Starting phenix.real_space_refine on Sun Jul 5 14:55:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymf_73105/07_2026/9ymf_73105.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymf_73105/07_2026/9ymf_73105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ymf_73105/07_2026/9ymf_73105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymf_73105/07_2026/9ymf_73105.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ymf_73105/07_2026/9ymf_73105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymf_73105/07_2026/9ymf_73105.map" } resolution = 3.45 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= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 290 5.49 5 S 124 5.16 5 C 16864 2.51 5 N 5050 2.21 5 O 5838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 28174 Number of models: 1 Model: "" Number of chains: 19 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: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} 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: "U" 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: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 706 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ALY:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} 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: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1008 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'ALY:plan-2': 3} Unresolved non-hydrogen planarities: 3 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: "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: "N" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3238 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 2 Chain: "K" Number of atoms: 5825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5825 Classifications: {'peptide': 732} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 698} Chain breaks: 2 Chain: "T" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2421 Classifications: {'peptide': 301} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 275} Chain: "P" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "Q" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 432 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "K" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 34 Unusual residues: {' ZN': 8} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24359 SG CYS K5477 94.428 89.849 69.437 1.00 26.59 S ATOM 24753 SG CYS K5525 97.246 90.346 66.525 1.00 30.06 S ATOM 24769 SG CYS K5527 96.736 87.144 68.349 1.00 26.14 S ATOM 24806 SG CYS K5532 94.119 88.567 65.942 1.00 32.30 S ATOM 19214 SG CYS K1380 69.662 75.965 46.943 1.00 83.14 S ATOM 19234 SG CYS K1383 68.672 79.370 48.782 1.00 76.36 S ATOM 19418 SG CYS K1408 67.589 78.778 45.248 1.00109.40 S ATOM 19590 SG CYS K1430 60.832 75.475 20.330 1.00174.68 S ATOM 19612 SG CYS K1433 62.915 76.039 17.201 1.00176.04 S ATOM 19789 SG CYS K1456 59.210 75.092 16.892 1.00191.65 S ATOM 19698 SG CYS K1445 53.277 74.587 30.764 1.00177.26 S ATOM 19720 SG CYS K1448 56.169 72.214 31.051 1.00169.43 S ATOM 19902 SG CYS K1471 53.389 71.507 28.478 1.00181.60 S ATOM 19931 SG CYS K1474 52.764 71.002 32.128 1.00184.98 S ATOM 19950 SG CYS K1477 37.892 70.810 32.469 1.00212.13 S ATOM 19973 SG CYS K1480 36.152 67.615 31.128 1.00209.55 S ATOM 20112 SG CYS K1498 36.466 70.608 28.909 1.00211.08 S ATOM 20129 SG CYS K1501 34.137 70.676 31.862 1.00217.85 S ATOM 20829 SG CYS K5032 73.809 80.056 64.903 1.00 73.53 S ATOM 20852 SG CYS K5035 71.863 78.296 67.568 1.00 74.20 S ATOM 21060 SG CYS K5062 70.139 81.287 65.680 1.00 80.63 S ATOM 21289 SG CYS K5092 69.637 84.229 76.546 1.00102.04 S ATOM 21309 SG CYS K5095 71.645 81.121 76.313 1.00105.55 S ATOM 21480 SG CYS K5117 68.075 81.076 74.978 1.00109.58 S ATOM 21370 SG CYS K5104 61.591 94.797 75.341 1.00130.50 S ATOM 21414 SG CYS K5109 63.433 94.835 78.704 1.00127.91 S ATOM 21609 SG CYS K5133 60.355 92.756 78.367 1.00126.74 S Time building chain proxies: 5.46, per 1000 atoms: 0.19 Number of scatterers: 28174 At special positions: 0 Unit cell: (159.96, 168.56, 167.