Starting phenix.real_space_refine on Sun Jul 5 10:34:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yl3_73071/07_2026/9yl3_73071.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yl3_73071/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9yl3_73071/07_2026/9yl3_73071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yl3_73071/07_2026/9yl3_73071.map" model { file = "/net/cci-nas-00/data/ceres_data/9yl3_73071/07_2026/9yl3_73071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yl3_73071/07_2026/9yl3_73071.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.29, per 1000 atoms: 0.20 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: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.38 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: 7.84 Time building geometry restraints manager: 2.78 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: 36989 1.46 - 2.92: 1452 2.92 - 4.39: 257 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: 14.070 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: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.280 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.550 ------------------------------------------------------------------------------- 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 : 0.636 7.310 38718 Z= 0.500 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 0.63574 / 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 : 1.038 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: 0.1800 time to fit residues: 46.3454 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 : 0.895 ------------------------------------------------------------------------------- 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: 10.9990 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... K5059 HIS K5111 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.103130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.068003 restraints weight = 116411.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.068421 restraints weight = 70172.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.068087 restraints weight = 45797.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.068107 restraints weight = 42522.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.068188 restraints weight = 39938.646| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27702 Z= 0.224 Angle : 0.658 9.395 38718 Z= 0.372 Chirality : 0.046 0.308 4317 Planarity : 0.005 0.073 3934 Dihedral : 24.732 161.681 6072 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.54 % Favored : 94.31 % Rotamer: Outliers : 3.44 % Allowed : 19.38 % Favored : 77.18 % 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: -1.36 (0.25), residues: 395 loop : -1.56 (0.15), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 74 TYR 0.021 0.002 TYR K5206 PHE 0.012 0.002 PHE D 70 TRP 0.025 0.001 TRP K1491 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (27702) covalent geometry : angle 0.65778 / 0.37 (38718) hydrogen bonds : bond 0.07326 / 4.90 ( 1051) hydrogen bonds : angle 5.73105 / 3.99 ( 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 207 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 130 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 1478 MET cc_start: 0.5981 (pmm) cc_final: 0.5115 (mpp) REVERT: K 5093 SER cc_start: 0.1358 (OUTLIER) cc_final: 0.0724 (t) REVERT: K 5177 MET cc_start: -0.0742 (ppp) cc_final: -0.0986 (ppp) REVERT: K 5274 MET cc_start: 0.2875 (ptt) cc_final: 0.0404 (mtt) REVERT: K 5332 MET cc_start: 0.5416 (OUTLIER) cc_final: 0.5165 (mpp) REVERT: O 11 LYS cc_start: 0.8138 (tmtt) cc_final: 0.7839 (tptt) REVERT: O 20 SER cc_start: 0.8252 (t) cc_final: 0.7887 (p) REVERT: O 71 LEU cc_start: 0.9166 (mp) cc_final: 0.8694 (tp) REVERT: A 94 GLU cc_start: 0.8010 (tp30) cc_final: 0.7627 (tp30) REVERT: B 52 GLU cc_start: 0.8284 (tp30) cc_final: 0.8065 (tp30) REVERT: C 91 GLU cc_start: 0.8373 (pm20) cc_final: 0.7934 (mm-30) REVERT: D 80 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9167 (tt) REVERT: G 92 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: N 13 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.5172 (m-80) REVERT: N 324 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.6376 (t0) REVERT: N 401 TYR cc_start: 0.6848 (t80) cc_final: 0.6616 (t80) REVERT: T 597 MET cc_start: 0.6667 (mmm) cc_final: 0.6214 (tpp) REVERT: P 54 ARG cc_start: 0.3214 (mtp180) cc_final: 0.2023 (mtm-85) REVERT: R 53 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.5095 (m-80) REVERT: R 92 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6329 (m-30) outliers start: 77 outliers final: 39 residues processed: 196 average time/residue: 0.1792 time to fit residues: 56.0546 Evaluate side-chains 161 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 114 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 92 GLU 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: 40.0000 chunk 196 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 263 optimal weight: 8.9990 chunk 257 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 267 optimal weight: 20.0000 chunk 79 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1497 HIS K5164 GLN K5194 HIS O 40 GLN A 108 ASN E 93 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.101917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.066274 restraints weight = 115766.