Starting phenix.real_space_refine on Sat Jul 4 23:44:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dch_46751/07_2026/9dch_46751.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dch_46751/07_2026/9dch_46751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dch_46751/07_2026/9dch_46751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dch_46751/07_2026/9dch_46751.map" model { file = "/net/cci-nas-00/data/ceres_data/9dch_46751/07_2026/9dch_46751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dch_46751/07_2026/9dch_46751.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 14 6.06 5 P 10 5.49 5 S 106 5.16 5 C 15367 2.51 5 N 4476 2.21 5 O 4460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24433 Number of models: 1 Model: "" Number of chains: 15 Chain: "G" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 219 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3124 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain breaks: 4 Unresolved non-hydrogen bonds: 589 Unresolved non-hydrogen angles: 737 Unresolved non-hydrogen dihedrals: 473 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLU:plan': 17, 'TYR:plan': 6, 'ARG:plan': 19, 'GLN:plan1': 15, 'PHE:plan': 2, 'ASN:plan1': 11, 'HIS:plan': 5, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 377 Chain: "B" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 2786 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'PTRANS': 17, 'TRANS': 405} Chain breaks: 9 Unresolved non-hydrogen bonds: 751 Unresolved non-hydrogen angles: 937 Unresolved non-hydrogen dihedrals: 602 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 13, 'GLU:plan': 20, 'TYR:plan': 3, 'ARG:plan': 15, 'HIS:plan': 5, 'ASN:plan1': 11, 'PHE:plan': 9} Unresolved non-hydrogen planarities: 407 Chain: "D" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2715 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 520 Unresolved non-hydrogen angles: 665 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 22, 'GLN:plan1': 8, 'ARG:plan': 4, 'HIS:plan': 3, 'ASN:plan1': 12, 'PHE:plan': 2, 'TYR:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 286 Chain: "F" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 695 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 5, 'PHE:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 95 Chain: "E" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 187 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 27} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2589 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 12, 'TRANS': 352} Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ASN:plan1': 6, 'GLU:plan': 12, 'GLN:plan1': 4, 'ARG:plan': 8, 'TYR:plan': 1, 'ASP:plan': 15, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 189 Chain: "H" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3128 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain breaks: 4 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 732 Unresolved non-hydrogen dihedrals: 470 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLU:plan': 17, 'TYR:plan': 6, 'ARG:plan': 19, 'GLN:plan1': 14, 'PHE:plan': 2, 'ASN:plan1': 11, 'HIS:plan': 5, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 373 Chain: "I" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 2789 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 215} Link IDs: {'PTRANS': 17, 'TRANS': 405} Chain breaks: 9 Unresolved non-hydrogen bonds: 748 Unresolved non-hydrogen angles: 933 Unresolved non-hydrogen dihedrals: 600 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 13, 'GLU:plan': 20, 'TYR:plan': 3, 'ARG:plan': 15, 'HIS:plan': 5, 'ASN:plan1': 11, 'PHE:plan': 9} Unresolved non-hydrogen planarities: 407 Chain: "K" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2718 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 517 Unresolved non-hydrogen angles: 661 Unresolved non-hydrogen dihedrals: 403 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 22, 'GLN:plan1': 8, 'ARG:plan': 4, 'HIS:plan': 3, 'ASN:plan1': 12, 'PHE:plan': 2, 'TYR:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 286 Chain: "M" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 695 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 5, 'PHE:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 95 Chain: "L" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 187 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 27} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "J" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2587 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 12, 'TRANS': 352} Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'ASN:plan1': 6, 'GLU:plan': 12, 'GLN:plan1': 4, 'ARG:plan': 8, 'TYR:plan': 1, 'ASP:plan': 15, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 189 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1873 SG CYS A 528 46.993 69.401 121.243 1.00 55.10 S ATOM 1918 SG CYS A 535 45.606 72.727 119.808 1.00 62.62 S ATOM 1941 SG CYS A 539 44.918 71.787 123.440 1.00 59.67 S ATOM 1873 SG CYS A 528 46.993 69.401 121.243 1.00 55.10 S ATOM 1954 SG CYS A 541 48.289 70.681 124.577 1.00 55.84 S ATOM 2006 SG CYS A 548 49.096 72.553 121.388 1.00 49.70 S ATOM 2041 SG CYS A 552 50.640 69.065 122.045 1.00 46.34 S ATOM 1918 SG CYS A 535 45.606 72.727 119.808 1.00 62.62 S ATOM 2006 SG CYS A 548 49.096 72.553 121.388 1.00 49.70 S ATOM 2052 SG CYS A 554 48.564 71.296 117.849 1.00 53.75 S ATOM 2075 SG CYS A 558 48.321 75.042 118.622 1.00 51.10 S ATOM 2121 SG CYS A 565 65.591 78.651 121.173 1.00 30.93 S ATOM 2138 SG CYS A 567 68.433 81.182 120.595 1.00 27.67 S ATOM 2167 SG CYS A 571 68.626 78.576 123.543 1.00 26.53 S ATOM 2206 SG CYS A 576 66.094 80.796 123.980 1.00 27.85 S ATOM 2167 SG CYS A 571 68.626 78.576 123.543 1.00 26.53 S ATOM 2277 SG CYS A 585 66.799 75.438 122.710 1.00 26.69 S ATOM 2329 SG CYS A 593 69.495 76.948 120.415 1.00 25.83 S ATOM 2403 SG CYS A 606 70.627 75.206 123.514 1.00 26.71 S ATOM 2121 SG CYS A 565 65.591 78.651 121.173 1.00 30.93 S ATOM 2219 SG CYS A 578 63.539 77.427 123.738 1.00 24.36 S ATOM 2277 SG CYS A 585 66.799 75.438 122.710 1.00 26.69 S ATOM 2308 SG CYS A 590 63.979 75.513 120.185 1.00 25.92 S ATOM 1096 SG CYS A 286 56.179 56.338 126.316 1.00 46.75 S ATOM 1118 SG CYS A 289 59.849 57.367 126.174 1.00 43.23 S ATOM 1160 SG CYS A 294 58.933 54.356 128.288 1.00 44.98 S ATOM 13973 SG CYS H 528 63.182 104.059 132.419 1.00 82.67 S ATOM 14018 SG CYS H 535 63.029 101.105 134.898 1.00 92.88 S ATOM 14041 SG CYS H 539 59.829 102.719 133.619 1.00 84.19 S ATOM 13973 SG CYS H 528 63.182 104.059 132.419 1.00 82.67 S ATOM 14054 SG CYS H 541 60.414 103.065 129.991 1.00 78.74 S ATOM 14106 SG CYS H 548 62.978 100.513 131.086 1.00 66.72 S ATOM 14141 SG CYS H 552 64.125 103.397 128.866 1.00 72.26 S ATOM 14018 SG CYS H 535 63.029 101.105 134.898 1.00 92.88 S ATOM 14106 SG CYS H 548 62.978 100.513 131.086 1.00 66.72 S ATOM 14152 SG CYS H 554 66.291 101.180 132.939 1.00 88.37 S ATOM 14175 SG CYS H 558 64.349 97.935 133.520 1.00 77.43 S ATOM 14221 SG CYS H 565 66.446 89.474 117.562 1.00 50.77 S ATOM 14238 SG CYS H 567 67.022 87.319 115.521 1.00 44.28 S ATOM 14267 SG CYS H 571 64.814 89.851 113.910 1.00 40.04 S ATOM 14306 SG CYS H 576 65.201 86.235 115.851 1.00 45.78 S ATOM 14267 SG CYS H 571 64.814 89.851 113.910 1.00 40.04 S ATOM 14377 SG CYS H 585 66.076 92.799 115.604 1.00 44.94 S ATOM 14429 SG CYS H 593 68.590 90.301 114.155 1.00 40.20 S ATOM 14503 SG CYS H 606 66.632 92.485 111.781 1.00 38.41 S ATOM 14221 SG CYS H 565 66.446 89.474 117.562 1.00 50.77 S ATOM 14319 SG CYS H 578 63.947 91.825 118.590 1.00 41.82 S ATOM 14377 SG CYS H 585 66.076 92.799 115.604 1.00 44.94 S ATOM 14408 SG CYS H 590 67.892 92.735 118.843 1.00 44.31 S ATOM 13192 SG CYS H 286 64.997 114.188 121.132 1.00 78.21 S ATOM 13214 SG CYS H 289 66.234 114.137 117.487 1.00 70.41 S ATOM 13256 SG CYS H 294 63.428 116.535 118.535 1.00 64.74 S Residues with excluded nonbonded symmetry interactions: 14 residue: pdb="ZN ZN A 801 " occ=0.00 residue: pdb="ZN ZN A 802 " occ=0.58 residue: pdb="ZN ZN A 803 " occ=0.10 residue: pdb="ZN ZN A 804 " occ=0.14 residue: pdb="ZN ZN A 805 " occ=0.71 residue: pdb="ZN ZN A 806 " occ=0.00 residue: pdb="ZN ZN A 807 " occ=0.11 residue: pdb="ZN ZN H 801 " occ=0.00 residue: pdb="ZN ZN H 802 " occ=0.17 residue: pdb="ZN ZN H 803 " occ=0.32 residue: pdb="ZN ZN H 804 " occ=0.74 residue: pdb="ZN ZN H 805 " occ=0.37 ... (remaining 2 not shown) Time building chain proxies: 5.31, per 1000 atoms: 0.22 Number of scatterers: 24433 At special positions: 0 Unit cell: (157.14, 177.51, 212.