Starting phenix.real_space_refine on Sat Aug 8 09:36:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yl3_73071/08_2026/9yl3_73071.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yl3_73071/08_2026/9yl3_73071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yl3_73071/08_2026/9yl3_73071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yl3_73071/08_2026/9yl3_73071.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yl3_73071/08_2026/9yl3_73071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yl3_73071/08_2026/9yl3_73071.map" } resolution = 3.5 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 119 5.16 5 C 15865 2.51 5 N 4767 2.21 5 O 5672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26713 Number of models: 1 Model: "" Number of chains: 27 Chain: "K" Number of atoms: 5517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5517 Classifications: {'peptide': 693} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 661} Chain breaks: 2 Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "F" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "N" Number of atoms: 2922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2922 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 2 Chain: "T" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2397 Classifications: {'peptide': 297} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 273} Chain: "P" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 372 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 5, 'TRANS': 41} Chain: "Q" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2326 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "G" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "J" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.18, per 1000 atoms: 0.16 Number of scatterers: 26713 At special positions: 0 Unit cell: (148.78, 165.98, 202.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 119 16.00 P 290 15.00 O 5672 8.00 N 4767 7.00 C 15865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.51 Conformation dependent library (CDL) restraints added in 603.5 milliseconds 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4868 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 36 sheets defined 33.0% alpha, 15.1% beta 145 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'K' and resid 1414 through 1421 removed outlier: 4.083A pdb=" N LEU K1418 " --> pdb=" O THR K1414 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU K1419 " --> pdb=" O LYS K1415 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS K1420 " --> pdb=" O VAL K1416 " (cutoff:3.500A) Processing helix chain 'K' and resid 1424 through 1428 Processing helix chain 'K' and resid 1438 through 1440 No H-bonds generated for 'chain 'K' and resid 1438 through 1440' Processing helix chain 'K' and resid 1498 through 1506 removed outlier: 3.724A pdb=" N LEU K1504 " --> pdb=" O PRO K1500 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL K1505 " --> pdb=" O CYS K1501 " (cutoff:3.500A) Processing helix chain 'K' and resid 1533 through 1535 No H-bonds generated for 'chain 'K' and resid 1533 through 1535' Processing helix chain 'K' and resid 1539 through 1549 Processing helix chain 'K' and resid 5007 through 5017 Processing helix chain 'K' and resid 5060 through 5065 removed outlier: 3.675A pdb=" N TRP K5065 " --> pdb=" O ASN K5061 " (cutoff:3.500A) Processing helix chain 'K' and resid 5079 through 5088 removed outlier: 3.605A pdb=" N LEU K5088 " --> pdb=" O LEU K5084 " (cutoff:3.500A) Processing helix chain 'K' and resid 5114 through 5121 removed outlier: 3.571A pdb=" N ARG K5120 " --> pdb=" O ALA K5116 " (cutoff:3.500A) Processing helix chain 'K' and resid 5160 through 5172 removed outlier: 3.994A pdb=" N ARG K5171 " --> pdb=" O SER K5167 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY K5172 " --> pdb=" O ILE K5168 " (cutoff:3.500A) Processing helix chain 'K' and resid 5192 through 5198 removed outlier: 3.731A pdb=" N MET K5196 " --> pdb=" O PRO K5193 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA K5197 " --> pdb=" O HIS K5194 " (cutoff:3.500A) Processing helix chain 'K' and resid 5259 through 5277 removed outlier: 3.706A pdb=" N ARG K5266 " --> pdb=" O ALA K5262 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE K5267 " --> pdb=" O VAL K5263 " (cutoff:3.500A) Proline residue: K5270 - end of helix removed outlier: 4.594A pdb=" N GLU K5277 " --> pdb=" O ALA K5273 " (cutoff:3.500A) Processing helix chain 'K' and resid 5284 through 5288 Processing helix chain 'K' and resid 5289 through 5294 Processing helix chain 'K' and resid 5298 through 5308 Processing helix chain 'K' and resid 5324 through 5328 Processing helix chain 'K' and resid 5383 through 5398 removed outlier: 3.957A pdb=" N ARG K5392 " --> pdb=" O TYR K5388 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N THR K5393 " --> pdb=" O ARG K5389 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP K5395 " --> pdb=" O LEU K5391 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS K5396 " --> pdb=" O ARG K5392 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN K5397 " --> pdb=" O THR K5393 " (cutoff:3.500A) Processing helix chain 'K' and resid 5433 through 5446 removed outlier: 3.860A pdb=" N LYS K5441 " --> pdb=" O ASN K5437 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE K5442 " --> pdb=" O ARG K5438 " (cutoff:3.500A) Processing helix chain 'K' and resid 5468 through 5472 Processing helix chain 'O' and resid 22 through 34 removed outlier: 3.661A pdb=" N VAL O 26 " --> pdb=" O THR O 22 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 41 removed outlier: 3.793A pdb=" N GLN O 40 " --> pdb=" O PRO O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.509A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.553A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.527A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.766A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.525A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.729A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.799A pdb=" N TYR B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.632A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 37 removed outlier: 3.652A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.915A pdb=" N GLU C 61 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 66 " --> pdb=" O ILE C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.646A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.605A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 47 removed outlier: 3.542A pdb=" N LYS D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.521A pdb=" N GLY D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.978A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.586A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.584A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.839A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.845A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.899A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.010A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.690A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.523A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 47 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.691A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR H 83 " --> pdb=" O ARG H 79 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.611A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.882A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 153 removed outlier: 3.516A pdb=" N LEU N 153 " --> pdb=" O ASP N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 234 removed outlier: 3.612A pdb=" N LEU N 231 " --> pdb=" O GLY N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 329 through 333 Processing helix chain 'T' and resid 354 through 358 Processing helix chain 'T' and resid 369 through 371 No H-bonds generated for 'chain 'T' and resid 369 through 371' Processing helix chain 'T' and resid 496 through 500 Processing helix chain 'T' and resid 525 through 533 removed outlier: 3.645A pdb=" N ALA T 529 " --> pdb=" O PHE T 525 " (cutoff:3.500A) Processing helix chain 'T' and resid 593 through 619 removed outlier: 3.536A pdb=" N MET T 597 " --> pdb=" O PRO T 593 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TRP T 599 " --> pdb=" O SER T 595 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY T 600 " --> pdb=" O ASP T 596 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL T 602 " --> pdb=" O GLY T 598 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP T 619 " --> pdb=" O GLU T 615 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 61 removed outlier: 3.902A pdb=" N THR P 60 " --> pdb=" O TYR