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.066839 restraints weight = 69221.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.066823 restraints weight = 45777.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066933 restraints weight = 40567.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.066883 restraints weight = 40397.660| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 27702 Z= 0.274 Angle : 0.690 8.861 38718 Z= 0.382 Chirality : 0.047 0.288 4317 Planarity : 0.005 0.048 3934 Dihedral : 25.178 162.442 6043 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.32 % Favored : 93.53 % Rotamer: Outliers : 4.69 % Allowed : 19.34 % Favored : 75.97 % 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: -1.74 (0.16), residues: 2564 helix: -0.29 (0.18), residues: 775 sheet: -1.20 (0.25), residues: 396 loop : -1.65 (0.15), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG T 461 TYR 0.034 0.002 TYR K5206 PHE 0.015 0.002 PHE A 67 TRP 0.033 0.002 TRP K1491 HIS 0.010 0.001 HIS K5059 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.27 (27702) covalent geometry : angle 0.69025 / 0.38 (38718) hydrogen bonds : bond 0.06890 / 4.56 ( 1051) hydrogen bonds : angle 5.37998 / 3.71 ( 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 222 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 117 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 1478 MET cc_start: 0.5910 (pmm) cc_final: 0.5114 (mpp) REVERT: K 5055 ASP cc_start: 0.1437 (OUTLIER) cc_final: 0.0610 (t0) REVERT: K 5093 SER cc_start: 0.1573 (OUTLIER) cc_final: 0.0877 (t) REVERT: K 5274 MET cc_start: 0.2867 (ptt) cc_final: 0.0394 (mtt) REVERT: K 5459 HIS cc_start: 0.8795 (OUTLIER) cc_final: 0.8425 (t70) REVERT: K 5485 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8375 (t) REVERT: O 11 LYS cc_start: 0.8193 (tmtt) cc_final: 0.7924 (tmtt) REVERT: O 18 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8596 (tm-30) REVERT: O 20 SER cc_start: 0.8379 (t) cc_final: 0.8162 (p) REVERT: O 71 LEU cc_start: 0.9127 (mp) cc_final: 0.8667 (mt) REVERT: A 94 GLU cc_start: 0.7986 (tp30) cc_final: 0.7565 (tp30) REVERT: C 91 GLU cc_start: 0.8370 (pm20) cc_final: 0.8029 (mm-30) REVERT: D 80 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9191 (tt) REVERT: H 35 GLU cc_start: 0.8556 (tp30) cc_final: 0.8220 (mm-30) REVERT: N 13 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.6051 (m-80) REVERT: N 53 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: N 183 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8225 (mp10) REVERT: N 231 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8738 (mm) REVERT: N 324 ASN cc_start: 0.7473 (OUTLIER) cc_final: 0.6496 (t0) REVERT: T 576 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7883 (mp) REVERT: T 597 MET cc_start: 0.7101 (mmm) cc_final: 0.6831 (tpp) REVERT: P 54 ARG cc_start: 0.3268 (mtp180) cc_final: 0.2551 (mtm180) REVERT: R 53 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.5446 (m-80) outliers start: 105 outliers final: 56 residues processed: 212 average time/residue: 0.1711 time to fit residues: 58.5512 Evaluate side-chains 174 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 106 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 5194 HIS 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 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 8 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 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 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 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 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 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 53 PHE Chi-restraints excluded: chain N residue 99 ASP 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 231 LEU 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 P residue 62 VAL 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 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: 0.9980 chunk 80 optimal weight: 0.6980 chunk 211 optimal weight: 20.0000 chunk 262 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 5 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 25 ASN T 448 GLN T 469 HIS T 605 HIS R 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.103533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.068720 restraints weight = 115413.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.069477 restraints weight = 64891.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.069077 restraints weight = 45109.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.069476 restraints weight = 37980.