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 14 29.99 S 106 16.00 P 10 15.00 O 4460 8.00 N 4476 7.00 C 15367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 457 " distance=2.03 Simple disulfide: pdb=" SG CYS H 325 " - pdb=" SG CYS H 457 " 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 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 530 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 539 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 535 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 528 " pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 528 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 541 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 548 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 552 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 535 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 558 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 554 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 548 " pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 571 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 565 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 567 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 576 " pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 593 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 571 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 585 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 606 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 565 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 585 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 590 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 578 " pdb=" ZN A 807 " pdb="ZN ZN A 807 " - pdb=" ND1 HIS A 297 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 289 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 294 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 286 " pdb=" ZN H 801 " pdb="ZN ZN H 801 " - pdb=" NE2 HIS H 530 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 539 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 535 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 528 " pdb=" ZN H 802 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 528 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 548 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 552 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 541 " pdb=" ZN H 803 " pdb="ZN ZN H 803 " - pdb=" SG CYS H 535 " pdb="ZN ZN H 803 " - pdb=" SG CYS H 558 " pdb="ZN ZN H 803 " - pdb=" SG CYS H 554 " pdb="ZN ZN H 803 " - pdb=" SG CYS H 548 " pdb=" ZN H 804 " pdb="ZN ZN H 804 " - pdb=" SG CYS H 567 " pdb="ZN ZN H 804 " - pdb=" SG CYS H 571 " pdb="ZN ZN H 804 " - pdb=" SG CYS H 565 " pdb="ZN ZN H 804 " - pdb=" SG CYS H 576 " pdb=" ZN H 805 " pdb="ZN ZN H 805 " - pdb=" SG CYS H 585 " pdb="ZN ZN H 805 " - pdb=" SG CYS H 593 " pdb="ZN ZN H 805 " - pdb=" SG CYS H 571 " pdb="ZN ZN H 805 " - pdb=" SG CYS H 606 " pdb=" ZN H 806 " pdb="ZN ZN H 806 " - pdb=" SG CYS H 565 " pdb="ZN ZN H 806 " - pdb=" SG CYS H 585 " pdb="ZN ZN H 806 " - pdb=" SG CYS H 578 " pdb="ZN ZN H 806 " - pdb=" SG CYS H 590 " pdb=" ZN H 807 " pdb="ZN ZN H 807 " - pdb=" ND1 HIS H 297 " pdb="ZN ZN H 807 " - pdb=" SG CYS H 294 " pdb="ZN ZN H 807 " - pdb=" SG CYS H 289 " pdb="ZN ZN H 807 " - pdb=" SG CYS H 286 " Number of angles added : 72 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6876 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 49 sheets defined 22.0% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 22 through 61 Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.567A pdb=" N THR A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 284' Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.861A pdb=" N THR A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 463 Processing helix chain 'A' and resid 467 through 482 Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 652 through 665 Processing helix chain 'A' and resid 687 through 691 removed outlier: 3.802A pdb=" N PHE A 691 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 107 Proline residue: B 93 - end of helix removed outlier: 3.553A pdb=" N ARG B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.786A pdb=" N LYS B 465 " --> pdb=" O TYR B 461 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 507 removed outlier: 3.723A pdb=" N HIS B 507 " --> pdb=" O GLN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.837A pdb=" N PHE B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 602 Processing helix chain 'B' and resid 607 through 625 Processing helix chain 'B' and resid 628 through 643 removed outlier: 4.030A pdb=" N ASN B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS B 634 " --> pdb=" O ASN B 630 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET B 637 " --> pdb=" O ASN B 633 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE B 639 " --> pdb=" O ALA B 635 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL B 640 " --> pdb=" O CYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 651 Processing helix chain 'B' and resid 652 through 662 Processing helix chain 'B' and resid 663 through 667 removed outlier: 3.567A pdb=" N ASN B 667 " --> pdb=" O HIS B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 689 removed outlier: 3.571A pdb=" N GLU B 683 " --> pdb=" O THR B 679 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET B 684 " --> pdb=" O LYS B 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 27 removed outlier: 3.790A pdb=" N LYS D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'F' and resid 193 through 210 removed outlier: 4.097A pdb=" N ALA F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 262 Processing helix chain 'F' and resid 276 through 281 removed outlier: 3.645A pdb=" N ASP F 281 " --> pdb=" O ALA F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 292 removed outlier: 3.917A pdb=" N LYS F 291 " --> pdb=" O MET F 288 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG F 292 " --> pdb=" O PRO F 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 288 through 292' Processing helix chain 'E' and resid 142 through 148 removed outlier: 3.723A pdb=" N ASP E 146 " --> pdb=" O THR E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.765A pdb=" N ARG E 164 " --> pdb=" O PHE E 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'C' and resid 339 through 343 Processing helix chain 'H' and resid 23 through 61 Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.512A pdb=" N THR H 283 " --> pdb=" O HIS H 279 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU H 284 " --> pdb=" O SER H 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 279 through 284' Processing helix chain 'H' and resid 336 through 347 Processing helix chain 'H' and resid 438 through 453 Processing helix chain 'H' and resid 456 through 463 Processing helix chain 'H' and resid 467 through 482 removed outlier: 3.540A pdb=" N SER H 479 " --> pdb=" O ARG H 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 544 Processing helix chain 'H' and resid 576 through 581 Processing helix chain 'H' and resid 609 through 614 Processing helix chain 'H' and resid 652 through 665 Processing helix chain 'H' and resid 687 through 691 removed outlier: 3.582A pdb=" N PHE H 691 " --> pdb=" O LYS H 688 " (cutoff:3.500A) Processing helix chain 'H' and resid 730 through 734 Processing helix chain 'I' and resid 81 through 107 Proline residue: I 93 - end of helix Processing helix chain 'I' and resid 131 through 133 No H-bonds generated for 'chain 'I' and resid 131 through 133' Processing helix chain 'I' and resid 134 through 139 Processing helix chain 'I' and resid 459 through 462 Processing helix chain 'I' and resid 463 through 471 removed outlier: 3.991A pdb=" N LYS I 468 " --> pdb=" O LEU I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 502 through 506 Processing helix chain 'I' and resid 539 through 544 removed outlier: 3.865A pdb=" N PHE I 543 " --> pdb=" O SER I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 575 through 580 removed outlier: 4.048A pdb=" N GLU I 580 " --> pdb=" O GLN I 577 " (cutoff:3.500A) Processing helix chain 'I' and resid 589 through 602 Processing helix chain 'I' and resid 607 through 625 Processing helix chain 'I' and resid 628 through 651 removed outlier: 3.884A pdb=" N ASN I 633 " --> pdb=" O ASP I 629 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS I 634 " --> pdb=" O ASN I 630 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET I 637 " --> pdb=" O ASN I 633 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE I 639 " --> pdb=" O ALA I 635 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL I 640 " --> pdb=" O CYS I 636 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU I 641 " --> pdb=" O MET I 637 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN I 642 " --> pdb=" O LEU I 638 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY I 644 " --> pdb=" O VAL I 640 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN I 645 " --> pdb=" O GLU I 641 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LYS I 646 " --> pdb=" O ASN I 642 " (cutoff:3.500A) Processing helix chain 'I' and resid 652 through 662 Processing helix chain 'I' and resid 663 through 667 Processing helix chain 'I' and resid 670 through 689 removed outlier: 4.052A pdb=" N MET I 684 " --> pdb=" O LYS I 680 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 27 removed outlier: 3.910A pdb=" N LYS K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN K 27 " --> pdb=" O ILE K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 355 through 362 Processing helix chain 'M' and resid 193 through 210 removed outlier: 4.545A pdb=" N ALA M 197 " --> pdb=" O GLN M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 262 