P 56 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 75 Processing helix chain 'P' and resid 81 through 91 removed outlier: 3.830A pdb=" N ALA P 85 " --> pdb=" O ILE P 81 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN P 91 " --> pdb=" O TYR P 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 69 removed outlier: 4.377A pdb=" N ASP Q 58 " --> pdb=" O ARG Q 54 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR Q 60 " --> pdb=" O TYR Q 56 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL Q 62 " --> pdb=" O ASP Q 58 " (cutoff:3.500A) Proline residue: Q 63 - end of helix removed outlier: 3.753A pdb=" N GLN Q 67 " --> pdb=" O PRO Q 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 86 removed outlier: 4.009A pdb=" N ALA Q 85 " --> pdb=" O GLU Q 82 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER Q 86 " --> pdb=" O PHE Q 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 1442 through 1444 Processing sheet with id=AA2, first strand: chain 'K' and resid 1520 through 1522 Processing sheet with id=AA3, first strand: chain 'K' and resid 5049 through 5053 removed outlier: 3.571A pdb=" N LEU K5052 " --> pdb=" O LEU K5056 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU K5056 " --> pdb=" O LEU K5052 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 5076 through 5077 Processing sheet with id=AA5, first strand: chain 'K' and resid 5102 through 5103 removed outlier: 3.567A pdb=" N TYR K5113 " --> pdb=" O SER K5102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 5124 through 5126 removed outlier: 4.237A pdb=" N MET K5124 " --> pdb=" O LEU K5132 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR K5130 " --> pdb=" O PHE K5126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 5179 through 5180 Processing sheet with id=AA8, first strand: chain 'K' and resid 5211 through 5217 removed outlier: 3.589A pdb=" N ALA K5212 " --> pdb=" O CYS K5230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 5399 through 5403 Processing sheet with id=AB1, first strand: chain 'K' and resid 5422 through 5426 removed outlier: 6.929A pdb=" N MET K5422 " --> pdb=" O SER K5498 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER K5498 " --> pdb=" O MET K5422 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE K5424 " --> pdb=" O ILE K5496 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE K5494 " --> pdb=" O TYR K5426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 5430 through 5432 removed outlier: 3.630A pdb=" N ILE K5431 " --> pdb=" O VAL K5460 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS K5459 " --> pdb=" O ILE K5455 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE K5455 " --> pdb=" O HIS K5459 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 12 through 16 removed outlier: 8.863A pdb=" N LEU O 67 " --> pdb=" O GLN O 2 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE O 4 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU O 69 " --> pdb=" O PHE O 4 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS O 6 " --> pdb=" O LEU O 69 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS O 68 " --> pdb=" O ILE O 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.957A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AB6, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB8, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.843A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AC1, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.526A pdb=" N ILE G 78 " --> pdb=" O GLY H 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'N' and resid 20 through 21 removed outlier: 3.829A pdb=" N VAL N 318 " --> pdb=" O LEU N 21 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP N 300 " --> pdb=" O ILE N 313 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 38 through 41 removed outlier: 3.646A pdb=" N LEU N 39 " --> pdb=" O TRP N 51 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLY N 46 " --> pdb=" O ALA N 64 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE N 62 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS N 60 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP N 52 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE N 58 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 69 through 74 removed outlier: 4.083A pdb=" N SER N 71 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE N 89 " --> pdb=" O SER N 85 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 110 through 116 removed outlier: 4.243A pdb=" N LYS N 112 " --> pdb=" O CYS N 126 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS N 122 " --> pdb=" O HIS N 116 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL N 143 " --> pdb=" O MET N 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 155 through 159 removed outlier: 3.598A pdb=" N VAL N 156 " --> pdb=" O GLY N 169 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN N 170 " --> pdb=" O LYS N 174 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS N 174 " --> pdb=" O ASN N 170 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS N 179 " --> pdb=" O LEU N 185 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU N 185 " --> pdb=" O LYS N 179 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 201 through 206 removed outlier: 7.051A pdb=" N ASN N 216 " --> pdb=" O LYS N 202 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE N 204 " --> pdb=" O LEU N 214 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU N 214 " --> pdb=" O ILE N 204 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N PHE N 206 " --> pdb=" O CYS N 212 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N CYS N 212 " --> pdb=" O PHE N 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN N 243 " --> pdb=" O VAL N 224 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 254 through 259 removed outlier: 6.679A pdb=" N GLY N 269 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYS N 257 " --> pdb=" O VAL N 267 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL N 267 " --> pdb=" O CYS N 257 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE N 259 " --> pdb=" O TYR N 265 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR N 265 " --> pdb=" O PHE N 259 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA N 275 " --> pdb=" O SER N 270 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS N 288 " --> pdb=" O ILE N 278 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLU N 280 " --> pdb=" O LEU N 286 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU N 286 " --> pdb=" O GLU N 280 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'T' and resid 373 through 375 removed outlier: 3.797A pdb=" N ILE T 344 " --> pdb=" O PHE T 520 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU T 518 " --> pdb=" O ALA T 346 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'T' and resid 393 through 394 removed outlier: 3.789A pdb=" N LYS T 393 " --> pdb=" O VAL T 402 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL T 402 " --> pdb=" O LYS T 393 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL T 401 " --> pdb=" O VAL T 574 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL T 574 " --> pdb=" O VAL T 401 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN T 491 " --> pdb=" O GLU T 540 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU T 540 " --> pdb=" O ASN T 491 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE T 541 " --> pdb=" O VAL T 552 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL T 552 " --> pdb=" O ILE T 541 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N PHE T 543 " --> pdb=" O GLN T 550 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL T 548 " --> pdb=" O LYS T 545 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'T' and resid 408 through 411 removed outlier: 3.598A pdb=" N SER T 408 " --> pdb=" O LEU T 568 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU T 568 " --> pdb=" O SER T 408 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE T 566 " --> pdb=" O VAL T 410 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS T 474 " --> pdb=" O LYS T 467 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 36 through 41 removed outlier: 6.107A pdb=" N LEU R 37 " --> pdb=" O LYS R 331 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS R 331 " --> pdb=" O LEU R 37 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE R 39 " --> pdb=" O LEU R 329 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 50 through 52 removed outlier: 3.581A pdb=" N LYS R 70 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS R 81 " --> pdb=" O ILE R 71 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLY R 73 " --> pdb=" O PHE R 79 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE R 79 " --> pdb=" O