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.069388 restraints weight = 37766.721| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27702 Z= 0.138 Angle : 0.593 10.071 38718 Z= 0.336 Chirality : 0.044 0.323 4317 Planarity : 0.004 0.048 3934 Dihedral : 25.076 159.540 6038 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 3.44 % Allowed : 20.59 % Favored : 75.97 % 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: -1.38 (0.16), residues: 2564 helix: 0.21 (0.19), residues: 761 sheet: -1.05 (0.25), residues: 411 loop : -1.54 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 342 TYR 0.021 0.001 TYR T 506 PHE 0.014 0.001 PHE K5241 TRP 0.013 0.001 TRP N 279 HIS 0.012 0.001 HIS K5194 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (27702) covalent geometry : angle 0.59293 / 0.34 (38718) hydrogen bonds : bond 0.05204 / 3.46 ( 1051) hydrogen bonds : angle 4.83122 / 3.33 ( 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 206 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 129 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: K 1478 MET cc_start: 0.5901 (pmm) cc_final: 0.5174 (mpp) REVERT: K 5093 SER cc_start: 0.1381 (OUTLIER) cc_final: 0.0672 (t) REVERT: K 5274 MET cc_start: 0.2839 (ptt) cc_final: 0.0409 (mtt) REVERT: O 2 GLN cc_start: 0.9201 (tt0) cc_final: 0.8441 (tp40) REVERT: O 11 LYS cc_start: 0.8150 (tmtt) cc_final: 0.7816 (tptt) REVERT: O 16 GLU cc_start: 0.8539 (tp30) cc_final: 0.8239 (mp0) REVERT: O 18 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8519 (tm-30) REVERT: O 25 ASN cc_start: 0.7975 (m110) cc_final: 0.7712 (t0) REVERT: A 94 GLU cc_start: 0.7915 (tp30) cc_final: 0.7438 (tp30) REVERT: C 91 GLU cc_start: 0.8289 (pm20) cc_final: 0.7913 (mm-30) REVERT: H 35 GLU cc_start: 0.8519 (tp30) cc_final: 0.8206 (mm-30) REVERT: N 13 TYR cc_start: 0.6952 (OUTLIER) cc_final: 0.5532 (m-80) REVERT: N 53 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: N 183 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8181 (mp10) REVERT: N 324 ASN cc_start: 0.7414 (OUTLIER) cc_final: 0.6728 (t0) REVERT: T 576 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7827 (mp) REVERT: T 597 MET cc_start: 0.7237 (mmm) cc_final: 0.6941 (tpp) REVERT: P 54 ARG cc_start: 0.3091 (mtp180) cc_final: 0.2446 (mtm180) REVERT: Q 79 ASN cc_start: 0.0873 (OUTLIER) cc_final: 0.0601 (m-40) REVERT: R 53 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.5060 (m-80) outliers start: 77 outliers final: 50 residues processed: 193 average time/residue: 0.1772 time to fit residues: 54.7995 Evaluate side-chains 175 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 117 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 1375 LEU 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 5338 CYS Chi-restraints excluded: chain K residue 5386 SER Chi-restraints excluded: chain K residue 5455 ILE 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 14 THR 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 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 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 67 GLN Chi-restraints excluded: chain Q residue 79 ASN 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 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: 10.0000 chunk 28 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 chunk 200 optimal weight: 0.0050 chunk 230 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN H 49 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.101795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.066176 restraints weight = 112138.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.066861 restraints weight = 69970.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.066720 restraints weight = 42991.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.066752 restraints weight = 39272.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.066841 restraints weight = 38177.968| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 27702 Z= 0.303 Angle : 0.714 9.677 38718 Z= 0.387 Chirality : 0.047 0.288 4317 Planarity : 0.005 0.047 3934 Dihedral : 25.438 161.127 6038 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.86 % Favored : 93.02 % Rotamer: Outliers : 4.64 % Allowed : 21.13 % Favored : 74.23 % 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: -1.60 (0.16), residues: 2564 helix: -0.09 (0.18), residues: 764 sheet: -0.94 (0.25), residues: 388 loop : -1.67 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 40 TYR 0.018 0.002 TYR G 50 PHE 0.018 0.002 PHE A 67 TRP 0.012 0.001 TRP R 156 HIS 0.006 0.002 HIS T 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.30 (27702) covalent geometry : angle 0.71438 / 0.39 (38718) hydrogen bonds : bond 0.06711 / 4.43 ( 1051) hydrogen bonds : angle 5.07070 / 3.49 ( 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 216 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 112 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: K 1478 MET cc_start: 0.5777 (pmm) cc_final: 0.4999 (mpp) REVERT: K 5055 ASP cc_start: 0.1404 (OUTLIER) cc_final: 0.0575 (t0) REVERT: K 5093 SER cc_start: 0.1374 (OUTLIER) cc_final: 0.0549 (t) REVERT: K 5274 MET cc_start: 0.2616 (ptt) cc_final: 0.0062 (mtt) REVERT: O 11 LYS cc_start: 0.8293 (tmtt) cc_final: 0.7944 (tptt) REVERT: O 29 LYS cc_start: 0.6223 (OUTLIER) cc_final: 0.5999 (ptpp) REVERT: A 94 GLU cc_start: 0.7998 (tp30) cc_final: 0.7502 (tp30) REVERT: C 38 ASN cc_start: 0.9449 (OUTLIER) cc_final: 0.9239 (p0) REVERT: C 91 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8060 (mm-30) REVERT: F 92 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7186 (tpp-160) REVERT: H 35 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8030 (mm-30) REVERT: H 101 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8303 (mp) REVERT: N 13 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6032 (m-80) REVERT: N 53 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: N 183 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8250 (mp10) REVERT: N 324 ASN cc_start: 0.7518 (OUTLIER) cc_final: 0.6534 (t0) REVERT: T 597 MET cc_start: 0.7428 (mmm) cc_final: 0.7219 (tpp) REVERT: P 54 ARG cc_start: 0.3129 (mtp180) cc_final: 0.2038 (mtm-85) REVERT: Q 79 ASN cc_start: 0.0876 (OUTLIER) cc_final: 0.0649 (m-40) REVERT: R 53 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.5548 (m-80) outliers start: 104 outliers final: 62 residues processed: 205 average time/residue: 0.1809 time to fit residues: 58.8576 Evaluate side-chains 181 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 105 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 5156 TYR 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 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 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 38 ASN 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 89 ILE Chi-restraints excluded: chain D residue 91 SER 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 92 ARG 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 35 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 101 LEU 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 128 MET 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 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 396 ASP 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 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: 0.5980 chunk 195 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 11 optimal weight: 40.0000 chunk 229 optimal weight: 0.0040 chunk 189 optimal weight: 0.9990 chunk 264 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 252 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 HIS T 469 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.103885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.068155 restraints weight = 112033.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.069504 restraints weight = 56970.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.068716 restraints weight = 38031.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.068842 restraints weight = 34867.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.068850 restraints weight = 34658.853| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27702 Z= 0.130 Angle : 0.596 12.069 38718 Z= 0.333 Chirality : 0.044 0.326 4317 Planarity : 0.004 0.049 3934 Dihedral : 25.214 157.356 6036 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.07 % Favored : 94.81 % Rotamer: Outliers : 3.31 % Allowed : 22.29 % Favored : 74.41 % 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: -1.28 (0.16), residues: 2564 helix: 0.33 (0.19), residues: 762 sheet: -1.03 (0.25), residues: 400 loop : -1.48 (0.15), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 67 TYR 0.020 0.001 TYR C 39 PHE 0.010 0.001 PHE K5241 TRP 0.015 0.001 TRP R 286 HIS 0.006 0.001 HIS T 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (27702) covalent geometry : angle 0.59586 / 0.33 (38718) hydrogen bonds : bond 0.04829 / 3.22 ( 1051) hydrogen bonds : angle 4.52925 / 3.12 ( 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 202 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 128 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: K 1478 MET cc_start: 0.5498 (pmm) cc_final: 0.4862 (mpp) REVERT: K 5055 ASP cc_start: 0.1645 (OUTLIER) cc_final: 0.0840 (t0) REVERT: K 5059 HIS cc_start: 0.3954 (OUTLIER) cc_final: 0.3592 (t-170) REVERT: K 5093 SER cc_start: 0.1691 (OUTLIER) cc_final: 0.1050 (t) REVERT: K 5274 MET cc_start: 0.3183 (ptt) cc_final: 0.0794 (mtt) REVERT: K 5536 MET cc_start: 0.3741 (tmm) cc_final: 0.3482 (tmm) REVERT: O 11 LYS cc_start: 0.8235 (tmtt) cc_final: 0.7884 (tptt) REVERT: O 29 LYS cc_start: 0.6090 (OUTLIER) cc_final: 0.5869 (ptpp) REVERT: O 71 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8627 (mt) REVERT: A 94 GLU cc_start: 0.7985 (tp30) cc_final: 0.7495 (tp30) REVERT: C 34 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8903 (mp) REVERT: C 91 GLU cc_start: 0.8273 (pm20) cc_final: 0.7895 (mm-30) REVERT: H 33 ARG cc_start: 0.6421 (OUTLIER) cc_final: 0.6075 (mtm-85) REVERT: H 35 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7999 (mm-30) REVERT: N 13 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.5089 (m-80) REVERT: N 53 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: N 183 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: N 324 ASN cc_start: 0.7414 (OUTLIER) cc_final: 0.6737 (t0) REVERT: P 54 ARG cc_start: 0.3246 (mtp180) cc_final: 0.2178 (mtm-85) REVERT: Q 79 ASN cc_start: 0.0908 (OUTLIER) cc_final: 0.0657 (m-40) REVERT: R 53 PHE cc_start: 0.6627 (OUTLIER) cc_final: 0.4984 (m-80) outliers start: 74 outliers final: 47 residues processed: 192 average time/residue: 0.1806 time to fit residues: 55.0571 Evaluate side-chains 182 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 121 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 5338 CYS Chi-restraints excluded: chain K residue 5386 SER Chi-restraints excluded: chain K residue 5464 THR 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 71 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 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 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 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 35 GLU 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 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 221 ILE 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 Q residue 79 ASN Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 107 ASP 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=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: 10.0000 chunk 212 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 94 optimal weight: 0.5980 chunk 165 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 278 optimal weight: 20.0000 chunk 251 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1525 HIS A 113 HIS C 38 ASN H 49 HIS ** Q 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.101279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.065400 restraints weight = 111541.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.066404 restraints weight = 66705.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.066049 restraints weight = 41372.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.066048 restraints weight = 38890.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.066134 restraints weight = 37298.228| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 27702 Z= 0.357 Angle : 0.768 11.478 38718 Z= 0.411 Chirality : 0.050 0.288 4317 Planarity : 0.005 0.052 3934 Dihedral : 25.622 160.286 6035 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.33 % Favored : 92.51 % Rotamer: Outliers : 4.51 % Allowed : 21.66 % Favored : 73.83 % 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: -1.68 (0.16), residues: 2564 helix: -0.16 (0.18), residues: 767 sheet: -1.13 (0.25), residues: 394 loop : -1.67 (0.15), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 116 TYR 0.021 0.002 TYR G 50 PHE 0.021 0.002 PHE A 67 TRP 0.015 0.002 TRP R 156 HIS 0.007 0.002 HIS T 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00815 / 0.36 (27702) covalent geometry : angle 0.76820 / 0.41 (38718) hydrogen bonds : bond 0.07048 / 4.66 ( 1051) hydrogen bonds : angle 5.01581 / 3.44 ( 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 216 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 115 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: K 1478 MET cc_start: 0.5748 (pmm) cc_final: 0.4971 (mpp) REVERT: K 5055 ASP cc_start: 0.1476 (OUTLIER) cc_final: 0.0616 (t0) REVERT: K 5059 HIS cc_start: 0.3737 (OUTLIER) cc_final: 0.3333 (t-170) REVERT: K 5061 ASN cc_start: 0.5199 (t0) cc_final: 0.4970 (t0) REVERT: K 5093 SER cc_start: 0.1587 (OUTLIER) cc_final: 0.0707 (t) REVERT: K 5274 MET cc_start: 0.2789 (ptt) cc_final: 0.0218 (mtt) REVERT: O 11 LYS cc_start: 0.8288 (tmtt) cc_final: 0.7952 (tptt) REVERT: O 29 LYS cc_start: 0.6229 (OUTLIER) cc_final: 0.5980 (ptpp) REVERT: A 94 GLU cc_start: 0.7975 (tp30) cc_final: 0.7483 (tp30) REVERT: C 34 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9020 (mp) REVERT: C 91 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8077 (mm-30) REVERT: F 92 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7256 (tpp-160) REVERT: H 35 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: N 53 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7959 (m-80) REVERT: N 183 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8245 (mp10) REVERT: N 324 ASN cc_start: 0.7514 (OUTLIER) cc_final: 0.6831 (t0) REVERT: T 597 MET cc_start: 0.7876 (tpp) cc_final: 0.7673 (tpp) REVERT: P 54 ARG cc_start: 0.3265 (mtp180) cc_final: 0.2617 (mtm180) REVERT: Q 79 ASN cc_start: 0.1222 (OUTLIER) cc_final: 0.0839 (m-40) REVERT: R 53 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.5654 (m-80) REVERT: R 92 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.6538 (m-30) REVERT: R 109 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8965 (mtmt) outliers start: 101 outliers final: 66 residues processed: 205 average time/residue: 0.1805 time to fit residues: 58.9499 Evaluate side-chains 187 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 106 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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 