Processing helix chain 'M' and resid 273 through 281 removed outlier: 4.497A pdb=" N LEU M 278 " --> pdb=" O LYS M 274 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU M 279 " --> pdb=" O ASP M 275 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP M 281 " --> pdb=" O ALA M 277 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 292 removed outlier: 4.409A pdb=" N LYS M 291 " --> pdb=" O MET M 288 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG M 292 " --> pdb=" O PRO M 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 288 through 292' Processing helix chain 'L' and resid 142 through 148 removed outlier: 3.861A pdb=" N ASP L 146 " --> pdb=" O THR L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 164 removed outlier: 3.787A pdb=" N ARG L 164 " --> pdb=" O PHE L 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 279 removed outlier: 3.573A pdb=" N MET J 271 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 85 removed outlier: 3.501A pdb=" N GLN A 94 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 100 removed outlier: 6.316A pdb=" N LYS A 99 " --> pdb=" O VAL C 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.200A pdb=" N SER A 114 " --> pdb=" O GLY A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 121 removed outlier: 6.270A pdb=" N PHE A 120 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 619 through 623 Processing sheet with id=AA6, first strand: chain 'A' and resid 642 through 645 removed outlier: 7.318A pdb=" N PHE A 642 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA A 717 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 644 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 185 through 188 Processing sheet with id=AA8, first strand: chain 'B' and resid 313 through 318 removed outlier: 3.703A pdb=" N LEU B 359 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR B 315 " --> pdb=" O PHE B 357 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE B 357 " --> pdb=" O TYR B 315 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL B 317 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 355 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 475 through 476 Processing sheet with id=AB1, first strand: chain 'B' and resid 557 through 560 removed outlier: 3.836A pdb=" N LEU B 529 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL D 35 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU D 34 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN D 403 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D 379 " --> pdb=" O VAL D 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 565 through 566 removed outlier: 4.013A pdb=" N TYR B 565 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 64 through 67 removed outlier: 6.929A pdb=" N ILE D 81 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 139 through 143 Processing sheet with id=AB5, first strand: chain 'D' and resid 193 through 196 Processing sheet with id=AB6, first strand: chain 'D' and resid 230 through 235 removed outlier: 3.870A pdb=" N ASP D 232 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 246 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 278 through 279 removed outlier: 3.565A pdb=" N CYS D 278 " --> pdb=" O GLY D 292 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR D 291 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA D 299 " --> pdb=" O THR D 291 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 320 through 323 removed outlier: 3.700A pdb=" N LEU D 333 " --> pdb=" O TRP D 345 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 219 through 220 Processing sheet with id=AC1, first strand: chain 'F' and resid 224 through 226 Processing sheet with id=AC2, first strand: chain 'C' and resid 82 through 87 removed outlier: 7.336A pdb=" N ARG C 436 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 99 through 101 removed outlier: 3.894A pdb=" N GLN C 100 " --> pdb=" O ALA C 114 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 114 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 113 " --> pdb=" O TYR C 124 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU C 131 " --> pdb=" O HIS C 127 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 151 through 154 removed outlier: 6.024A pdb=" N ILE C 172 " --> pdb=" O HIS C 185 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS C 185 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE C 174 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 193 through 198 removed outlier: 3.986A pdb=" N GLU C 195 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 227 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN C 219 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU C 225 " --> pdb=" O ASN C 219 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N GLN C 292 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL C 226 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE C 294 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE C 228 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 242 through 244 removed outlier: 3.710A pdb=" N MET C 252 " --> pdb=" O ASP C 243 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 251 " --> pdb=" O TRP C 263 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 309 through 311 removed outlier: 3.780A pdb=" N SER C 323 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS C 332 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE C 352 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.854A pdb=" N ALA C 378 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR C 387 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 388 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR C 402 " --> pdb=" O VAL C 388 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 114 through 115 removed outlier: 5.829A pdb=" N SER H 114 " --> pdb=" O GLY H 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'H' and resid 619 through 623 Processing sheet with id=AD2, first strand: chain 'H' and resid 642 through 645 removed outlier: 7.182A pdb=" N PHE H 642 " --> pdb=" O ALA H 717 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA H 717 " --> pdb=" O PHE H 642 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER H 644 " --> pdb=" O ILE H 715 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET H 705 " --> pdb=" O ARG H 712 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 649 through 651 Processing sheet with id=AD4, first strand: chain 'I' and resid 185 through 188 removed outlier: 4.056A pdb=" N GLU I 185 " --> pdb=" O ARG I 253 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 313 through 318 removed outlier: 3.733A pdb=" N LEU I 359 " --> pdb=" O GLY I 313 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE I 357 " --> pdb=" O TYR I 315 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL I 317 " --> pdb=" O LEU I 355 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU I 355 " --> pdb=" O VAL I 317 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 429 through 433 removed outlier: 6.051A pdb=" N PHE I 429 " --> pdb=" O ILE I 487 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL I 489 " --> pdb=" O PHE I 429 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLN I 431 " --> pdb=" O VAL I 489 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE I 491 " --> pdb=" O GLN I 431 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU I 433 " --> pdb=" O ILE I 491 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 557 through 560 removed outlier: 3.856A pdb=" N LEU I 529 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL K 35 " --> pdb=" O LEU I 529 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU K 34 " --> pdb=" O GLN K 403 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP K 379 " --> pdb=" O VAL K 393 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 565 through 566 removed outlier: 3.982A pdb=" N TYR I 565 " --> pdb=" O LEU I 574 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 64 through 67 removed outlier: 5.393A pdb=" N LEU K 79 " --> pdb=" O LYS K 120 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS K 120 " --> pdb=" O LEU K 79 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE K 81 " --> pdb=" O GLU K 118 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 139 through 143 Processing sheet with id=AE2, first strand: chain 'K' and resid 193 through 196 Processing sheet with id=AE3, first strand: chain 'K' and resid 230 through 235 removed outlier: 4.316A pdb=" N ASP K 232 " --> pdb=" O VAL K 246 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL K 246 " --> pdb=" O ASP K 232 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 322 through 325 Processing sheet with id=AE5, first strand: chain 'M' and resid 219 through 220 removed outlier: 3.529A pdb=" N VAL M 267 " --> pdb=" O VAL M 220 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 224 through 226 Processing sheet with id=AE7, first strand: chain 'J' and resid 82 through 87 removed outlier: 7.152A pdb=" N ARG J 436 " --> pdb=" O VAL J 85 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER J 87 " --> pdb=" O ILE J 434 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE J 434 " --> pdb=" O SER J 87 