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 124 16.00 P 290 15.00 O 5838 8.00 N 5050 7.00 C 16864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS K1424 " - pdb=" SG CYS K1427 " distance=2.03 Simple disulfide: pdb=" SG CYS K1526 " - pdb=" SG CYS K1556 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K5601 " pdb="ZN ZN K5601 " - pdb=" SG CYS K5527 " pdb="ZN ZN K5601 " - pdb=" SG CYS K5532 " pdb="ZN ZN K5601 " - pdb=" SG CYS K5525 " pdb="ZN ZN K5601 " - pdb=" SG CYS K5477 " pdb=" ZN K5602 " pdb="ZN ZN K5602 " - pdb=" ND1 HIS K1405 " pdb="ZN ZN K5602 " - pdb=" SG CYS K1408 " pdb="ZN ZN K5602 " - pdb=" SG CYS K1383 " pdb="ZN ZN K5602 " - pdb=" SG CYS K1380 " pdb=" ZN K5603 " pdb="ZN ZN K5603 " - pdb=" ND1 HIS K1453 " pdb="ZN ZN K5603 " - pdb=" SG CYS K1430 " pdb="ZN ZN K5603 " - pdb=" SG CYS K1433 " pdb="ZN ZN K5603 " - pdb=" SG CYS K1456 " pdb=" ZN K5604 " pdb="ZN ZN K5604 " - pdb=" SG CYS K1448 " pdb="ZN ZN K5604 " - pdb=" SG CYS K1474 " pdb="ZN ZN K5604 " - pdb=" SG CYS K1471 " pdb="ZN ZN K5604 " - pdb=" SG CYS K1445 " pdb=" ZN K5605 " pdb="ZN ZN K5605 " - pdb=" SG CYS K1501 " pdb="ZN ZN K5605 " - pdb=" SG CYS K1498 " pdb="ZN ZN K5605 " - pdb=" SG CYS K1480 " pdb="ZN ZN K5605 " - pdb=" SG CYS K1477 " pdb=" ZN K5606 " pdb="ZN ZN K5606 " - pdb=" ND1 HIS K5059 " pdb="ZN ZN K5606 " - pdb=" SG CYS K5032 " pdb="ZN ZN K5606 " - pdb=" SG CYS K5035 " pdb="ZN ZN K5606 " - pdb=" SG CYS K5062 " pdb=" ZN K5607 " pdb="ZN ZN K5607 " - pdb=" ND1 HIS K5114 " pdb="ZN ZN K5607 " - pdb=" SG CYS K5095 " pdb="ZN ZN K5607 " - pdb=" SG CYS K5092 " pdb="ZN ZN K5607 " - pdb=" SG CYS K5117 " pdb=" ZN K5608 " pdb="ZN ZN K5608 " - pdb=" ND1 HIS K5136 " pdb="ZN ZN K5608 " - pdb=" SG CYS K5109 " pdb="ZN ZN K5608 " - pdb=" SG CYS K5133 " pdb="ZN ZN K5608 " - pdb=" SG CYS K5104 " Number of angles added : 33 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5246 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 36 sheets defined 31.8% alpha, 16.9% beta 144 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'O' and resid 22 through 34 removed outlier: 3.622A pdb=" N VAL O 26 " --> pdb=" O THR O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'U' and resid 22 through 34 removed outlier: 3.721A pdb=" N VAL U 26 " --> pdb=" O THR U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 60 Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.535A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 4.178A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.567A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.831A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.601A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.495A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.674A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.527A pdb=" N TYR D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) removed outlier: 4.038A 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: 3.894A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.906A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.087A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.624A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.264A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.791A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.417A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.629A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.688A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.869A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.834A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.572A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.692A pdb=" N ALA H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 234 Processing helix chain 'N' and resid 324 through 328 removed outlier: 4.053A pdb=" N ASN N 328 " --> pdb=" O GLN N 325 " (cutoff:3.500A) Processing helix chain 'N' and resid 348 through 353 removed outlier: 4.631A pdb=" N PHE N 352 " --> pdb=" O GLU N 349 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP N 353 " --> pdb=" O SER N 350 " (cutoff:3.500A) Processing helix chain 'N' and resid 469 through 473 removed outlier: 3.924A pdb=" N VAL N 473 " --> pdb=" O LEU N 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 1414 through 1421 removed outlier: 3.750A pdb=" N LEU K1418 " --> pdb=" O THR K1414 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU K1419 " --> pdb=" O LYS K1415 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS K1420 " --> pdb=" O VAL K1416 " (cutoff:3.500A) Processing helix chain 'K' and resid 1498 through 1503 Processing helix chain 'K' and resid 1533 through 1536 removed outlier: 4.032A pdb=" N SER K1536 " --> pdb=" O GLY K1533 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1533 through 1536' Processing helix chain 'K' and resid 1539 through 1549 removed outlier: 3.810A pdb=" N VAL K1543 " --> pdb=" O THR K1539 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU K1544 " --> pdb=" O GLU K1540 " (cutoff:3.500A) Processing helix chain 'K' and resid 5007 through 5017 Processing helix chain 'K' and resid 5060 through 5065 Processing helix chain 'K' and resid 5079 through 5090 removed outlier: 4.143A pdb=" N LEU K5089 " --> pdb=" O HIS K5085 " (cutoff:3.500A) Processing helix chain 'K' and resid 5114 through 5121 Processing helix chain 'K' and resid 5160 through 5172 removed outlier: 4.241A pdb=" N ARG K5171 " --> pdb=" O SER K5167 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY K5172 " --> pdb=" O ILE