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 49 LEU 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 B residue 96 THR Chi-restraints excluded: chain C residue 30 VAL 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 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL 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 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 90 LEU 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 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 35 GLU 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 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 137 LEU Chi-restraints excluded: chain N residue 183 GLN Chi-restraints excluded: chain N residue 184 ASP 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 317 VAL 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 P residue 62 VAL 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 92 ASP Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 117 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 184 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 267 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1492 GLN E 68 GLN Q 67 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.102215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.067099 restraints weight = 114844.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.066961 restraints weight = 66561.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.067249 restraints weight = 51100.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.067556 restraints weight = 39358.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.067549 restraints weight = 38777.518| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27702 Z= 0.159 Angle : 0.622 12.247 38718 Z= 0.342 Chirality : 0.044 0.321 4317 Planarity : 0.004 0.052 3934 Dihedral : 25.430 156.659 6035 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.58 % Favored : 94.31 % Rotamer: Outliers : 3.62 % Allowed : 22.91 % Favored : 73.47 % 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: -1.37 (0.16), residues: 2564 helix: 0.23 (0.19), residues: 757 sheet: -0.93 (0.25), residues: 403 loop : -1.57 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 92 TYR 0.017 0.001 TYR Q 56 PHE 0.015 0.001 PHE N 336 TRP 0.015 0.001 TRP R 286 HIS 0.006 0.001 HIS T 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (27702) covalent geometry : angle 0.62219 / 0.34 (38718) hydrogen bonds : bond 0.05134 / 3.41 ( 1051) hydrogen bonds : angle 4.52748 / 3.11 ( 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: 81 poor density : 120 time to evaluate : 0.923 Fit side-chains REVERT: K 1478 MET cc_start: 0.5486 (pmm) cc_final: 0.4735 (mpp) REVERT: K 5055 ASP cc_start: 0.1632 (OUTLIER) cc_final: 0.0762 (t0) REVERT: K 5059 HIS cc_start: 0.3872 (OUTLIER) cc_final: 0.3562 (t-170) REVERT: K 5093 SER cc_start: 0.1829 (OUTLIER) cc_final: 0.1051 (t) REVERT: K 5274 MET cc_start: 0.2941 (ptt) cc_final: 0.0430 (mtt) REVERT: O 11 LYS cc_start: 0.8236 (tmtt) cc_final: 0.7903 (tptt) REVERT: O 29 LYS cc_start: 0.6280 (OUTLIER) cc_final: 0.6047 (ptpp) REVERT: A 94 GLU cc_start: 0.8014 (tp30) cc_final: 0.7504 (tp30) REVERT: C 34 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8957 (mp) REVERT: C 91 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7933 (mm-30) REVERT: E 59 GLU cc_start: 0.8255 (pm20) cc_final: 0.7890 (pm20) REVERT: H 35 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7990 (mm-30) REVERT: N 53 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7873 (m-80) REVERT: N 324 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.6716 (t0) REVERT: P 54 ARG cc_start: 0.3104 (mtp180) cc_final: 0.2397 (mtm180) REVERT: Q 79 ASN cc_start: 0.1243 (OUTLIER) cc_final: 0.0867 (m-40) REVERT: R 53 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.5242 (m-80) outliers start: 81 outliers final: 59 residues processed: 190 average time/residue: 0.1713 time to fit residues: 51.9225 Evaluate side-chains 186 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 116 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 105 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 29 ILE 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 49 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 39 ILE 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 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 35 GLU 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 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 192 THR Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 324 ASN 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 T residue 576 ILE Chi-restraints excluded: chain Q residue 56 TYR 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 217 VAL Chi-restraints excluded: chain R residue 266 PHE Chi-restraints excluded: chain R residue 318 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 140 optimal weight: 0.6980 chunk 11 optimal weight: 0.0670 chunk 103 optimal weight: 0.1980 chunk 151 optimal weight: 20.0000 chunk 149 optimal weight: 40.0000 chunk 273 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 19 optimal weight: 0.0000 chunk 36 optimal weight: 4.9990 chunk 242 optimal weight: 10.0000 chunk 250 optimal weight: 0.5980 overall best weight: 0.