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER J 417 " --> pdb=" O ILE J 426 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL J 428 " --> pdb=" O GLN J 415 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN J 415 " --> pdb=" O VAL J 428 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 100 through 101 removed outlier: 3.809A pdb=" N GLN J 100 " --> pdb=" O ALA J 114 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE J 113 " --> pdb=" O TYR J 124 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR J 124 " --> pdb=" O PHE J 113 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN J 136 " --> pdb=" O LEU J 123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 149 through 155 removed outlier: 3.762A pdb=" N ALA J 166 " --> pdb=" O THR J 149 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS J 160 " --> pdb=" O ASP J 155 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN J 181 " --> pdb=" O ASN J 176 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 193 through 198 removed outlier: 4.098A pdb=" N GLU J 195 " --> pdb=" O VAL J 209 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL J 209 " --> pdb=" O GLU J 195 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU J 215 " --> pdb=" O ILE J 228 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE J 228 " --> pdb=" O LEU J 215 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU J 217 " --> pdb=" O VAL J 226 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN J 292 " --> pdb=" O VAL J 226 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 239 through 242 removed outlier: 3.650A pdb=" N SER J 241 " --> pdb=" O CYS J 254 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 309 through 311 removed outlier: 3.546A pdb=" N TRP J 331 " --> pdb=" O ILE J 319 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER J 321 " --> pdb=" O VAL J 329 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER J 323 " --> pdb=" O ALA J 327 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA J 327 " --> pdb=" O SER J 323 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE J 356 " --> pdb=" O ILE J 328 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY J 354 " --> pdb=" O CYS J 330 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS J 332 " --> pdb=" O ILE J 352 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE J 352 " --> pdb=" O LYS J 332 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 368 through 370 removed outlier: 3.586A pdb=" N LEU J 379 " --> pdb=" O TYR J 387 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR J 387 " --> pdb=" O LEU J 379 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR J 402 " --> pdb=" O VAL J 388 " (cutoff:3.500A) 742 hydrogen bonds defined for protein. 2037 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: 4.04 Time building geometry restraints manager: 2.10 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: 8305 1.34 - 1.46: 6201 1.46 - 1.59: 10383 1.59 - 1.71: 18 1.71 - 1.83: 134 Bond restraints: 25041 Sorted by residual: bond pdb=" CA CYS H 576 " pdb=" C CYS H 576 " ideal model delta sigma weight residual 1.523 1.561 -0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N ASN H 572 " pdb=" CA ASN H 572 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.33e-02 5.65e+03 7.68e+00 bond pdb=" N ARG A 566 " pdb=" CA ARG A 566 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.66e+00 bond pdb=" N ASN A 572 " pdb=" CA ASN A 572 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.33e-02 5.65e+03 6.61e+00 bond pdb=" N LYS H 574 " pdb=" CA LYS H 574 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.35e-02 5.49e+03 4.73e+00 ... (remaining 25036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 34341 4.14 - 8.28: 47 8.28 - 12.41: 3 12.41 - 16.55: 1 16.55 - 20.69: 1 Bond angle restraints: 34393 Sorted by residual: angle pdb=" C GLN A 575 " pdb=" CA GLN A 575 " pdb=" CB GLN A 575 " ideal model delta sigma weight residual 110.96 90.27 20.69 1.54e+00 4.22e-01 1.80e+02 angle pdb=" N ARG A 566 " pdb=" CA ARG A 566 " pdb=" C ARG A 566 " ideal model delta sigma weight residual 112.26 103.19 9.07 1.32e+00 5.74e-01 4.72e+01 angle pdb=" C ALA E 141 " pdb=" CA ALA E 141 " pdb=" CB ALA E 141 " ideal model delta sigma weight residual 116.54 110.02 6.52 1.15e+00 7.56e-01 3.22e+01 angle pdb=" C CYS H 576 " pdb=" N PRO H 577 " pdb=" CA PRO H 577 " ideal model delta sigma weight residual 119.84 126.69 -6.85 1.25e+00 6.40e-01 3.01e+01 angle pdb=" C CYS H 576 " pdb=" CA CYS H 576 " pdb=" CB CYS H 576 " ideal model delta sigma weight residual 109.82 118.83 -9.01 1.65e+00 3.67e-01 2.98e+01 ... (remaining 34388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13330 17.93 - 35.85: 944 35.85 - 53.78: 282 53.78 - 71.70: 59 71.70 - 89.63: 10 Dihedral angle restraints: 14625 sinusoidal: 4123 harmonic: 10502 Sorted by residual: dihedral pdb=" C GLN A 575 " pdb=" N GLN A 575 " pdb=" CA GLN A 575 " pdb=" CB GLN A 575 " ideal model delta harmonic sigma weight residual -122.60 -100.39 -22.21 0 2.50e+00 1.60e-01 7.89e+01 dihedral pdb=" CB CYS A 325 " pdb=" SG CYS A 325 " pdb=" SG CYS A 457 " pdb=" CB CYS A 457 " ideal model delta sinusoidal sigma weight residual 93.00 142.83 -49.83 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" C CYS H 576 " pdb=" N CYS H 576 " pdb=" CA CYS H 576 " pdb=" CB CYS H 576 " ideal model delta harmonic sigma weight residual -122.60 -133.71 11.11 0 2.50e+00 1.60e-01 1.98e+01 ... (remaining 14622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3499 0.069 - 0.139: 422 0.139 - 0.208: 6 0.208 - 0.277: 1 0.277 - 0.347: 1 Chirality restraints: 3929 Sorted by residual: chirality pdb=" CA GLN A 575 " pdb=" N GLN A 575 " pdb=" C GLN A 575 " pdb=" CB GLN A 575 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA CYS H 576 " pdb=" N CYS H 576 " pdb=" C CYS H 576 " pdb=" CB CYS H 576 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB THR A 344 " pdb=" CA THR A 344 " pdb=" OG1 THR A 344 " pdb=" CG2 THR A 344 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.57e-01 ... (remaining 3926 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 566 " -0.483 9.50e-02 1.11e+02 2.17e-01 2.87e+01 pdb=" NE ARG H 566 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG H 566 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG H 566 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 566 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 566 " 0.330 9.50e-02 1.11e+02 1.48e-01 1.37e+01 pdb=" NE ARG A 566 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 566 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 566 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 566 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 99 " 0.018 2.00e-02 2.50e+03 2.39e-02 9.96e+00 pdb=" CG PHE I 99 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE I 99 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE I 99 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE I 99 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 99 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE I 99 " -0.008 2.00e-02 2.50e+03 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2479 2.75 - 3.28: 24053 3.28 - 3.82: 40251 3.82 - 4.36: 42425 4.36 - 4.90: 75306 Nonbonded interactions: 184514 Sorted by model distance: nonbonded pdb=" OG1 THR I 523 " pdb=" O HIS I 561 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR K 46 " pdb=" O ASN K 128 " model vdw 2.210 3.040 nonbonded pdb=" NZ LYS C 332 " pdb=" O LYS C 335 " model vdw 2.211 3.120 nonbonded pdb=" O TRP K 49 " pdb=" OH TYR K 132 " model vdw 2.211 3.040 nonbonded pdb=" O SER I 662 " pdb=" OG SER I 662 " model vdw 2.217 3.040 ... (remaining 184509 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' selection = (chain 'H' and (resid 22 through 330 or (resid 331 and (name N or name CA or nam \ e C or name O or name CB )) or resid 332 through 807)) } ncs_group { reference = chain 'B' selection = (chain 'I' and (resid 80 through 138 or (resid 139 through 162 and (name N or na \ me CA or name C or name O or name CB )) or resid 163 through 689)) } ncs_group { reference = (chain 'C' and (resid 77 through 208 or (resid 209 through 210 and (name N or na \ me CA or name C or name O or name CB )) or resid 211 through 441)) selection = chain 'J' } ncs_group { reference = chain 'D' selection = (chain 'K' and (resid 3 through 203 or (resid 204 and (name N or name CA or name \ C or name O or name CB )) or resid 205 through 411)) } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'M' } 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=0.00 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: 2.030 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: 0.050 Set scattering table: 0.060 Process input model: 21.570 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4745 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25099 Z= 0.136 Angle : 0.685 54.611 34469 Z= 0.325 Chirality : 0.042 0.347 3929 Planarity : 0.005 0.217 4537 Dihedral : 14.772 89.628 7743 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.17 % Favored : 91.66 % Rotamer: Outliers : 2.18 % Allowed : 26.22 % Favored : 71.60 % Cbeta Deviations : 0.06 % 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: -1.21 (0.15), residues: 3502 helix: 1.70 (0.21), residues: 666 sheet: -1.46 (0.21), residues: 634 loop : -1.46 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 461 TYR 0.015 0.001 TYR I 643 PHE 0.054 0.001 PHE I 99 TRP 0.017 0.001 TRP J 314 HIS 0.010 0.001 HIS A 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (25041) covalent geometry : angle 0.55621 / 0.32 (34393) SS BOND : bond 0.00250 / 0.13 ( 2) SS BOND : angle 0.75418 / 0.88 ( 4) hydrogen bonds : bond 0.23206 / 19.19 ( 742) hydrogen bonds : angle 8.17538 / 6.34 ( 2037) metal coordination : bond 0.00843 / 0.81 ( 56) metal coordination : angle 8.75424 / 8.65 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 315 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.5937 (ppp) cc_final: 0.5689 (ppp) REVERT: A 285 PHE cc_start: 0.3738 (p90) cc_final: 0.3453 (p90) outliers start: 39 outliers final: 18 residues processed: 345 average time/residue: 0.1458 time to fit residues: 79.7229 Evaluate side-chains 243 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain K residue 277 ASN Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain J residue 356 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 9.