GLY R 73 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 90 through 95 removed outlier: 3.700A pdb=" N VAL R 103 " --> pdb=" O ALA R 94 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS R 112 " --> pdb=" O SER R 104 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER R 106 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THR R 110 " --> pdb=" O SER R 106 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS R 123 " --> pdb=" O ILE R 113 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ASP R 115 " --> pdb=" O CYS R 121 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N CYS R 121 " --> pdb=" O ASP R 115 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 132 through 137 removed outlier: 3.560A pdb=" N CYS R 134 " --> pdb=" O GLY R 147 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG R 154 " --> pdb=" O SER R 146 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 185 through 189 removed outlier: 3.533A pdb=" N ARG R 196 " --> pdb=" O SER R 188 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS R 195 " --> pdb=" O THR R 208 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR R 208 " --> pdb=" O CYS R 195 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE R 197 " --> pdb=" O LEU R 206 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 217 through 219 removed outlier: 3.655A pdb=" N PHE R 219 " --> pdb=" O ALA R 232 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR R 233 " --> pdb=" O THR R 237 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR R 237 " --> pdb=" O THR R 233 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS R 250 " --> pdb=" O LEU R 240 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 264 through 267 removed outlier: 7.084A pdb=" N VAL R 283 " --> pdb=" O LYS R 296 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS R 296 " --> pdb=" O VAL R 283 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE R 285 " --> pdb=" O VAL R 294 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 6.62 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7310 1.33 - 1.46: 6191 1.46 - 1.58: 13464 1.58 - 1.70: 578 1.70 - 1.82: 159 Bond restraints: 27702 Sorted by residual: bond pdb=" N GLU P 75 " pdb=" CA GLU P 75 " ideal model delta sigma weight residual 1.460 1.489 -0.029 8.20e-03 1.49e+04 1.21e+01 bond pdb=" C1' DC I 26 " pdb=" N1 DC I 26 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.17e+01 bond pdb=" C3' DC J 126 " pdb=" C2' DC J 126 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C1' DT I 87 " pdb=" N1 DT I 87 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.90e+00 bond pdb=" C1' DT I 68 " pdb=" N1 DT I 68 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.28e+00 ... (remaining 27697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 36973 1.46 - 2.92: 1467 2.92 - 4.39: 258 4.39 - 5.85: 17 5.85 - 7.31: 3 Bond angle restraints: 38718 Sorted by residual: angle pdb=" N PHE N 386 " pdb=" CA PHE N 386 " pdb=" C PHE N 386 " ideal model delta sigma weight residual 113.02 105.71 7.31 1.20e+00 6.94e-01 3.71e+01 angle pdb=" CA ASP N 390 " pdb=" C ASP N 390 " pdb=" O ASP N 390 " ideal model delta sigma weight residual 121.10 116.20 4.90 1.10e+00 8.26e-01 1.99e+01 angle pdb=" N3 DT J 79 " pdb=" C4 DT J 79 " pdb=" O4 DT J 79 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 68 " pdb=" C4 DT I 68 " pdb=" O4 DT I 68 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 38713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.38: 14094 32.38 - 64.75: 1751 64.75 - 97.13: 62 97.13 - 129.51: 1 129.51 - 161.88: 3 Dihedral angle restraints: 15911 sinusoidal: 8361 harmonic: 7550 Sorted by residual: dihedral pdb=" CA TYR N 13 " pdb=" C TYR N 13 " pdb=" N PRO N 14 " pdb=" CA PRO N 14 " ideal model delta harmonic sigma weight residual -180.00 -157.39 -22.61 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA PRO C 26 " pdb=" C PRO C 26 " pdb=" N VAL C 27 " pdb=" CA VAL C 27 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 58.12 161.88 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 15908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3084 0.037 - 0.074: 671 0.074 - 0.111: 238 0.111 - 0.148: 254 0.148 - 0.185: 70 Chirality restraints: 4317 Sorted by residual: chirality pdb=" C3' DG J 82 " pdb=" C4' DG J 82 " pdb=" O3' DG J 82 " pdb=" C2' DG J 82 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" C3' DG I 71 " pdb=" C4' DG I 71 " pdb=" O3' DG I 71 " pdb=" C2' DG I 71 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" C3' DC J 54 " pdb=" C4' DC J 54 " pdb=" O3' DC J 54 " pdb=" C2' DC J 54 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.04e-01 ... (remaining 4314 not shown) Planarity restraints: 3934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 76 " -0.260 9.50e-02 1.11e+02 1.16e-01 8.33e+00 pdb=" NE ARG P 76 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG P 76 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG P 76 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG P 76 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS P 74 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C LYS P 74 " -0.049 2.00e-02 2.50e+03 pdb=" O LYS P 74 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU P 75 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 61 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" CD GLU C 61 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU C 61 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU C 61 " -0.013 2.00e-02 2.50e+03 ... (remaining 3931 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6005 2.79 - 3.32: 25891 3.32 - 3.85: 46707 3.85 - 4.37: 54266 4.37 - 4.90: 84103 Nonbonded interactions: 216972 Sorted by model distance: nonbonded pdb=" O ASP E 81 " pdb=" OD1 ASP E 81 " model vdw 2.263 3.040 nonbonded pdb=" O TYR C 57 " pdb=" OE1 GLU C 61 " model vdw 2.381 3.040 nonbonded pdb=" O ASN H 67 " pdb=" OE1 GLU H 71 " model vdw 2.409 3.040 nonbonded pdb=" N GLN N 273 " pdb=" OE1 GLN N 273 " model vdw 2.411 3.120 nonbonded pdb=" O ASN D 67 " pdb=" OE1 GLU D 71 " model vdw 2.422 3.040 ... (remaining 216967 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 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 19 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } ncs_group { reference = (chain 'P' and resid 52 through 96) selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.140 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.440 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27702 Z= 0.355 Angle : 0.639 7.310 38718 Z= 0.503 Chirality : 0.051 0.185 4317 Planarity : 0.004 0.116 3934 Dihedral : 22.601 161.883 11043 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.54 % Favored : 94.19 % Rotamer: Outliers : 1.65 % Allowed : 18.94 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.97 (0.16), residues: 2564 helix: -0.76 (0.19), residues: 738 sheet: -1.82 (0.25), residues: 395 loop : -1.42 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.025 0.001 TYR D 40 PHE 0.006 0.001 PHE P 95 TRP 0.007 0.001 TRP N 279 HIS 0.004 0.001 HIS T 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.36 (27702) covalent geometry : angle 0.63884 / 0.50 (38718) hydrogen bonds : bond 0.23106 / 15.60 ( 1051) hydrogen bonds : angle 8.28714 / 5.78 ( 2637) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 1478 MET cc_start: 0.5605 (pmm) cc_final: 0.4741 (mpp) REVERT: K 5177 MET cc_start: -0.0010 (ppp) cc_final: -0.0416 (ppp) REVERT: K 5274 MET cc_start: 0.2762 (ptt) cc_final: 0.0100 (mtt) REVERT: O 11 LYS cc_start: 0.7753 (tmtt) cc_final: 0.7492 (tmtt) REVERT: O 20 SER cc_start: 0.7541 (t) cc_final: 0.7318 (p) REVERT: B 52 GLU cc_start: 0.8477 (tp30) cc_final: 0.8165 (tp30) REVERT: C 91 GLU cc_start: 0.8621 (pm20) cc_final: 0.7988 (mm-30) REVERT: E 48 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8630 (tt) REVERT: N 13 TYR cc_start: 0.6465 (OUTLIER) cc_final: 0.4915 (m-80) REVERT: N 135 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8165 (mm) REVERT: P 54 ARG cc_start: 0.1499 (mtp180) cc_final: 0.0753 (mtm-85) REVERT: P 75 GLU cc_start: 0.4653 (OUTLIER) cc_final: 0.4287 (tt0) REVERT: Q 69 LEU cc_start: 0.7064 (pp) cc_final: 0.6827 (pp) REVERT: R 53 PHE cc_start: 0.6386 (OUTLIER) cc_final: 0.4815 (m-80) outliers start: 37 outliers final: 27 residues processed: 163 average time/residue: 0.1665 time to fit residues: 42.8711 Evaluate side-chains 147 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1385 SER Chi-restraints excluded: chain K residue 5130 THR Chi-restraints excluded: chain K residue 5338 CYS Chi-restraints excluded: chain K residue 5386 SER Chi-restraints excluded: chain K residue 5482 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain N residue 13 TYR Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 381 ASP Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain T residue 572 CYS Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 121 CYS Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain R residue 266 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1393 HIS K5059 HIS K5111 ASN K5194 HIS K5526 HIS O 40 GLN O 60 ASN E 85 GLN N 142 HIS ** T 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 577 ASN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 314 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.103117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.067716 restraints weight = 116372.