K5168 " (cutoff:3.500A) Processing helix chain 'K' and resid 5259 through 5277 removed outlier: 3.623A pdb=" N ARG K5266 " --> pdb=" O ALA K5262 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE K5267 " --> pdb=" O VAL K5263 " (cutoff:3.500A) Proline residue: K5270 - end of helix removed outlier: 3.919A 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 5295 Processing helix chain 'K' and resid 5298 through 5308 Processing helix chain 'K' and resid 5383 through 5395 removed outlier: 3.624A pdb=" N GLN K5387 " --> pdb=" O SER K5383 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG K5390 " --> pdb=" O SER K5386 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG K5392 " --> pdb=" O TYR K5388 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR K5393 " --> pdb=" O ARG K5389 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP K5395 " --> pdb=" O LEU K5391 " (cutoff:3.500A) Processing helix chain 'K' and resid 5433 through 5446 removed outlier: 3.899A pdb=" N ASN K5437 " --> pdb=" O ASN K5433 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG K5438 " --> pdb=" O GLU K5434 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU K5445 " --> pdb=" O LYS K5441 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN K5446 " --> pdb=" O ILE K5442 " (cutoff:3.500A) Processing helix chain 'K' and resid 5468 through 5472 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 501 removed outlier: 3.668A pdb=" N LYS T 500 " --> pdb=" O THR T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 525 through 532 Processing helix chain 'T' and resid 593 through 595 No H-bonds generated for 'chain 'T' and resid 593 through 595' Processing helix chain 'T' and resid 596 through 619 removed outlier: 5.225A pdb=" N VAL T 602 " --> pdb=" O GLY T 598 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU T 607 " --> pdb=" O VAL T 603 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA T 608 " --> pdb=" O GLU T 604 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR T 612 " --> pdb=" O ALA T 608 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS T 613 " --> pdb=" O ASP T 609 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 59 removed outlier: 3.853A pdb=" N GLN P 59 " --> pdb=" O ALA P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 76 removed outlier: 3.737A pdb=" N LEU P 65 " --> pdb=" O VAL P 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA P 70 " --> pdb=" O LEU P 66 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU P 75 " --> pdb=" O VAL P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 91 removed outlier: 3.909A pdb=" N PHE P 83 " --> pdb=" O ASN P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 97 removed outlier: 3.945A pdb=" N ASP P 97 " --> pdb=" O ALA P 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 59 removed outlier: 3.631A pdb=" N LEU Q 57 " --> pdb=" O THR Q 53 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN Q 59 " --> pdb=" O ALA Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 75 removed outlier: 3.773A pdb=" N VAL Q 71 " --> pdb=" O GLN Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 91 removed outlier: 3.928A pdb=" N PHE Q 83 " --> pdb=" O ASN Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 97 removed outlier: 3.972A pdb=" N ASP Q 97 " --> pdb=" O ALA Q 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 12 through 16 removed outlier: 8.627A pdb=" N LEU O 67 " --> pdb=" O GLN O 2 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE O 4 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU O 69 " --> pdb=" O PHE O 4 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS O 6 " --> pdb=" O LEU O 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 12 through 16 removed outlier: 3.722A pdb=" N VAL U 5 " --> pdb=" O ILE U 13 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU U 15 " --> pdb=" O ILE U 3 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N LEU U 67 " --> pdb=" O GLN U 2 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE U 4 " --> pdb=" O LEU U 67 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU U 69 " --> pdb=" O PHE U 4 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS U 6 " --> pdb=" O LEU U 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.349A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.543A pdb=" N ILE C 78 " --> pdb=" O GLY D 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.892A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.161A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'R' and resid 36 through 41 removed outlier: 6.138A pdb=" N LEU R 37 " --> pdb=" O LYS R 331 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS R 331 " --> pdb=" O LEU R 37 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE R 39 " --> pdb=" O LEU R 329 