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 620 HIS K 277 ASN ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.128194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.110445 restraints weight = 125671.210| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 5.17 r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4372 r_free = 0.4372 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4372 r_free = 0.4372 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.4372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 25099 Z= 0.216 Angle : 0.746 38.874 34469 Z= 0.355 Chirality : 0.045 0.223 3929 Planarity : 0.005 0.048 4537 Dihedral : 6.670 63.770 3914 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.11 % Favored : 89.75 % Rotamer: Outliers : 4.37 % Allowed : 23.81 % Favored : 71.82 % 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: -1.53 (0.14), residues: 3502 helix: 1.25 (0.20), residues: 674 sheet: -1.67 (0.20), residues: 640 loop : -1.61 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 461 TYR 0.022 0.002 TYR H 731 PHE 0.036 0.002 PHE A 474 TRP 0.030 0.002 TRP D 402 HIS 0.012 0.002 HIS B 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (25041) covalent geometry : angle 0.64978 / 0.35 (34393) SS BOND : bond 0.00417 / 0.21 ( 2) SS BOND : angle 3.72960 / 5.49 ( 4) hydrogen bonds : bond 0.05175 / 4.37 ( 742) hydrogen bonds : angle 6.79028 / 5.18 ( 2037) metal coordination : bond 0.01964 / 1.58 ( 56) metal coordination : angle 7.98263 / 7.66 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 239 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 TRP cc_start: 0.0817 (OUTLIER) cc_final: -0.4393 (p-90) REVERT: C 196 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7249 (tt) REVERT: C 271 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7664 (ppp) REVERT: C 332 LYS cc_start: 0.7689 (tptt) cc_final: 0.7405 (tptt) REVERT: I 117 TYR cc_start: 0.3477 (OUTLIER) cc_final: 0.0755 (t80) REVERT: I 661 VAL cc_start: 0.8838 (t) cc_final: 0.8554 (p) REVERT: J 414 ARG cc_start: 0.8319 (mmp-170) cc_final: 0.6573 (tpt170) outliers start: 78 outliers final: 37 residues processed: 296 average time/residue: 0.1418 time to fit residues: 68.1428 Evaluate side-chains 259 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 356 PHE Chi-restraints excluded: chain J residue 375 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 309 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 275 optimal weight: 40.0000 chunk 316 optimal weight: 40.0000 chunk 145 optimal weight: 4.9990 chunk 282 optimal weight: 20.0000 chunk 131 optimal weight: 6.9990 chunk 94 optimal weight: 0.0980 chunk 297 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 694 HIS D 78 HIS ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 ASN H 118 GLN ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 527 HIS I 655 ASN ** K 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.126748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.108865 restraints weight = 125917.895| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 5.11 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4336 r_free = 0.4336 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4336 r_free = 0.4336 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 25099 Z= 0.195 Angle : 0.708 45.913 34469 Z= 0.330 Chirality : 0.044 0.217 3929 Planarity : 0.004 0.045 4537 Dihedral : 6.658 63.834 3903 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.17 % Favored : 90.66 % Rotamer: Outliers : 4.65 % Allowed : 23.75 % Favored : 71.60 % 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: -1.69 (0.14), residues: 3502 helix: 1.18 (0.20), residues: 676 sheet: -1.73 (0.20), residues: 664 loop : -1.75 (0.13), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 150 TYR 0.042 0.002 TYR H 731 PHE 0.026 0.002 PHE I 99 TRP 0.014 0.002 TRP K 382 HIS 0.010 0.001 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (25041) covalent geometry : angle 0.60714 / 0.32 (34393) SS BOND : bond 0.00241 / 0.12 ( 2) SS BOND : angle 1.84066 / 2.93 ( 4) hydrogen bonds : bond 0.05067 / 4.27 ( 742) hydrogen bonds : angle 6.40256 / 4.89 ( 2037) metal coordination : bond 0.01808 / 1.45 ( 56) metal coordination : angle 7.96388 / 7.71 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 224 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 TRP cc_start: 0.0864 (OUTLIER) cc_final: -0.0156 (m-90) REVERT: A 729 PHE cc_start: 0.6912 (m-80) cc_final: 0.6046 (m-10) REVERT: B 113 ARG cc_start: 0.2621 (ttm170) cc_final: -0.1028 (tpt-90) REVERT: B 514 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.6389 (p90) REVERT: C 271 MET cc_start: 0.8021 (ppp) cc_final: 0.7678 (ppp) REVERT: C 332 LYS cc_start: 0.7713 (tptt) cc_final: 0.7463 (tptt) REVERT: C 369 SER cc_start: 0.6789 (m) cc_final: 0.6250 (p) REVERT: C 375 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8359 (mttp) REVERT: H 333 LEU cc_start: 0.4582 (mp) cc_final: 0.3993 (mt) REVERT: I 117 TYR cc_start: 0.3615 (OUTLIER) cc_final: 0.1063 (t80) outliers start: 83 outliers final: 55 residues processed: 293 average time/residue: 0.1481 time to fit residues: 70.9062 Evaluate side-chains 269 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 210 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 514 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 278 TYR Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 437 TRP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 598 THR Chi-restraints excluded: chain I residue 600 ILE Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 356 PHE Chi-restraints excluded: chain J residue 375 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 195 optimal weight: 3.9990 chunk 153 optimal weight: 0.3980 chunk 293 optimal weight: 7.9990 chunk 224 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 351 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 347 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 ASN ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 527 HIS K 192 HIS ** K 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.125756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.108578 restraints weight = 128543.098| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 5.12 r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4346 r_free = 0.4346 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4346 r_free = 0.4346 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5781 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25099 Z= 0.145 Angle : 0.645 37.732 34469 Z= 0.301 Chirality : 0.043 0.167 3929 Planarity : 0.004 0.044 4537 Dihedral : 6.606 63.823 3903 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.39 % Favored : 90.46 % Rotamer: Outliers : 5.21 % Allowed : 23.47 % Favored : 71.32 % 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: -1.62 (0.14), residues: 3502 helix: 1.35 (0.20), residues: 676 sheet: -1.70 (0.20), residues: 640 loop : -1.75 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 236 TYR 0.025 0.001 TYR H 731 PHE 0.019 0.001 PHE I 99 TRP 0.020 0.002 TRP J 389 HIS 0.007 0.001 HIS D 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (25041) covalent geometry : angle 0.56135 / 0.30 (34393) SS BOND : bond 0.01520 / 0.76 ( 2) SS BOND : angle 1.27139 / 1.94 ( 4) hydrogen bonds : bond 0.04113 / 3.49 ( 742) hydrogen bonds : angle 6.05172 / 4.62 ( 2037) metal coordination : bond 0.01372 / 1.13 ( 56) metal coordination : angle 6.98153 / 6.80 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 226 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 TRP cc_start: 0.1010 (OUTLIER) cc_final: -0.0051 (m-90) REVERT: A 457 CYS cc_start: 0.3628 (OUTLIER) cc_final: 0.3130 (p) REVERT: B 113 ARG cc_start: 0.2698 (ttm170) cc_final: -0.0745 (tpt-90) REVERT: D 25 LYS cc_start: 0.6307 (mttt) cc_final: 0.6007 (mttm) REVERT: C 213 HIS cc_start: 0.6965 (m-70) cc_final: 0.6743 (m-70) REVERT: C 271 MET cc_start: 0.8029 (ppp) cc_final: 0.7732 (ppp) REVERT: C 332 LYS cc_start: 0.7963 (tptt) cc_final: 0.7705 (tptt) REVERT: C 369 SER cc_start: 0.6906 (m) cc_final: 0.6472 (p) REVERT: H 333 LEU cc_start: 0.4970 (mp) cc_final: 0.4441 (mt) REVERT: I 117 TYR cc_start: 0.3148 (OUTLIER) cc_final: 0.0557 (t80) REVERT: I 661 VAL cc_start: 0.8857 (t) cc_final: 0.8588 (p) REVERT: K 409 TYR cc_start: 0.5960 (OUTLIER) cc_final: 0.5214 (t80) outliers start: 93 outliers final: 59 residues processed: 303 average time/residue: 0.1281 time to fit residues: 64.6307 Evaluate side-chains 277 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 214 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 278 TYR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 437 TRP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 192 HIS Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 345 TRP Chi-restraints excluded: chain K residue 409 TYR Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 283 ASN Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 356 PHE Chi-restraints excluded: chain J residue 389 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 168 optimal weight: 10.0000 chunk 316 optimal weight: 0.2980 chunk 61 optimal weight: 0.1980 chunk 347 optimal weight: 0.0970 chunk 34 optimal weight: 0.0670 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 109 optimal weight: 0.0000 overall best weight: 0.