 (ttp) REVERT: B 132 MET cc_start: 0.8577 (mpp) cc_final: 0.8059 (mpp) REVERT: B 782 GLN cc_start: 0.8699 (tp40) cc_final: 0.8148 (tp-100) REVERT: D 89 MET cc_start: 0.8660 (tpp) cc_final: 0.8229 (mmp) REVERT: D 240 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.9015 (mp) REVERT: D 358 MET cc_start: 0.8697 (mmm) cc_final: 0.8434 (mmt) REVERT: D 430 MET cc_start: 0.8285 (pmm) cc_final: 0.7956 (pmm) REVERT: D 470 LYS cc_start: 0.9287 (tppt) cc_final: 0.9043 (pttp) REVERT: D 702 MET cc_start: 0.8263 (mmm) cc_final: 0.7890 (tpp) REVERT: D 789 MET cc_start: 0.8754 (tpp) cc_final: 0.8439 (mmm) outliers start: 21 outliers final: 18 residues processed: 167 average time/residue: 0.1324 time to fit residues: 38.4381 Evaluate side-chains 173 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 678 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 220 optimal weight: 0.9990 chunk 219 optimal weight: 0.5980 chunk 228 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 278 optimal weight: 0.7980 chunk 294 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 257 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 780 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.068538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.056071 restraints weight = 100985.169| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.36 r_work: 0.3125 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24804 Z= 0.113 Angle : 0.509 13.158 33874 Z= 0.254 Chirality : 0.042 0.340 4017 Planarity : 0.003 0.051 4248 Dihedral : 3.716 29.202 3915 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.83 % Allowed : 13.69 % Favored : 85.48 % 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: 0.64 (0.16), residues: 3191 helix: 1.82 (0.14), residues: 1390 sheet: -0.83 (0.28), residues: 380 loop : -0.60 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 92 TYR 0.010 0.001 TYR A 647 PHE 0.013 0.001 PHE C 533 TRP 0.010 0.001 TRP C 56 HIS 0.004 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00259 (24766) covalent geometry : angle 0.49913 (33774) SS BOND : bond 0.00155 ( 14) SS BOND : angle 0.64615 ( 28) hydrogen bonds : bond 0.03226 ( 1156) hydrogen bonds : angle 4.32499 ( 3366) link_NAG-ASN : bond 0.00448 ( 24) link_NAG-ASN : angle 2.18728 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4928.72 seconds wall clock time: 85 minutes 18.08 seconds (5118.08 seconds total)