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU R 329 " --> pdb=" O PHE R 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 48 through 53 removed outlier: 3.689A pdb=" N SER R 50 " --> pdb=" O SER R 63 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS R 81 " --> pdb=" O ILE R 71 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY R 73 " --> pdb=" O PHE R 79 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N PHE R 79 " --> pdb=" O GLY R 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 90 through 95 removed outlier: 4.078A pdb=" N SER R 106 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR R 110 " --> pdb=" O SER R 106 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE R 113 " --> pdb=" O LYS R 123 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS R 123 " --> pdb=" O ILE R 113 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP R 115 " --> pdb=" O CYS R 121 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N CYS R 121 " --> pdb=" O ASP R 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 134 through 137 removed outlier: 3.658A pdb=" N ILE R 144 " --> pdb=" O TRP R 156 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL R 153 " --> pdb=" O LEU R 167 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP R 157 " --> pdb=" O CYS R 163 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N CYS R 163 " --> pdb=" O ASP R 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 174 through 179 removed outlier: 3.936A pdb=" N ALA R 176 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER R 190 " --> pdb=" O LEU R 194 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU R 194 " --> pdb=" O SER R 190 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS R 207 " --> pdb=" O ILE R 197 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP R 199 " --> pdb=" O CYS R 205 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS R 205 " --> pdb=" O ASP R 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 217 through 222 removed outlier: 3.946A pdb=" N THR R 237 " --> pdb=" O THR R 233 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU R 238 " --> pdb=" O THR R 251 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR R 251 " --> pdb=" O LEU R 238 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU R 240 " --> pdb=" O LEU R 249 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 264 through 267 removed outlier: 6.635A pdb=" N ASN R 287 " --> pdb=" O ILE R 293 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE R 293 " --> pdb=" O ASN R 287 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 20 through 21 removed outlier: 4.397A pdb=" N VAL N 318 " --> pdb=" O LEU N 21 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP N 300 " --> pdb=" O ILE N 313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 27 through 32 removed outlier: 4.107A pdb=" N THR N 29 " --> pdb=" O GLY N 42 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS N 43 " --> pdb=" O ARG N 47 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ARG N 47 " --> pdb=" O CYS N 43 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE N 48 " --> pdb=" O ILE N 61 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE N 61 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE N 50 " --> pdb=" O ALA N 59 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY N 57 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 69 through 74 removed outlier: 3.937A pdb=" N ILE N 89 " --> pdb=" O SER N 85 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN N 102 " --> pdb=" O GLN N 92 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASP N 94 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N CYS N 100 " --> pdb=" O ASP N 94 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS N 453 " --> pdb=" O ASP N 101 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG N 103 " --> pdb=" O LYS N 453 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 110 through 115 removed outlier: 7.208A pdb=" N CYS N 126 " --> pdb=" O LEU N 111 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL N 113 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU N 124 " --> pdb=" O VAL N 113 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N TYR N 115 " --> pdb=" O LYS N 122 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LYS N 122 " --> pdb=" O TYR N 115 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 157 through 159 removed outlier: 3.929A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LYS N 179 " --> pdb=" O LEU N 185 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU N 185 " --> pdb=" O LYS N 179 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 201 through 206 removed outlier: 3.887A pdb=" N GLN N 243 " --> pdb=" O VAL N 224 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 