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 HIS D 343 ASN C 221 GLN ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 HIS K 370 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.127684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.110715 restraints weight = 128492.705| |-----------------------------------------------------------------------------| r_work (start): 0.4394 rms_B_bonded: 5.17 r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4394 r_free = 0.4394 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4394 r_free = 0.4394 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5689 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25099 Z= 0.107 Angle : 0.602 29.677 34469 Z= 0.283 Chirality : 0.042 0.150 3929 Planarity : 0.004 0.038 4537 Dihedral : 6.460 63.800 3903 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.05 % Favored : 91.83 % Rotamer: Outliers : 3.75 % Allowed : 25.21 % Favored : 71.04 % 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: -1.40 (0.14), residues: 3502 helix: 1.63 (0.21), residues: 668 sheet: -1.42 (0.20), residues: 666 loop : -1.67 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 150 TYR 0.026 0.001 TYR H 731 PHE 0.024 0.001 PHE I 86 TRP 0.043 0.002 TRP D 402 HIS 0.021 0.001 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (25041) covalent geometry : angle 0.53396 / 0.28 (34393) SS BOND : bond 0.00650 / 0.32 ( 2) SS BOND : angle 0.82724 / 0.96 ( 4) hydrogen bonds : bond 0.03592 / 3.03 ( 742) hydrogen bonds : angle 5.70331 / 4.36 ( 2037) metal coordination : bond 0.00764 / 0.78 ( 56) metal coordination : angle 6.12203 / 6.08 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 231 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 TRP cc_start: 0.0675 (OUTLIER) cc_final: -0.0178 (m-90) REVERT: B 113 ARG cc_start: 0.2565 (ttm170) cc_final: -0.0471 (ttt90) REVERT: D 25 LYS cc_start: 0.6186 (mttt) cc_final: 0.5902 (mttp) REVERT: C 271 MET cc_start: 0.8040 (ppp) cc_final: 0.7816 (ppp) REVERT: C 369 SER cc_start: 0.6961 (m) cc_final: 0.6673 (p) REVERT: H 110 MET cc_start: 0.7076 (ppp) cc_final: 0.6582 (ppp) REVERT: H 293 ASP cc_start: 0.7950 (t0) cc_final: 0.7709 (t0) REVERT: H 333 LEU cc_start: 0.4876 (mp) cc_final: 0.4376 (mt) REVERT: I 117 TYR cc_start: 0.2512 (OUTLIER) cc_final: -0.0096 (t80) REVERT: I 661 VAL cc_start: 0.8837 (t) cc_final: 0.8573 (p) REVERT: K 409 TYR cc_start: 0.5936 (OUTLIER) cc_final: 0.5185 (t80) REVERT: M 268 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.6650 (t70) outliers start: 67 outliers final: 48 residues processed: 285 average time/residue: 0.1306 time to fit residues: 63.2368 Evaluate side-chains 265 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 282 HIS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 614 MET Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 278 TYR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 437 TRP Chi-restraints excluded: chain H residue 621 LEU Chi-restraints excluded: chain H residue 715 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 248 TYR Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 192 HIS Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 345 TRP Chi-restraints excluded: chain K residue 409 TYR Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 283 ASN Chi-restraints excluded: chain J residue 356 PHE Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain J residue 389 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 54 optimal weight: 40.0000 chunk 93 optimal weight: 0.0980 chunk 53 optimal weight: 50.0000 chunk 291 optimal weight: 20.0000 chunk 299 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 HIS ** B 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS D 27 ASN ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 HIS D 343 ASN ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 685 GLN K 343 ASN J 326 ASN J 381 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.123704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.106858 restraints weight = 125652.004| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 5.49 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4292 r_free = 0.4292 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4294 r_free = 0.4294 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.4294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 25099 Z= 0.215 Angle : 0.710 39.364 34469 Z= 0.341 Chirality : 0.045 0.276 3929 Planarity : 0.005 0.049 4537 Dihedral : 6.720 63.847 3902 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.91 % Favored : 89.92 % Rotamer: Outliers : 5.55 % Allowed : 24.54 % Favored : 69.92 % 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: -1.72 (0.14), residues: 3502 helix: 1.05 (0.20), residues: 678 sheet: -1.61 (0.19), residues: 704 loop : -1.78 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 236 TYR 0.020 0.002 TYR B 495 PHE 0.040 0.002 PHE B 476 TRP 0.080 0.003 TRP D 345 HIS 0.035 0.002 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (25041) covalent geometry : angle 0.62880 / 0.34 (34393) SS BOND : bond 0.00663 / 0.33 ( 2) SS BOND : angle 0.88486 / 0.92 ( 4) hydrogen bonds : bond 0.04646 / 3.90 ( 742) hydrogen bonds : angle 6.08976 / 4.68 ( 2037) metal coordination : bond 0.02086 / 1.61 ( 56) metal coordination : angle 7.25159 / 7.29 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 210 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.6498 (ppp) cc_final: 0.6194 (ppp) REVERT: A 437 TRP cc_start: 0.1463 (OUTLIER) cc_final: 0.0016 (m-90) REVERT: A 457 CYS cc_start: 0.3342 (OUTLIER) cc_final: 0.2866 (p) REVERT: A 550 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5378 (pttm) REVERT: B 113 ARG cc_start: 0.3162 (ttm170) cc_final: 0.0229 (ttt90) REVERT: B 587 LYS cc_start: 0.5424 (tptp) cc_final: 0.4660 (mptt) REVERT: D 25 LYS cc_start: 0.6467 (mttt) cc_final: 0.6168 (mttp) REVERT: C 244 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6853 (m-80) REVERT: C 252 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5442 (tpt) REVERT: C 271 MET cc_start: 0.8136 (ppp) cc_final: 0.7865 (ppp) REVERT: C 332 LYS cc_start: 0.8069 (tptt) cc_final: 0.7694 (tptt) REVERT: C 369 SER cc_start: 0.7084 (m) cc_final: 0.6685 (p) REVERT: H 83 CYS cc_start: 0.7976 (p) cc_final: 0.7757 (t) REVERT: H 333 LEU cc_start: 0.5278 (mp) cc_final: 0.4829 (mt) REVERT: H 615 SER cc_start: 0.5215 (OUTLIER) cc_final: 0.4951 (m) REVERT: I 117 TYR cc_start: 0.3236 (OUTLIER) cc_final: 0.0730 (t80) REVERT: I 595 LYS cc_start: 0.3378 (OUTLIER) cc_final: 0.2981 (tttt) REVERT: I 643 TYR cc_start: 0.4763 (m-80) cc_final: 0.4553 (m-80) REVERT: K 195 SER cc_start: 0.6291 (OUTLIER) cc_final: 0.5931 (p) REVERT: K 409 TYR cc_start: 0.6027 (OUTLIER) cc_final: 0.5445 (t80) outliers start: 99 outliers final: 64 residues processed: 300 average time/residue: 0.1337 time to fit residues: 66.9949 Evaluate side-chains 276 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 202 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 437 TRP Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 449 HIS Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 595 LYS Chi-restraints excluded: chain I residue 600 ILE Chi-restraints excluded: chain I residue 639 PHE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 192 HIS Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 345 TRP Chi-restraints excluded: chain K residue 409 TYR Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 237 ASP Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 356 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 334 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 351 optimal weight: 7.9990 chunk 331 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 HIS D 64 HIS ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 HIS D 272 HIS ** F 