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.068044 restraints weight = 67017.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.068050 restraints weight = 45299.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.068120 restraints weight = 38480.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.068162 restraints weight = 38901.566| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27702 Z= 0.222 Angle : 0.677 9.653 38718 Z= 0.380 Chirality : 0.046 0.345 4317 Planarity : 0.005 0.064 3934 Dihedral : 24.755 160.241 6072 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.54 % Favored : 94.31 % Rotamer: Outliers : 3.48 % Allowed : 19.38 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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 (0.16), residues: 2564 helix: -0.30 (0.18), residues: 770 sheet: -1.34 (0.25), residues: 394 loop : -1.57 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K5432 TYR 0.022 0.002 TYR D 40 PHE 0.013 0.002 PHE D 70 TRP 0.026 0.002 TRP K1491 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (27702) covalent geometry : angle 0.67715 / 0.38 (38718) hydrogen bonds : bond 0.06924 / 4.62 ( 1051) hydrogen bonds : angle 5.63658 / 3.92 ( 2637) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 130 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 1478 MET cc_start: 0.6059 (pmm) cc_final: 0.5172 (mpp) REVERT: K 5177 MET cc_start: -0.0694 (ppp) cc_final: -0.0966 (ppp) REVERT: K 5274 MET cc_start: 0.2739 (ptt) cc_final: 0.0263 (mtt) REVERT: K 5332 MET cc_start: 0.5510 (mpp) cc_final: 0.5243 (mpp) REVERT: O 11 LYS cc_start: 0.8111 (tmtt) cc_final: 0.7807 (tptt) REVERT: O 20 SER cc_start: 0.8260 (t) cc_final: 0.7918 (p) REVERT: O 71 LEU cc_start: 0.9141 (mp) cc_final: 0.8638 (mp) REVERT: A 94 GLU cc_start: 0.8003 (tp30) cc_final: 0.7615 (tp30) REVERT: B 52 GLU cc_start: 0.8282 (tp30) cc_final: 0.8058 (tp30) REVERT: C 91 GLU cc_start: 0.8390 (pm20) cc_final: 0.7965 (mm-30) REVERT: D 80 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9181 (tt) REVERT: N 13 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.5145 (m-80) REVERT: N 324 ASN cc_start: 0.7387 (OUTLIER) cc_final: 0.6393 (t0) REVERT: N 401 TYR cc_start: 0.6844 (t80) cc_final: 0.6613 (t80) REVERT: T 597 MET cc_start: 0.6734 (mmm) cc_final: 0.6299 (tpp) REVERT: P 54 ARG cc_start: 0.3100 (mtp180) cc_final: 0.1967 (mtm-85) REVERT: R 53 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.5075 (m-80) REVERT: R 92 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6341 (m-30) outliers start: 78 outliers final: 41 residues processed: 198 average time/residue: 0.1556 time to fit residues: 49.6168 Evaluate side-chains 159 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5058 VAL Chi-restraints excluded: chain K residue 5103 SER Chi-restraints excluded: chain K residue 5130 THR Chi-restraints excluded: chain K residue 5194 HIS Chi-restraints excluded: chain K residue 5338 CYS Chi-restraints excluded: chain K residue 5386 SER Chi-restraints excluded: chain K residue 5464 THR Chi-restraints excluded: chain K residue 5482 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain N residue 13 TYR Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 192 THR Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 324 ASN Chi-restraints excluded: chain T residue 571 SER Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 266 PHE Chi-restraints excluded: chain R residue 318 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 8 optimal weight: 7.9990 chunk 196 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 chunk 144 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 267 optimal weight: 20.0000 chunk 79 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1497 HIS K5164 GLN O 40 GLN A 108 ASN ** T 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 ASN ** 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 = 0.4169 r_free = 0.4169 target = 0.102610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.066982 restraints weight = 115967.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.067888 restraints weight = 65783.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.067589 restraints weight = 47236.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067587 restraints weight = 39660.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067599 restraints weight = 39856.650| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27702 Z= 0.226 Angle : 0.652 9.381 38718 Z= 0.363 Chirality : 0.046 0.328 4317 Planarity : 0.004 0.050 3934 Dihedral : 24.996 160.782 6042 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.01 % Favored : 93.88 % Rotamer: Outliers : 4.02 % Allowed : 19.52 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.59 (0.16), residues: 2564 helix: -0.11 (0.18), residues: 767 sheet: -1.17 (0.25), residues: 392 loop : -1.57 (0.15), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.027 0.002 TYR K5206 PHE 0.015 0.002 PHE T 520 TRP 0.021 0.001 TRP K1491 HIS 0.017 0.001 HIS K5194 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (27702) covalent geometry : angle 0.65173 / 0.36 (38718) hydrogen bonds : bond 0.06364 / 4.21 ( 1051) hydrogen bonds : angle 5.26153 / 3.63 ( 2637) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 117 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 1478 MET cc_start: 0.5960 (pmm) cc_final: 0.5181 (mpp) REVERT: K 5055 ASP cc_start: 0.1447 (OUTLIER) cc_final: 0.0671 (t0) REVERT: K 5093 SER cc_start: 0.1379 (OUTLIER) cc_final: 0.0714 (t) REVERT: K 5274 MET cc_start: 0.2957 (ptt) cc_final: 0.0484 (mtt) REVERT: K 5332 MET cc_start: 0.5584 (OUTLIER) cc_final: 0.5300 (mpp) REVERT: K 5459 HIS cc_start: 0.8738 (OUTLIER) cc_final: 0.8363 (t70) REVERT: K 5485 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8383 (t) REVERT: O 11 LYS cc_start: 0.8167 (tmtt) cc_final: 0.7863 (tmtt) REVERT: O 18 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8576 (tm-30) REVERT: O 20 SER cc_start: 0.8354 (t) cc_final: 0.8115 (p) REVERT: O 71 LEU cc_start: 0.9095 (mp) cc_final: 0.8645 (mt) REVERT: A 94 GLU cc_start: 0.7969 (tp30) cc_final: 0.7561 (tp30) REVERT: C 91 GLU cc_start: 0.8388 (pm20) cc_final: 0.8017 (mm-30) REVERT: D 80 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9175 (tt) REVERT: N 13 TYR cc_start: 0.6979 (OUTLIER) cc_final: 0.5579 (m-80) REVERT: N 183 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8182 (mp10) REVERT: N 324 ASN cc_start: 0.7464 (OUTLIER) cc_final: 0.6479 (t0) REVERT: T 576 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7840 (mp) REVERT: T 597 MET cc_start: 0.7037 (mmm) cc_final: 0.6741 (tpp) REVERT: P 54 ARG cc_start: 0.3168 (mtp180) cc_final: 0.2523 (mtm180) REVERT: R 53 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.5241 (m-80) outliers start: 90 outliers final: 51 residues processed: 198 average time/residue: 0.1618 time to fit residues: 51.6307 Evaluate side-chains 173 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 111 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1375 LEU Chi-restraints excluded: chain K residue 5055 ASP Chi-restraints excluded: chain K residue 5058 VAL Chi-restraints excluded: chain K residue 5093 SER Chi-restraints excluded: chain K residue 5103 SER Chi-restraints excluded: chain K residue 5130 THR Chi-restraints excluded: chain K residue 5332 MET Chi-restraints excluded: chain K residue 5338 CYS Chi-restraints excluded: chain K residue 5386 SER Chi-restraints excluded: chain K residue 5455 ILE Chi-restraints excluded: chain K residue 5459 HIS Chi-restraints excluded: chain K residue 5464 THR Chi-restraints excluded: chain K residue 5482 VAL Chi-restraints excluded: chain K residue 5485 VAL Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain N residue 13 TYR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 183 GLN Chi-restraints excluded: chain N residue 192 THR Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 324 ASN Chi-restraints excluded: chain T residue 572 CYS Chi-restraints excluded: chain T residue 576 ILE Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 266 PHE Chi-restraints excluded: chain R residue 318 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 127 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 262 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 195 optimal weight: 0.0170 chunk 42 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 25 ASN O 40 GLN E 93 GLN ** T 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 469 HIS T 605 HIS R 225 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.103843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.069106 restraints weight = 115668.