254 through 259 removed outlier: 4.188A pdb=" N LYS N 256 " --> pdb=" O GLY N 269 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA N 275 " --> pdb=" O SER N 270 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS N 288 " --> pdb=" O ILE N 278 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU N 280 " --> pdb=" O LEU N 286 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU N 286 " --> pdb=" O GLU N 280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 343 through 344 removed outlier: 6.627A pdb=" N VAL N 343 " --> pdb=" O ILE K5430 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N ARG K5432 " --> pdb=" O VAL N 343 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE K5461 " --> pdb=" O ARG K5454 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG K5454 " --> pdb=" O ILE K5461 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 1364 through 1368 Processing sheet with id=AC7, first strand: chain 'K' and resid 1443 through 1444 Processing sheet with id=AC8, first strand: chain 'K' and resid 1520 through 1522 Processing sheet with id=AC9, first strand: chain 'K' and resid 5049 through 5053 removed outlier: 6.901A pdb=" N LEU K5056 " --> pdb=" O LEU K5052 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 5076 through 5077 Processing sheet with id=AD2, first strand: chain 'K' and resid 5124 through 5125 removed outlier: 3.623A pdb=" N MET K5124 " --> pdb=" O LEU K5132 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 5187 through 5190 removed outlier: 3.711A pdb=" N GLY K5189 " --> pdb=" O GLY K5209 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLY K5209 " --> pdb=" O GLY K5189 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N VAL K5208 " --> pdb=" O GLU K5234 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU K5234 " --> pdb=" O VAL K5208 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR K5210 " --> pdb=" O ILE K5232 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE K5232 " --> pdb=" O TYR K5210 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 5399 through 5403 Processing sheet with id=AD5, first strand: chain 'K' and resid 5422 through 5426 removed outlier: 6.394A pdb=" N MET K5422 " --> pdb=" O SER K5498 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER K5498 " --> pdb=" O MET K5422 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE K5424 " --> pdb=" O ILE K5496 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE K5494 " --> pdb=" O TYR K5426 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 5474 through 5475 removed outlier: 6.515A pdb=" N ASN K5474 " --> pdb=" O TYR K5510 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'T' and resid 373 through 375 removed outlier: 4.857A pdb=" N LEU T 518 " --> pdb=" O ALA T 346 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA T 510 " --> pdb=" O GLU T 521 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T' and resid 383 through 388 removed outlier: 5.563A pdb=" N ASP T 387 " --> pdb=" O ARG T 411 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR T 569 " --> pdb=" O ALA T 435 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA T 435 " --> pdb=" O TYR T 569 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU T 438 " --> pdb=" O TRP T 460 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP T 440 " --> pdb=" O TYR T 458 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 393 through 394 removed outlier: 3.667A pdb=" N LYS T 393 " --> pdb=" O VAL T 402 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER T 575 " --> pdb=" O VAL T 427 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL T 427 " --> pdb=" O SER T 575 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN T 577 " --> pdb=" O ILE T 425 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ILE T 425 " --> pdb=" O ASN T 577 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE T 543 " --> pdb=" O VAL T 552 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL T 552 " --> pdb=" O PHE T 543 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS T 545 " --> pdb=" O GLN T 550 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN T 550 " --> pdb=" O LYS T 545 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2265 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 8.88 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8283 1.34 - 1.46: 8159 1.46 - 1.59: 12148 1.59 - 1.71: 578 1.71 - 1.84: 168 Bond restraints: 29336 Sorted by residual: bond pdb=" C1' DT J 57 " pdb=" N1 DT J 57 " ideal model delta sigma weight residual 1.468 1.557 -0.089 1.40e-02 5.10e+03 4.08e+01 bond pdb=" C1' DT J 15 " pdb=" N1 DT J 15 " ideal model delta sigma weight residual 1.468 1.555 -0.087 1.40e-02 5.10e+03 3.89e+01 bond pdb=" C1' DC I 36 " pdb=" N1 DC I 36 " ideal model delta sigma weight