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 HIS I 126 ASN ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.120678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.103488 restraints weight = 120980.184| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 5.19 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4240 r_free = 0.4240 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4241 r_free = 0.4241 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (17 function evaluations) r_final: 0.4241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 25099 Z= 0.276 Angle : 0.834 49.503 34469 Z= 0.404 Chirality : 0.047 0.225 3929 Planarity : 0.006 0.051 4537 Dihedral : 7.235 63.876 3900 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.82 % Favored : 87.98 % Rotamer: Outliers : 6.44 % Allowed : 24.15 % Favored : 69.41 % 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: -2.30 (0.14), residues: 3502 helix: 0.47 (0.20), residues: 652 sheet: -1.74 (0.20), residues: 654 loop : -2.20 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG E 150 TYR 0.026 0.003 TYR I 499 PHE 0.063 0.003 PHE I 86 TRP 0.063 0.003 TRP D 345 HIS 0.034 0.002 HIS I 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.27 (25041) covalent geometry : angle 0.73387 / 0.40 (34393) SS BOND : bond 0.00652 / 0.33 ( 2) SS BOND : angle 0.81922 / 0.94 ( 4) hydrogen bonds : bond 0.05560 / 4.59 ( 742) hydrogen bonds : angle 6.68628 / 5.13 ( 2037) metal coordination : bond 0.02374 / 1.85 ( 56) metal coordination : angle 8.69150 / 8.47 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 220 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6789 (tt0) REVERT: A 437 TRP cc_start: 0.1702 (OUTLIER) cc_final: -0.0109 (m-90) REVERT: A 457 CYS cc_start: 0.3900 (OUTLIER) cc_final: 0.3450 (p) REVERT: A 530 HIS cc_start: 0.3386 (p90) cc_final: 0.3177 (p90) REVERT: B 113 ARG cc_start: 0.3705 (ttm170) cc_final: 0.1006 (tpt-90) REVERT: B 514 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7153 (p90) REVERT: B 587 LYS cc_start: 0.5982 (tptp) cc_final: 0.5356 (mptt) REVERT: C 101 PHE cc_start: 0.6542 (OUTLIER) cc_final: 0.5137 (t80) REVERT: C 236 ARG cc_start: 0.4846 (mmp-170) cc_final: 0.3765 (mtm180) REVERT: C 244 TYR cc_start: 0.7577 (OUTLIER) cc_final: 0.7041 (m-80) REVERT: C 252 MET cc_start: 0.6090 (OUTLIER) cc_final: 0.5620 (tpt) REVERT: C 271 MET cc_start: 0.8130 (ppp) cc_final: 0.7855 (ppp) REVERT: C 293 LYS cc_start: 0.7970 (mptt) cc_final: 0.7677 (mptt) REVERT: C 358 TYR cc_start: 0.1256 (OUTLIER) cc_final: 0.0367 (p90) REVERT: C 369 SER cc_start: 0.7221 (m) cc_final: 0.6765 (p) REVERT: H 110 MET cc_start: 0.7328 (ppp) cc_final: 0.6314 (ppp) REVERT: H 333 LEU cc_start: 0.5709 (mp) cc_final: 0.5367 (mt) REVERT: I 595 LYS cc_start: 0.3560 (OUTLIER) cc_final: 0.3175 (tttt) REVERT: K 409 TYR cc_start: 0.5885 (OUTLIER) cc_final: 0.5455 (t80) REVERT: J 438 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7427 (m-30) outliers start: 115 outliers final: 81 residues processed: 312 average time/residue: 0.1310 time to fit residues: 68.4916 Evaluate side-chains 299 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 208 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 83 HIS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 514 PHE Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 630 ASN Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 437 TRP Chi-restraints excluded: chain H residue 582 VAL Chi-restraints excluded: chain H residue 611 ILE Chi-restraints excluded: chain H residue 729 PHE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 449 HIS Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 595 LYS Chi-restraints excluded: chain I residue 598 THR Chi-restraints excluded: chain I residue 600 ILE Chi-restraints excluded: chain I residue 663 MET Chi-restraints excluded: chain I residue 667 ASN Chi-restraints excluded: chain I residue 688 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 345 TRP Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 409 TYR Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 283 ASN Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 356 PHE Chi-restraints excluded: chain J residue 402 THR Chi-restraints excluded: chain J residue 438 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 316 optimal weight: 0.8980 chunk 216 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 228 optimal weight: 8.9990 chunk 312 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 274 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 302 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 HIS D 200 HIS ** D 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 GLN ** C 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.122859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.106044 restraints weight = 121364.430| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 5.17 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4293 r_free = 0.4293 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4293 r_free = 0.4293 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25099 Z= 0.153 Angle : 0.705 41.098 34469 Z= 0.329 Chirality : 0.044 0.212 3929 Planarity : 0.004 0.045 4537 Dihedral : 6.865 63.841 3898 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.71 % Favored : 90.09 % Rotamer: Outliers : 4.59 % Allowed : 26.61 % Favored : 68.80 % 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: -2.05 (0.14), residues: 3502 helix: 0.75 (0.20), residues: 676 sheet: -1.64 (0.20), residues: 666 loop : -2.07 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 52 TYR 0.026 0.002 TYR H 731 PHE 0.020 0.002 PHE I 86 TRP 0.055 0.002 TRP H 599 HIS 0.017 0.001 HIS B 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (25041) covalent geometry : angle 0.61622 / 0.32 (34393) SS BOND : bond 0.00783 / 0.39 ( 2) SS BOND : angle 0.99599 / 1.46 ( 4) hydrogen bonds : bond 0.04353 / 3.65 ( 742) hydrogen bonds : angle 6.28651 / 4.86 ( 2037) metal coordination : bond 0.01389 / 1.15 ( 56) metal coordination : angle 7.49633 / 7.25 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 212 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.6163 (ppp) cc_final: 0.5880 (ppp) REVERT: A 437 TRP cc_start: 0.1476 (OUTLIER) cc_final: 0.0049 (m-90) REVERT: A 457 CYS cc_start: 0.3788 (OUTLIER) cc_final: 0.3381 (p) REVERT: A 530 HIS cc_start: 0.3343 (p90) cc_final: 0.3083 (p90) REVERT: A 550 LYS cc_start: 0.6133 (OUTLIER) cc_final: 0.5456 (pttm) REVERT: B 113 ARG cc_start: 0.3351 (ttm170) cc_final: 0.0424 (tpt-90) REVERT: B 514 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7003 (p90) REVERT: B 572 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7077 (mm) REVERT: B 587 LYS cc_start: 0.6193 (tptp) cc_final: 0.5873 (mptt) REVERT: C 101 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.5020 (t80) REVERT: C 244 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6959 (m-80) REVERT: C 252 MET cc_start: 0.5899 (OUTLIER) cc_final: 0.5224 (tpt) REVERT: C 271 MET cc_start: 0.8058 (ppp) cc_final: 0.7794 (ppp) REVERT: C 293 LYS cc_start: 0.7953 (mptt) cc_final: 0.7703 (mptt) REVERT: C 358 TYR cc_start: 0.1169 (OUTLIER) cc_final: 0.0419 (p90) REVERT: C 369 SER cc_start: 0.7123 (m) cc_final: 0.6874 (p) REVERT: H 293 ASP cc_start: 0.8386 (t0) cc_final: 0.8116 (t0) REVERT: H 333 LEU cc_start: 0.5723 (mp) cc_final: 0.5404 (mt) REVERT: K 409 TYR cc_start: 0.5795 (OUTLIER) cc_final: 0.5341 (t80) REVERT: J 438 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7116 (m-30) outliers start: 82 outliers final: 59 residues processed: 278 average time/residue: 0.1285 time to fit residues: 59.7356 Evaluate side-chains 282 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 212 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 83 HIS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 514 PHE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 278 TYR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 437 TRP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 449 HIS Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 598 THR Chi-restraints excluded: chain I residue 688 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 345 TRP Chi-restraints excluded: chain K residue 409 TYR Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain J residue 80 TYR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 283 ASN Chi-restraints excluded: chain J residue 438 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 6 optimal weight: 50.0000 chunk 322 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 317 optimal weight: 9.9990 chunk 237 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 53 optimal weight: 40.0000 chunk 273 optimal weight: 20.0000 chunk 159 optimal weight: 7.9990 chunk 282 optimal weight: 50.0000 chunk 188 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS D 200 HIS ** D 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.121705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.104880 restraints weight = 120568.430| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 5.18 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 25099 Z= 0.190 Angle : 0.731 42.824 34469 Z= 0.344 Chirality : 0.044 