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.069765 restraints weight = 65088.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.069332 restraints weight = 41399.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.069586 restraints weight = 38875.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.069556 restraints weight = 37220.668| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27702 Z= 0.134 Angle : 0.589 11.476 38718 Z= 0.331 Chirality : 0.044 0.353 4317 Planarity : 0.004 0.049 3934 Dihedral : 24.969 158.072 6040 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 3.44 % Allowed : 20.41 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.32 (0.16), residues: 2564 helix: 0.27 (0.19), residues: 768 sheet: -1.00 (0.25), residues: 401 loop : -1.51 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.018 0.001 TYR K5206 PHE 0.012 0.001 PHE K5241 TRP 0.013 0.001 TRP K1491 HIS 0.022 0.001 HIS K5059 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (27702) covalent geometry : angle 0.58854 / 0.33 (38718) hydrogen bonds : bond 0.05031 / 3.34 ( 1051) hydrogen bonds : angle 4.72963 / 3.26 ( 2637) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 132 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: K 1478 MET cc_start: 0.5891 (pmm) cc_final: 0.5179 (mpp) REVERT: K 5055 ASP cc_start: 0.1407 (OUTLIER) cc_final: 0.0660 (t0) REVERT: K 5093 SER cc_start: 0.1195 (OUTLIER) cc_final: 0.0546 (t) REVERT: K 5274 MET cc_start: 0.3014 (ptt) cc_final: 0.0602 (mtt) REVERT: K 5332 MET cc_start: 0.5953 (OUTLIER) cc_final: 0.5633 (mpp) REVERT: O 2 GLN cc_start: 0.9167 (tt0) cc_final: 0.8419 (tp40) REVERT: O 11 LYS cc_start: 0.8136 (tmtt) cc_final: 0.7839 (tmtt) REVERT: O 16 GLU cc_start: 0.8654 (tp30) cc_final: 0.8310 (mp0) REVERT: O 18 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8537 (tm-30) REVERT: O 25 ASN cc_start: 0.7934 (m110) cc_final: 0.7678 (t0) REVERT: O 71 LEU cc_start: 0.9107 (mp) cc_final: 0.8638 (mt) REVERT: A 94 GLU cc_start: 0.7931 (tp30) cc_final: 0.7450 (tp30) REVERT: C 91 GLU cc_start: 0.8270 (pm20) cc_final: 0.7897 (mm-30) REVERT: H 35 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8063 (mm-30) REVERT: N 13 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.5155 (m-80) REVERT: N 53 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: N 183 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8165 (mp10) REVERT: N 324 ASN cc_start: 0.7368 (OUTLIER) cc_final: 0.6674 (t0) REVERT: T 576 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7797 (mp) REVERT: T 597 MET cc_start: 0.7238 (mmm) cc_final: 0.6918 (tpp) REVERT: P 54 ARG cc_start: 0.3071 (mtp180) cc_final: 0.2098 (mtm-85) REVERT: R 53 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.4979 (m-80) outliers start: 77 outliers final: 42 residues processed: 198 average time/residue: 0.1622 time to fit residues: 51.6063 Evaluate side-chains 167 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1375 LEU Chi-restraints excluded: chain K residue 5055 ASP Chi-restraints excluded: chain K residue 5058 VAL Chi-restraints excluded: chain K residue 5093 SER Chi-restraints excluded: chain K residue 5103 SER Chi-restraints excluded: chain K residue 5130 THR Chi-restraints excluded: chain K residue 5332 MET Chi-restraints excluded: chain K residue 5338 CYS Chi-restraints excluded: chain K residue 5386 SER Chi-restraints excluded: chain K residue 5399 VAL Chi-restraints excluded: chain K residue 5464 THR Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain N residue 13 TYR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 183 GLN Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 324 ASN Chi-restraints excluded: chain T residue 572 CYS Chi-restraints excluded: chain T residue 576 ILE Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 266 PHE Chi-restraints excluded: chain R residue 318 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 254 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 228 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 200 optimal weight: 0.0020 chunk 230 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 overall best weight: 3.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 HIS ** T 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.102315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.066431 restraints weight = 112709.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.067316 restraints weight = 63650.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.067007 restraints weight = 41658.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.067070 restraints weight = 40193.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.067122 restraints weight = 37467.086| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 27702 Z= 0.267 Angle : 0.687 11.232 38718 Z= 0.373 Chirality : 0.047 0.325 4317 Planarity : 0.005 0.046 3934 Dihedral : 25.275 159.721 6037 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.40 % Favored : 93.49 % Rotamer: Outliers : 4.42 % Allowed : 20.95 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.45 (0.16), residues: 2564 helix: 0.09 (0.19), residues: 765 sheet: -0.89 (0.25), residues: 388 loop : -1.61 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 74 TYR 0.018 0.002 TYR T 506 PHE 0.018 0.002 PHE A 67 TRP 0.010 0.001 TRP R 156 HIS 0.006 0.001 HIS T 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.27 (27702) covalent geometry : angle 0.68726 / 0.37 (38718) hydrogen bonds : bond 0.06335 / 4.19 ( 1051) hydrogen bonds : angle 4.93338 / 3.40 ( 2637) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 120 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: K 1478 MET cc_start: 0.5753 (pmm) cc_final: 0.5032 (mpp) REVERT: K 5055 ASP cc_start: 0.1438 (OUTLIER) cc_final: 0.0608 (t0) REVERT: K 5093 SER cc_start: 0.1573 (OUTLIER) cc_final: 0.0843 (t) REVERT: K 5274 MET cc_start: 0.2897 (ptt) cc_final: 0.0431 (mtt) REVERT: K 5332 MET cc_start: 0.5696 (OUTLIER) cc_final: 0.5416 (mpp) REVERT: O 11 LYS cc_start: 0.8208 (tmtt) cc_final: 0.7882 (tptt) REVERT: O 29 LYS cc_start: 0.6177 (OUTLIER) cc_final: 0.5943 (ptpp) REVERT: O 71 LEU cc_start: 0.9160 (mp) cc_final: 0.8683 (mt) REVERT: A 94 GLU cc_start: 0.8050 (tp30) cc_final: 0.7515 (tp30) REVERT: C 91 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8029 (mm-30) REVERT: E 59 GLU cc_start: 0.8214 (pm20) cc_final: 0.7872 (pm20) REVERT: N 13 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.5997 (m-80) REVERT: N 53 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: N 183 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8246 (mp10) REVERT: N 324 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.6742 (t0) REVERT: N 359 LYS cc_start: -0.3542 (OUTLIER) cc_final: -0.3844 (mtmm) REVERT: T 576 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7846 (mp) REVERT: T 597 MET cc_start: 0.7436 (mmm) cc_final: 0.7174 (tpp) REVERT: P 54 ARG cc_start: 0.3322 (mtp180) cc_final: 0.2604 (mtm180) REVERT: Q 79 ASN cc_start: 0.0773 (OUTLIER) cc_final: 0.0524 (m-40) REVERT: R 53 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.5523 (m-80) outliers start: 99 outliers final: 65 residues processed: 204 average time/residue: 0.1457 time to fit residues: 48.1242 Evaluate side-chains 189 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 111 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1375 LEU Chi-restraints excluded: chain K residue 5055 ASP Chi-restraints excluded: chain K residue 5058 VAL Chi-restraints excluded: chain K residue 5093 SER Chi-restraints excluded: chain K residue 5103 SER Chi-restraints excluded: chain K residue 5130 THR Chi-restraints excluded: chain K residue 5332 MET Chi-restraints excluded: chain K residue 5338 CYS Chi-restraints excluded: chain K residue 5386 SER Chi-restraints excluded: chain K residue 5399 VAL Chi-restraints excluded: chain K residue 5464 THR Chi-restraints excluded: chain K residue 5476 SER Chi-restraints excluded: chain K residue 5482 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 29 LYS Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain N residue 13 TYR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 183 GLN Chi-restraints excluded: chain N residue 192 THR Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 324 ASN Chi-restraints excluded: chain N residue 359 LYS Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain T residue 572 CYS Chi-restraints excluded: chain T residue 576 ILE Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain Q residue 79 ASN Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 266 PHE Chi-restraints excluded: chain R residue 318 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 168 optimal weight: 0.0010 chunk 195 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 11 optimal weight: 50.0000 chunk 229 optimal weight: 20.0000 chunk 189 optimal weight: 0.9980 chunk 264 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 448 GLN T 469 HIS ** R 86 HIS ** 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 = 0.4193 r_free = 0.4193 target = 0.103687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.068267 restraints weight = 112702.