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 40 GLN E 39 HIS F 75 HIS Q 67 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.103729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.069714 restraints weight = 115737.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.070454 restraints weight = 65789.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.070005 restraints weight = 41896.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.070164 restraints weight = 37998.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.070189 restraints weight = 37062.154| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27702 Z= 0.123 Angle : 0.601 13.675 38718 Z= 0.332 Chirality : 0.043 0.324 4317 Planarity : 0.004 0.055 3934 Dihedral : 25.239 155.943 6033 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.42 % Favored : 94.50 % Rotamer: Outliers : 2.64 % Allowed : 23.98 % Favored : 73.38 % 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: -1.08 (0.16), residues: 2564 helix: 0.52 (0.19), residues: 764 sheet: -0.82 (0.25), residues: 407 loop : -1.41 (0.15), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 54 TYR 0.013 0.001 TYR D 40 PHE 0.033 0.001 PHE T 520 TRP 0.020 0.001 TRP R 286 HIS 0.006 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 (27702) covalent geometry : angle 0.60086 / 0.33 (38718) hydrogen bonds : bond 0.04282 / 2.85 ( 1051) hydrogen bonds : angle 4.15507 / 2.87 ( 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 197 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 138 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: K 1478 MET cc_start: 0.5648 (pmm) cc_final: 0.4997 (mpp) REVERT: K 5055 ASP cc_start: 0.1390 (OUTLIER) cc_final: 0.0476 (t0) REVERT: K 5059 HIS cc_start: 0.3764 (OUTLIER) cc_final: 0.3490 (t-170) REVERT: K 5061 ASN cc_start: 0.4336 (t0) cc_final: 0.4074 (t0) REVERT: K 5093 SER cc_start: 0.1599 (OUTLIER) cc_final: 0.0709 (t) REVERT: K 5274 MET cc_start: 0.2469 (ptt) cc_final: -0.0030 (mtt) REVERT: O 11 LYS cc_start: 0.8240 (tmtt) cc_final: 0.7948 (tmtt) REVERT: O 29 LYS cc_start: 0.6127 (OUTLIER) cc_final: 0.5893 (ptpp) REVERT: O 71 LEU cc_start: 0.9172 (mp) cc_final: 0.8724 (mt) REVERT: A 94 GLU cc_start: 0.7928 (tp30) cc_final: 0.7433 (tp30) REVERT: C 34 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8885 (mp) REVERT: C 91 GLU cc_start: 0.8266 (pm20) cc_final: 0.7864 (mm-30) REVERT: G 81 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8489 (tpt170) REVERT: H 35 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: N 53 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: N 288 LYS cc_start: 0.5019 (pttt) cc_final: 0.4594 (pttt) REVERT: N 324 ASN cc_start: 0.7078 (OUTLIER) cc_final: 0.6398 (t0) REVERT: P 54 ARG cc_start: 0.2972 (mtp180) cc_final: 0.1996 (mtm-85) REVERT: P 67 GLN cc_start: 0.9449 (mp10) cc_final: 0.9161 (mm-40) REVERT: Q 79 ASN cc_start: 0.0838 (OUTLIER) cc_final: 0.0416 (m110) REVERT: R 53 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.5009 (m-80) outliers start: 59 outliers final: 36 residues processed: 190 average time/residue: 0.1726 time to fit residues: 51.9808 Evaluate side-chains 173 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 5338 CYS Chi-restraints excluded: chain K residue 5386 SER Chi-restraints excluded: chain K residue 5464 THR 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 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 39 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 91 SER 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 96 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 81 ARG Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 35 GLU 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 193 THR Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 324 ASN 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 53 PHE 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 236 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 85 optimal weight: 0.0170 chunk 73 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 31 optimal weight: 0.0570 chunk 130 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 271 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 chunk 202 optimal weight: 0.0770 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K5194 HIS A 93 GLN E 76 GLN P 94 GLN Q 67 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.104298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.069686 restraints weight = 112601.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.070700 restraints weight = 63508.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.070085 restraints weight = 40514.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.070134 restraints weight = 39164.