0.175 3929 Planarity : 0.005 0.063 4537 Dihedral : 6.857 63.853 3896 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.88 % Favored : 88.92 % Rotamer: Outliers : 4.71 % Allowed : 26.72 % Favored : 68.57 % 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: -2.10 (0.14), residues: 3502 helix: 0.71 (0.20), residues: 676 sheet: -1.65 (0.20), residues: 666 loop : -2.10 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 522 TYR 0.020 0.002 TYR B 495 PHE 0.022 0.002 PHE D 108 TRP 0.039 0.002 TRP D 345 HIS 0.009 0.001 HIS B 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (25041) covalent geometry : angle 0.64216 / 0.34 (34393) SS BOND : bond 0.00565 / 0.28 ( 2) SS BOND : angle 1.11404 / 1.53 ( 4) hydrogen bonds : bond 0.04625 / 3.88 ( 742) hydrogen bonds : angle 6.24237 / 4.81 ( 2037) metal coordination : bond 0.01788 / 1.40 ( 56) metal coordination : angle 7.65856 / 7.58 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 208 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 TRP cc_start: 0.1718 (OUTLIER) cc_final: 0.0237 (m-90) REVERT: A 457 CYS cc_start: 0.3869 (OUTLIER) cc_final: 0.3400 (p) REVERT: A 530 HIS cc_start: 0.3456 (p90) cc_final: 0.3121 (p90) REVERT: A 550 LYS cc_start: 0.6094 (OUTLIER) cc_final: 0.5394 (pttm) REVERT: B 113 ARG cc_start: 0.3493 (ttm170) cc_final: 0.0723 (ttt90) REVERT: B 474 PHE cc_start: 0.4865 (OUTLIER) cc_final: 0.4653 (p90) REVERT: B 514 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7113 (p90) REVERT: D 25 LYS cc_start: 0.6280 (mttt) cc_final: 0.6068 (mttp) REVERT: C 101 PHE cc_start: 0.6455 (OUTLIER) cc_final: 0.5075 (t80) REVERT: C 244 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6851 (m-80) REVERT: C 252 MET cc_start: 0.5883 (OUTLIER) cc_final: 0.5405 (tpt) REVERT: C 271 MET cc_start: 0.7940 (ppp) cc_final: 0.7690 (ppp) REVERT: C 293 LYS cc_start: 0.7933 (mptt) cc_final: 0.7691 (mptt) REVERT: C 358 TYR cc_start: 0.1207 (OUTLIER) cc_final: 0.0427 (p90) REVERT: C 369 SER cc_start: 0.7138 (m) cc_final: 0.6906 (p) REVERT: H 293 ASP cc_start: 0.8349 (t0) cc_final: 0.8073 (t0) REVERT: H 333 LEU cc_start: 0.5762 (mp) cc_final: 0.5450 (mt) REVERT: I 595 LYS cc_start: 0.3525 (OUTLIER) cc_final: 0.3116 (tttt) REVERT: K 409 TYR cc_start: 0.5811 (OUTLIER) cc_final: 0.5434 (t80) REVERT: J 438 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7218 (m-30) outliers start: 84 outliers final: 63 residues processed: 276 average time/residue: 0.1336 time to fit residues: 61.2903 Evaluate side-chains 281 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 206 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 514 PHE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 437 TRP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 449 HIS Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 595 LYS Chi-restraints excluded: chain I residue 598 THR Chi-restraints excluded: chain I residue 656 PHE Chi-restraints excluded: chain I residue 688 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 345 TRP Chi-restraints excluded: chain K residue 409 TYR Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain J residue 80 TYR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 356 PHE Chi-restraints excluded: chain J residue 402 THR Chi-restraints excluded: chain J residue 438 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 35 optimal weight: 0.7980 chunk 308 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 328 optimal weight: 9.9990 chunk 187 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 291 optimal weight: 30.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 HIS D 200 HIS ** D 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.122893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.106203 restraints weight = 120112.049| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 5.18 r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5924 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25099 Z= 0.143 Angle : 0.676 37.331 34469 Z= 0.318 Chirality : 0.043 0.203 3929 Planarity : 0.004 0.043 4537 Dihedral : 6.724 63.835 3896 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.25 % Favored : 90.58 % Rotamer: Outliers : 4.03 % Allowed : 27.68 % Favored : 68.29 % 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: -1.96 (0.14), residues: 3502 helix: 0.90 (0.20), residues: 678 sheet: -1.59 (0.20), residues: 664 loop : -2.03 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 52 TYR 0.022 0.002 TYR H 731 PHE 0.021 0.002 PHE I 86 TRP 0.034 0.002 TRP D 345 HIS 0.007 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (25041) covalent geometry : angle 0.59713 / 0.31 (34393) SS BOND : bond 0.00626 / 0.31 ( 2) SS BOND : angle 0.95248 / 1.29 ( 4) hydrogen bonds : bond 0.04076 / 3.41 ( 742) hydrogen bonds : angle 6.02811 / 4.66 ( 2037) metal coordination : bond 0.01327 / 1.09 ( 56) metal coordination : angle 6.94968 / 6.90 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 209 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 CYS cc_start: 0.7828 (t) cc_final: 0.7570 (t) REVERT: A 110 MET cc_start: 0.6110 (ppp) cc_final: 0.5863 (ppp) REVERT: A 437 TRP cc_start: 0.1666 (OUTLIER) cc_final: 0.0363 (m-90) REVERT: A 457 CYS cc_start: 0.3805 (OUTLIER) cc_final: 0.3377 (p) REVERT: A 550 LYS cc_start: 0.5984 (OUTLIER) cc_final: 0.5319 (pttm) REVERT: B 113 ARG cc_start: 0.3263 (ttm170) cc_final: 0.0472 (ttt90) REVERT: B 474 PHE cc_start: 0.4842 (OUTLIER) cc_final: 0.4577 (p90) REVERT: C 101 PHE cc_start: 0.6441 (OUTLIER) cc_final: 0.5074 (t80) REVERT: C 213 HIS cc_start: 0.6362 (m-70) cc_final: 0.5939 (t-90) REVERT: C 220 ILE cc_start: 0.6223 (OUTLIER) cc_final: 0.5929 (mp) REVERT: C 236 ARG cc_start: 0.5101 (mmp-170) cc_final: 0.4821 (mmp80) REVERT: C 252 MET cc_start: 0.5854 (OUTLIER) cc_final: 0.5196 (tpt) REVERT: C 271 MET cc_start: 0.7928 (ppp) cc_final: 0.7672 (ppp) REVERT: C 293 LYS cc_start: 0.7972 (mptt) cc_final: 0.7736 (mptt) REVERT: C 358 TYR cc_start: 0.1285 (OUTLIER) cc_final: 0.0524 (p90) REVERT: H 293 ASP cc_start: 0.8267 (t0) cc_final: 0.7990 (t0) REVERT: H 333 LEU cc_start: 0.5796 (mp) cc_final: 0.5508 (mt) REVERT: H 545 GLN cc_start: 0.8768 (tp40) cc_final: 0.8498 (tp40) REVERT: I 661 VAL cc_start: 0.8871 (t) cc_final: 0.8571 (p) REVERT: K 409 TYR cc_start: 0.5667 (OUTLIER) cc_final: 0.5287 (t80) REVERT: J 438 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7074 (m-30) outliers start: 72 outliers final: 59 residues processed: 271 average time/residue: 0.1205 time to fit residues: 55.3225 Evaluate side-chains 273 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 316 HIS Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 358 TYR Chi-restraints excluded: chain C residue 364 TRP Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 437 TRP Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 117 TYR Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 449 HIS Chi-restraints excluded: chain I residue 466 HIS Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 583 SER Chi-restraints excluded: chain I residue 598 THR Chi-restraints excluded: chain I residue 656 PHE Chi-restraints excluded: chain I residue 688 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 345 TRP Chi-restraints excluded: chain K residue 409 TYR Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 268 HIS Chi-restraints excluded: chain J residue 80 TYR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 283 ASN Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain J residue 402 THR Chi-restraints excluded: chain J residue 438 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 327 optimal weight: 0.9980 chunk 295 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 234 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 291 optimal weight: 0.2980 chunk 237 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 HIS D 272 HIS ** C 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.122343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.105552 restraints weight = 120962.694| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 5.18 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25099 Z= 0.156 Angle : 0.686 37.979 34469 Z= 0.322 Chirality : 0.044 0.184 3929 Planarity : 0.004 0.044 4537 Dihedral : 6.694 63.836 3896 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.68 % Favored : 89.12 % Rotamer: Outliers : 4.43 % Allowed : 27.28 % Favored : 68.29 % 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: -1.95 (0.14), residues: 3502 helix: 0.89 (0.20), residues: 678 sheet: -1.49 (0.20), residues: 668 loop : -2.06 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 52 TYR 0.018 0.002 TYR B 495 PHE 0.024 0.002 PHE A 285 TRP 0.035 0.002 TRP D 345 HIS 0.008 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (25041) covalent geometry : angle 0.60780 / 0.32 (34393) SS BOND : bond 0.00517 / 0.26 ( 2) SS BOND : angle 1.00980 / 1.28 ( 4) hydrogen bonds : bond 0.04161 / 3.48 ( 742) hydrogen bonds : angle 5.93002 / 4.60 ( 2037) metal coordination : bond 0.01500 / 1.21 ( 56) metal coordination : angle 6.96672 / 6.99 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6952.02 seconds wall clock time: 119 minutes 6.53 seconds (7146.53 seconds total)