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.069764 restraints weight = 60661.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.068365 restraints weight = 40037.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.068969 restraints weight = 39945.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.068999 restraints weight = 32878.824| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27702 Z= 0.140 Angle : 0.595 11.910 38718 Z= 0.330 Chirality : 0.044 0.353 4317 Planarity : 0.004 0.048 3934 Dihedral : 25.121 156.455 6037 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.07 % Favored : 94.81 % Rotamer: Outliers : 3.62 % Allowed : 21.62 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.24 (0.16), residues: 2564 helix: 0.40 (0.19), residues: 762 sheet: -0.98 (0.25), residues: 403 loop : -1.49 (0.15), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 40 TYR 0.018 0.001 TYR D 40 PHE 0.016 0.001 PHE T 520 TRP 0.013 0.001 TRP R 286 HIS 0.006 0.001 HIS T 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (27702) covalent geometry : angle 0.59480 / 0.33 (38718) hydrogen bonds : bond 0.04819 / 3.21 ( 1051) hydrogen bonds : angle 4.51642 / 3.11 ( 2637) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 123 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: K 1478 MET cc_start: 0.5683 (pmm) cc_final: 0.5002 (mpp) REVERT: K 5055 ASP cc_start: 0.1428 (OUTLIER) cc_final: 0.0597 (t0) REVERT: K 5059 HIS cc_start: 0.3980 (OUTLIER) cc_final: 0.3687 (t-170) REVERT: K 5093 SER cc_start: 0.1603 (OUTLIER) cc_final: 0.0909 (t) REVERT: K 5274 MET cc_start: 0.2973 (ptt) cc_final: 0.0560 (mtt) REVERT: K 5332 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5967 (mpp) REVERT: O 11 LYS cc_start: 0.8192 (tmtt) cc_final: 0.7857 (tptt) REVERT: O 29 LYS cc_start: 0.6108 (OUTLIER) cc_final: 0.5876 (ptpp) REVERT: O 71 LEU cc_start: 0.9117 (mp) cc_final: 0.8651 (mt) REVERT: A 94 GLU cc_start: 0.7960 (tp30) cc_final: 0.7475 (tp30) REVERT: C 34 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8935 (mp) REVERT: C 91 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7894 (mm-30) REVERT: F 92 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7135 (tpp-160) REVERT: H 33 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.5960 (mtm-85) REVERT: N 13 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.5849 (m-80) REVERT: N 53 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: N 183 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8145 (mp10) REVERT: N 324 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.6682 (t0) REVERT: T 339 ASP cc_start: 0.8316 (t0) cc_final: 0.7928 (m-30) REVERT: T 576 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7806 (mp) REVERT: P 54 ARG cc_start: 0.3154 (mtp180) cc_final: 0.2115 (mtm-85) REVERT: Q 79 ASN cc_start: 0.0823 (OUTLIER) cc_final: 0.0548 (m-40) REVERT: R 53 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.5040 (m-80) outliers start: 81 outliers final: 52 residues processed: 192 average time/residue: 0.1741 time to fit residues: 53.3120 Evaluate side-chains 185 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 117 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1375 LEU Chi-restraints excluded: chain K residue 5055 ASP Chi-restraints excluded: chain K residue 5058 VAL Chi-restraints excluded: chain K residue 5059 HIS Chi-restraints excluded: chain K residue 5093 SER Chi-restraints excluded: chain K residue 5103 SER Chi-restraints excluded: chain K residue 5130 THR Chi-restraints excluded: chain K residue 5332 MET Chi-restraints excluded: chain K residue 5338 CYS Chi-restraints excluded: chain K residue 5386 SER Chi-restraints excluded: chain K residue 5464 THR Chi-restraints excluded: chain K residue 5482 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 29 LYS Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain N residue 13 TYR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 183 GLN Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 324 ASN Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain T residue 333 GLU Chi-restraints excluded: chain T residue 576 ILE Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain Q residue 79 ASN Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 266 PHE Chi-restraints excluded: chain R residue 318 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 268 optimal weight: 20.0000 chunk 230 optimal weight: 5.9990 chunk 66 optimal weight: 0.0870 chunk 212 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 165 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 278 optimal weight: 20.0000 chunk 251 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 overall best weight: 2.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1492 GLN K1525 HIS ** R 86 HIS ** 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 = 0.4175 r_free = 0.4175 target = 0.102628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.066977 restraints weight = 111739.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.067840 restraints weight = 62117.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.068386 restraints weight = 38101.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.067820 restraints weight = 40799.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.067939 restraints weight = 36221.742| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27702 Z= 0.212 Angle : 0.647 11.726 38718 Z= 0.350 Chirality : 0.045 0.335 4317 Planarity : 0.004 0.049 3934 Dihedral : 25.281 157.573 6035 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.36 % Favored : 93.53 % Rotamer: Outliers : 4.02 % Allowed : 22.20 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.30 (0.16), residues: 2564 helix: 0.29 (0.19), residues: 762 sheet: -0.99 (0.25), residues: 398 loop : -1.50 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 74 TYR 0.014 0.002 TYR T 612 PHE 0.015 0.001 PHE T 520 TRP 0.009 0.001 TRP R 156 HIS 0.006 0.001 HIS T 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (27702) covalent geometry : angle 0.64743 / 0.35 (38718) hydrogen bonds : bond 0.05522 / 3.65 ( 1051) hydrogen bonds : angle 4.57382 / 3.14 ( 2637) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 119 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 1478 MET cc_start: 0.5682 (pmm) cc_final: 0.4982 (mpp) REVERT: K 5055 ASP cc_start: 0.1520 (OUTLIER) cc_final: 0.0645 (t0) REVERT: K 5059 HIS cc_start: 0.3962 (OUTLIER) cc_final: 0.3638 (t-170) REVERT: K 5093 SER cc_start: 0.1522 (OUTLIER) cc_final: 0.0772 (t) REVERT: K 5274 MET cc_start: 0.2842 (ptt) cc_final: 0.0332 (mtt) REVERT: K 5332 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5919 (mpp) REVERT: O 11 LYS cc_start: 0.8282 (tmtt) cc_final: 0.7940 (tptt) REVERT: O 29 LYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5849 (ptpp) REVERT: O 71 LEU cc_start: 0.9153 (mp) cc_final: 0.8672 (mt) REVERT: A 94 GLU cc_start: 0.7983 (tp30) cc_final: 0.7459 (tp30) REVERT: C 34 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9025 (mp) REVERT: C 91 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7995 (mm-30) REVERT: E 59 GLU cc_start: 0.8193 (pm20) cc_final: 0.7711 (pm20) REVERT: F 92 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7177 (tpp-160) REVERT: H 101 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8217 (mp) REVERT: N 13 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.5402 (m-80) REVERT: N 53 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: N 183 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8209 (mp10) REVERT: N 324 ASN cc_start: 0.7340 (OUTLIER) cc_final: 0.6649 (t0) REVERT: T 597 MET cc_start: 0.7847 (tpp) cc_final: 0.7621 (tpp) REVERT: P 54 ARG cc_start: 0.3199 (mtp180) cc_final: 