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.070211 restraints weight = 37427.117| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27702 Z= 0.118 Angle : 0.593 11.897 38718 Z= 0.325 Chirality : 0.043 0.322 4317 Planarity : 0.004 0.055 3934 Dihedral : 25.241 156.296 6033 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 2.23 % Allowed : 24.65 % Favored : 73.11 % 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: -0.99 (0.16), residues: 2564 helix: 0.64 (0.19), residues: 758 sheet: -0.75 (0.25), residues: 407 loop : -1.38 (0.15), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.014 0.001 TYR T 506 PHE 0.030 0.001 PHE T 520 TRP 0.017 0.001 TRP R 286 HIS 0.006 0.001 HIS T 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.12 (27702) covalent geometry : angle 0.59252 / 0.33 (38718) hydrogen bonds : bond 0.04184 / 2.78 ( 1051) hydrogen bonds : angle 4.08591 / 2.81 ( 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 177 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 127 time to evaluate : 0.930 Fit side-chains REVERT: K 1478 MET cc_start: 0.5580 (pmm) cc_final: 0.5008 (mpp) REVERT: K 5055 ASP cc_start: 0.1502 (OUTLIER) cc_final: 0.0611 (t0) REVERT: K 5059 HIS cc_start: 0.3989 (OUTLIER) cc_final: 0.3669 (t-170) REVERT: K 5061 ASN cc_start: 0.4336 (t0) cc_final: 0.3973 (t0) REVERT: K 5274 MET cc_start: 0.2883 (ptt) cc_final: 0.0408 (mtt) REVERT: O 11 LYS cc_start: 0.8237 (tmtt) cc_final: 0.7949 (tmtt) REVERT: O 29 LYS cc_start: 0.6086 (OUTLIER) cc_final: 0.5843 (ptpp) REVERT: O 71 LEU cc_start: 0.9153 (mp) cc_final: 0.8694 (mt) REVERT: A 94 GLU cc_start: 0.7883 (tp30) cc_final: 0.7331 (tp30) REVERT: C 34 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8892 (mp) REVERT: C 91 GLU cc_start: 0.8239 (pm20) cc_final: 0.7870 (mm-30) REVERT: G 81 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8469 (tpt170) REVERT: H 35 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7829 (mm-30) REVERT: N 53 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: N 288 LYS cc_start: 0.5069 (pttt) cc_final: 0.4646 (pttt) REVERT: N 324 ASN cc_start: 0.6904 (OUTLIER) cc_final: 0.6230 (t0) REVERT: T 521 GLU cc_start: 0.5008 (OUTLIER) cc_final: 0.4521 (pp20) REVERT: T 597 MET cc_start: 0.7920 (tpp) cc_final: 0.7552 (tpp) REVERT: P 54 ARG cc_start: 0.2985 (mtp180) cc_final: 0.2337 (mtm180) REVERT: P 67 GLN cc_start: 0.9408 (mp10) cc_final: 0.9156 (mm-40) REVERT: Q 79 ASN cc_start: 0.0993 (OUTLIER) cc_final: 0.0613 (m110) REVERT: R 53 PHE cc_start: 0.6698 (OUTLIER) cc_final: 0.5091 (m-80) REVERT: R 109 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8899 (mtmt) outliers start: 50 outliers final: 34 residues processed: 172 average time/residue: 0.1912 time to fit residues: 51.9801 Evaluate side-chains 167 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 5338 CYS Chi-restraints excluded: chain K residue 5386 SER Chi-restraints excluded: chain K residue 5464 THR 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 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 89 ILE 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 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 81 ARG Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 35 GLU 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 193 THR Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 324 ASN 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 53 PHE Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 133 PHE 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: 20.0000 chunk 54 optimal weight: 7.9990 chunk 16 optimal weight: 30.0000 chunk 94 optimal weight: 0.6980 chunk 19 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 228 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 364 GLN Q 67 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 = 0.4151 r_free = 0.4151 target = 0.101643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.066783 restraints weight = 114552.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.067054 restraints weight = 71348.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.066491 restraints weight = 51868.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.066561 restraints weight = 42391.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.066741 restraints weight = 40042.373| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27702 Z= 0.236 Angle : 0.675 11.062 38718 Z= 0.362 Chirality : 0.045 0.307 4317 Planarity : 0.004 0.054 3934 Dihedral : 25.514 158.822 6033 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 2.64 % Allowed : 24.48 % Favored : 72.89 % 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: -1.22 (0.16), residues: 2564 helix: 0.33 (0.19), residues: 761 sheet: -0.91 (0.25), residues: 388 loop : -1.44 (0.15), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.021 0.002 TYR D 40 PHE 0.024 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 0.00531 / 0.24 (27702) covalent geometry : angle 0.67481 / 0.36 (38718) hydrogen bonds : bond 0.05561 / 3.69 ( 1051) hydrogen bonds : angle 4.39747 / 3.03 ( 2637) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5615.54 seconds wall clock time: 97 minutes 39.60 seconds (5859.60 seconds total)