0.2102 (mtm-85) REVERT: Q 79 ASN cc_start: 0.1091 (OUTLIER) cc_final: 0.0881 (m-40) REVERT: R 53 PHE cc_start: 0.6862 (OUTLIER) cc_final: 0.5336 (m-80) outliers start: 90 outliers final: 57 residues processed: 195 average time/residue: 0.1611 time to fit residues: 50.1029 Evaluate side-chains 185 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 113 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1375 LEU Chi-restraints excluded: chain K residue 5055 ASP Chi-restraints excluded: chain K residue 5058 VAL Chi-restraints excluded: chain K residue 5059 HIS Chi-restraints excluded: chain K residue 5093 SER Chi-restraints excluded: chain K residue 5103 SER Chi-restraints excluded: chain K residue 5130 THR Chi-restraints excluded: chain K residue 5332 MET Chi-restraints excluded: chain K residue 5338 CYS Chi-restraints excluded: chain K residue 5386 SER Chi-restraints excluded: chain K residue 5464 THR Chi-restraints excluded: chain K residue 5476 SER Chi-restraints excluded: chain K residue 5482 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 29 LYS Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain N residue 13 TYR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 183 GLN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 324 ASN Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain T residue 333 GLU Chi-restraints excluded: chain T residue 572 CYS Chi-restraints excluded: chain Q residue 79 ASN Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 266 PHE Chi-restraints excluded: chain R residue 318 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 184 optimal weight: 0.7980 chunk 203 optimal weight: 0.0020 chunk 37 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 94 optimal weight: 0.0970 chunk 267 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 174 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.104278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.068731 restraints weight = 112463.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.069183 restraints weight = 57386.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.069123 restraints weight = 42022.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.069433 restraints weight = 32648.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.069419 restraints weight = 30484.672| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27702 Z= 0.122 Angle : 0.591 11.943 38718 Z= 0.325 Chirality : 0.043 0.358 4317 Planarity : 0.004 0.050 3934 Dihedral : 25.100 154.487 6035 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.80 % Favored : 95.09 % Rotamer: Outliers : 3.08 % Allowed : 22.87 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.06 (0.16), residues: 2564 helix: 0.62 (0.19), residues: 755 sheet: -0.89 (0.25), residues: 406 loop : -1.41 (0.15), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 42 TYR 0.016 0.001 TYR D 40 PHE 0.021 0.001 PHE N 336 TRP 0.016 0.001 TRP R 286 HIS 0.006 0.001 HIS T 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.12 (27702) covalent geometry : angle 0.59063 / 0.33 (38718) hydrogen bonds : bond 0.04372 / 2.92 ( 1051) hydrogen bonds : angle 4.20375 / 2.89 ( 2637) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 132 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: K 1478 MET cc_start: 0.5502 (pmm) cc_final: 0.4949 (mpp) REVERT: K 5055 ASP cc_start: 0.1677 (OUTLIER) cc_final: 0.0860 (t0) REVERT: K 5059 HIS cc_start: 0.3935 (OUTLIER) cc_final: 0.3665 (t-170) REVERT: K 5274 MET cc_start: 0.3195 (ptt) cc_final: 0.0796 (mtt) REVERT: K 5332 MET cc_start: 0.6482 (OUTLIER) cc_final: 0.6183 (mpp) REVERT: O 11 LYS cc_start: 0.8196 (tmtt) cc_final: 0.7885 (tmtt) REVERT: O 29 LYS cc_start: 0.6009 (OUTLIER) cc_final: 0.5776 (ptpp) REVERT: O 71 LEU cc_start: 0.9059 (mp) cc_final: 0.8604 (mt) REVERT: A 94 GLU cc_start: 0.7941 (tp30) cc_final: 0.7403 (tp30) REVERT: C 34 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8930 (mp) REVERT: C 91 GLU cc_start: 0.8164 (pm20) cc_final: 0.7874 (mm-30) REVERT: F 92 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7254 (tpp-160) REVERT: H 35 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7996 (mm-30) REVERT: H 59 MET cc_start: 0.9226 (tpp) cc_final: 0.9016 (tpp) REVERT: N 53 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: N 135 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8059 (mt) REVERT: N 183 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8197 (mp10) REVERT: N 288 LYS cc_start: 0.5268 (pttt) cc_final: 0.4905 (pttt) REVERT: N 324 ASN cc_start: 0.7179 (OUTLIER) cc_final: 0.6521 (t0) REVERT: P 54 ARG cc_start: 0.3151 (mtp180) cc_final: 0.2126 (mtm-85) REVERT: Q 66 LEU cc_start: 0.8458 (mt) cc_final: 0.8048 (pp) REVERT: Q 79 ASN cc_start: 0.0908 (OUTLIER) cc_final: 0.0641 (m-40) REVERT: R 53 PHE cc_start: 0.6503 (OUTLIER) cc_final: 0.4861 (m-80) outliers start: 69 outliers final: 47 residues processed: 190 average time/residue: 0.1846 time to fit residues: 55.4262 Evaluate side-chains 181 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 122 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1375 LEU Chi-restraints excluded: chain K residue 5055 ASP Chi-restraints excluded: chain K residue 5058 VAL Chi-restraints excluded: chain K residue 5059 HIS Chi-restraints excluded: chain K residue 5093 SER Chi-restraints excluded: chain K residue 5130 THR Chi-restraints excluded: chain K residue 5332 MET Chi-restraints excluded: chain K residue 5338 CYS Chi-restraints excluded: chain K residue 5386 SER Chi-restraints excluded: chain K residue 5464 THR Chi-restraints excluded: chain K residue 5476 SER Chi-restraints excluded: chain K residue 5482 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 29 LYS Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain N residue 13 TYR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 183 GLN Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 324 ASN Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain T residue 358 LEU Chi-restraints excluded: chain T residue 572 CYS Chi-restraints excluded: chain Q residue 79 ASN Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 266 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 140 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 103 optimal weight: 0.0970 chunk 151 optimal weight: 20.0000 chunk 149 optimal weight: 40.0000 chunk 273 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 242 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 183 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.103161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.067279 restraints weight = 112108.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.067893 restraints weight = 58712.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.067313 restraints weight = 42466.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.067805 restraints weight = 38387.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.067919 restraints weight = 30201.361| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27702 Z= 0.184 Angle : 0.626 12.292 38718 Z= 0.338 Chirality : 0.044 0.342 4317 Planarity : 0.004 0.050 3934 Dihedral : 25.254 156.089 6035 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.77 % Favored : 94.11 % Rotamer: Outliers : 3.53 % Allowed : 22.73 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.12 (0.16), residues: 2564 helix: 0.51 (0.19), residues: 756 sheet: -0.91 (0.25), residues: 399 loop : -1.42 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 29 TYR 0.016 0.001 TYR N 401 PHE 0.013 0.001 PHE A 67 TRP 0.009 0.001 TRP T 421 HIS 0.006 0.001 HIS T 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (27702) covalent geometry : angle 0.62601 / 0.34 (38718) hydrogen bonds : bond 0.05020 / 3.32 ( 1051) hydrogen bonds : angle 4.29481 / 2.95 ( 2637) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 121 time to evaluate : 0.737 Fit side-chains REVERT: K 1478 MET cc_start: 0.5567 (pmm) cc_final: 0.4980 (mpp) REVERT: K 5055 ASP cc_start: 0.1691 (OUTLIER) cc_final: 0.0841 (t0) REVERT: K 5059 HIS cc_start: 0.3925 (OUTLIER) cc_final: 0.3627 (t-170) REVERT: K 5274 MET cc_start: 0.3150 (ptt) cc_final: 0.0702 (mtt) REVERT: K 5332 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.6106 (mpp) REVERT: O 11 LYS cc_start: 0.8246 (tmtt) cc_final: 0.7895 (tptt) REVERT: O 29 LYS cc_start: 0.6027 (OUTLIER) cc_final: 0.5782 (ptpp) REVERT: O 71 LEU cc_start: 0.9074 (mp) cc_final: 0.8622 (mt) REVERT: A 94 GLU cc_start: 0.7964 (tp30) cc_final: 0.7407 (tp30) REVERT: C 34 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8994 (mp) REVERT: C 91 GLU cc_start: 0.8262 (pm20) cc_final: 0.7977 (mm-30) REVERT: F 92 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7359 (tpp-160) REVERT: N 53 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: N 135 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7944 (mt) REVERT: N 288 LYS cc_start: 0.5319 (pttt) cc_final: 0.4884 (pttm) REVERT: N 324 ASN cc_start: 0.7215 (OUTLIER) cc_final: 0.6552 (t0) REVERT: T 521 GLU cc_start: 0.5727 (OUTLIER) cc_final: 0.5307 (pp20) REVERT: T 597 MET cc_start: 0.7770 (tpp) cc_final: 0.7378 (tpp) REVERT: P 54 ARG cc_start: 0.3154 (mtp180) cc_final: 0.2135 (mtm-85) REVERT: Q 79 ASN cc_start: 0.0870 (OUTLIER) cc_final: 0.0587 (m-40) REVERT: R 53 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.5109 (m-80) outliers start: 79 outliers final: 55 residues processed: 189 average time/residue: 0.1720 time to fit residues: 51.9653 Evaluate side-chains 187 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 120 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1375 LEU Chi-restraints excluded: chain K residue 5055 ASP Chi-restraints excluded: chain K residue 5058 VAL Chi-restraints excluded: chain K residue 5059 HIS Chi-restraints excluded: chain K residue 5093 SER Chi-restraints excluded: chain K residue 5103 SER Chi-restraints excluded: chain K residue 5130 THR Chi-restraints excluded: chain K residue 5332 MET Chi-restraints excluded: chain K residue 5338 CYS Chi-restraints excluded: chain K residue 5386 SER Chi-restraints excluded: chain K residue 5464 THR Chi-restraints excluded: chain K residue 5476 SER Chi-restraints excluded: chain K residue 5482 VAL Chi-restraints excluded: chain O residue 29 LYS Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain N residue 13 TYR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 324 ASN Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain T residue 333 GLU Chi-restraints excluded: chain T residue 521 GLU Chi-restraints excluded: chain T residue 572 CYS Chi-restraints excluded: chain Q residue 79 ASN Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 266 PHE Chi-restraints excluded: chain R residue 318 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 236 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 130 optimal weight: 0.0270 chunk 33 optimal weight: 0.5980 chunk 271 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 202 optimal weight: 0.0070 overall best weight: 1.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.103575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.067867 restraints weight = 111694.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.068972 restraints weight = 57626.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.068951 restraints weight = 35941.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.068604 restraints weight = 36713.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.068548 restraints weight = 33498.122| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27702 Z= 0.152 Angle : 0.616 11.389 38718 Z= 0.334 Chirality : 0.043 0.350 4317 Planarity : 0.004 0.050 3934 Dihedral : 25.240 155.042 6035 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.23 % Favored : 94.66 % Rotamer: Outliers : 3.17 % Allowed : 22.96 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.09 (0.16), residues: 2564 helix: 0.55 (0.19), residues: 757 sheet: -0.89 (0.25), residues: 399 loop : -1.40 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K5432 TYR 0.018 0.001 TYR T 506 PHE 0.036 0.001 PHE T 520 TRP 0.011 0.001 TRP K1491 HIS 0.006 0.001 HIS T 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (27702) covalent geometry : angle 0.61566 / 0.33 (38718) hydrogen bonds : bond 0.04690 / 3.11 ( 1051) hydrogen bonds : angle 4.21440 / 2.90 ( 2637) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5128 Ramachandran restraints generated. 2564 Oldfield, 0 Emsley, 2564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 123 time to evaluate : 0.943 Fit side-chains REVERT: K 1478 MET cc_start: 0.5561 (pmm) cc_final: 0.4976 (mpp) REVERT: K 5055 ASP cc_start: 0.1695 (OUTLIER) cc_final: 0.0820 (t0) REVERT: K 5059 HIS cc_start: 0.4028 (OUTLIER) cc_final: 0.3752 (t-170) REVERT: K 5274 MET cc_start: 0.3167 (ptt) cc_final: 0.0726 (mtt) REVERT: K 5332 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.6167 (mpp) REVERT: O 11 LYS cc_start: 0.8216 (tmtt) cc_final: 0.7928 (tmtt) REVERT: O 29 LYS cc_start: 0.6060 (OUTLIER) cc_final: 0.5816 (ptpp) REVERT: O 71 LEU cc_start: 0.9109 (mp) cc_final: 0.8643 (mt) REVERT: A 94 GLU cc_start: 0.7918 (tp30) cc_final: 0.7384 (tp30) REVERT: C 34 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8971 (mp) REVERT: C 91 GLU cc_start: 0.8231 (pm20) cc_final: 0.7929 (mm-30) REVERT: F 92 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7293 (tpp-160) REVERT: H 35 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7967 (mm-30) REVERT: N 53 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: N 135 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7916 (mt) REVERT: N 288 LYS cc_start: 0.5305 (pttt) cc_final: 0.4869 (pttm) REVERT: N 324 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6473 (t0) REVERT: T 521 GLU cc_start: 0.5369 (OUTLIER) cc_final: 0.4988 (pp20) REVERT: T 597 MET cc_start: 0.7908 (tpp) cc_final: 0.7569 (tpp) REVERT: P 54 ARG cc_start: 0.3159 (mtp180) cc_final: 0.2139 (mtm-85) REVERT: Q 79 ASN cc_start: 0.0970 (OUTLIER) cc_final: 0.0700 (m-40) REVERT: R 53 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.5098 (m-80) outliers start: 71 outliers final: 54 residues processed: 183 average time/residue: 0.1786 time to fit residues: 52.0283 Evaluate side-chains 186 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 120 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1375 LEU Chi-restraints excluded: chain K residue 1515 VAL Chi-restraints excluded: chain K residue 5055 ASP Chi-restraints excluded: chain K residue 5058 VAL Chi-restraints excluded: chain K residue 5059 HIS Chi-restraints excluded: chain K residue 5093 SER Chi-restraints excluded: chain K residue 5103 SER Chi-restraints excluded: chain K residue 5130 THR Chi-restraints excluded: chain K residue 5332 MET Chi-restraints excluded: chain K residue 5338 CYS Chi-restraints excluded: chain K residue 5386 SER Chi-restraints excluded: chain K residue 5464 THR Chi-restraints excluded: chain K residue 5476 SER Chi-restraints excluded: chain K residue 5482 VAL Chi-restraints excluded: chain O residue 29 LYS Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain N residue 13 TYR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain N residue 99 ASP Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 324 ASN Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain T residue 333 GLU Chi-restraints excluded: chain T residue 521 GLU Chi-restraints excluded: chain T residue 572 CYS Chi-restraints excluded: chain Q residue 79 ASN Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 266 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 58 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 16 optimal weight: 40.0000 chunk 94 optimal weight: 0.6980 chunk 19 optimal weight: 20.0000 chunk 79 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 228 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K5194 HIS N 364 GLN ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** 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 = 0.4177 r_free = 0.4177 target = 0.102789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.066802 restraints weight = 111322.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.067544 restraints weight = 57517.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.066763 restraints weight = 42837.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.067132 restraints weight = 36043.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.067291 restraints weight = 30842.122| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27702 Z= 0.192 Angle : 0.640 11.198 38718 Z= 0.344 Chirality : 0.044 0.346 4317 Planarity : 0.004 0.050 3934 Dihedral : 25.362 156.519 6035 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.12 % Favored : 93.76 % Rotamer: Outliers : 3.48 % Allowed : 22.91 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.18 (0.16), residues: 2564 helix: 0.44 (0.19), residues: 757 sheet: -0.88 (0.25), residues: 400 loop : -1.46 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 29 TYR 0.015 0.001 TYR D 40 PHE 0.039 0.002 PHE T 520 TRP 0.013 0.001 TRP K1491 HIS 0.006 0.001 HIS T 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (27702) covalent geometry : angle 0.64003 / 0.34 (38718) hydrogen bonds : bond 0.05176 / 3.43 ( 1051) hydrogen bonds : angle 4.30060 / 2.96 ( 2637) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5437.61 seconds wall clock time: 94 minutes 25.69 seconds (5665.69 seconds total)