residual 1.468 1.554 -0.086 1.40e-02 5.10e+03 3.73e+01 bond pdb=" C1' DC J 16 " pdb=" N1 DC J 16 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.19e+01 bond pdb=" C1' DC J 85 " pdb=" N1 DC J 85 " ideal model delta sigma weight residual 1.468 1.545 -0.077 1.40e-02 5.10e+03 3.06e+01 ... (remaining 29331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 40399 3.02 - 6.03: 501 6.03 - 9.05: 20 9.05 - 12.07: 3 12.07 - 15.08: 1 Bond angle restraints: 40924 Sorted by residual: angle pdb=" C SER E 10 " pdb=" N THR E 11 " pdb=" CA THR E 11 " ideal model delta sigma weight residual 121.19 136.27 -15.08 1.59e+00 3.96e-01 9.00e+01 angle pdb=" O4' DG J 82 " pdb=" C4' DG J 82 " pdb=" C3' DG J 82 " ideal model delta sigma weight residual 106.00 102.83 3.17 6.00e-01 2.78e+00 2.79e+01 angle pdb=" O5' DT J 15 " pdb=" C5' DT J 15 " pdb=" C4' DT J 15 " ideal model delta sigma weight residual 109.40 113.27 -3.87 8.00e-01 1.56e+00 2.34e+01 angle pdb=" O4' DG I 100 " pdb=" C4' DG I 100 " pdb=" C3' DG I 100 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.33e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 ... (remaining 40919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.53: 15203 33.53 - 67.06: 1642 67.06 - 100.60: 74 100.60 - 134.13: 0 134.13 - 167.66: 4 Dihedral angle restraints: 16923 sinusoidal: 8793 harmonic: 8130 Sorted by residual: dihedral pdb=" CA ASN K5373 " pdb=" C ASN K5373 " pdb=" N THR K5374 " pdb=" CA THR K5374 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CB CYS K1526 " pdb=" SG CYS K1526 " pdb=" SG CYS K1556 " pdb=" CB CYS K1556 " ideal model delta sinusoidal sigma weight residual -86.00 -128.99 42.99 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" CB CYS K1424 " pdb=" SG CYS K1424 " pdb=" SG CYS K1427 " pdb=" CB CYS K1427 " ideal model delta sinusoidal sigma weight residual 93.00 135.86 -42.86 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 16920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3462 0.049 - 0.097: 642 0.097 - 0.146: 408 0.146 - 0.194: 56 0.194 - 0.243: 1 Chirality restraints: 4569 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 -2.49 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE G 79 " pdb=" N ILE G 79 " pdb=" C ILE G 79 " pdb=" CB ILE G 79 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" C3' DG J 39 " pdb=" C4' DG J 39 " pdb=" O3' DG J 39 " pdb=" C2' DG J 39 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 4566 not shown) Planarity restraints: 4224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE ALY E 23 " -0.233 2.00e-02 2.50e+03 1.95e-01 4.76e+02 pdb=" NZ ALY E 23 " 0.324 2.00e-02 2.50e+03 pdb=" CH ALY E 23 " 0.063 2.00e-02 2.50e+03 pdb=" OH ALY E 23 " 0.010 2.00e-02 2.50e+03 pdb=" CH3 ALY E 23 " -0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 105 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" CD GLU D 105 " -0.051 2.00e-02 2.50e+03 pdb=" OE1 GLU D 105 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU D 105 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 69 " -0.032 2.00e-02 2.50e+03 1.45e-02 5.75e+00 pdb=" N9 DA I 69 " 0.032 2.00e-02 2.50e+03 pdb=" C8 DA I 69 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 69 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 69 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 69 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 69 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 69 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 69 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 69 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 69 " 0.003 2.00e-02 2.50e+03 ... (remaining 4221 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 12352 2.97 - 3.46: 28241 3.46 - 3.94: 47151 3.94 - 4.42: 54168 4.42 - 4.90: 82321 Nonbonded interactions: 224233 Sorted by model distance: nonbonded pdb=" N ALY E 23 " pdb=" O ALY E 23 " model vdw 2.492 2.496 nonbonded pdb=" O2' SAH K5609 " pdb=" O3' SAH K5609 " model vdw 2.503 2.432 nonbonded pdb=" O5' DA I 135 " pdb=" O4' DA I 135 " model vdw 2.544 2.432 nonbonded pdb=" O GLU D 105 " pdb=" OE1 GLU D 105 " model vdw 2.563 3.040 nonbonded pdb=" O SER O 20 " pdb=" OG SER O 20 " model vdw 2.566 3.040 ... (remaining 224228 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 '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 'O' selection = chain 'U' } ncs_group { reference = chain 'P' selection = (chain 'Q' and (resid 46 through 98 or (resid 99 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 33.720 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 : 0.006 0.089 29370 Z= 0.444 Angle : 0.820 15.084 40961 Z= 0.575 Chirality : 0.052 0.243 4569 Planarity : 0.006 0.195 4224 Dihedral : 22.513 167.659 11671 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.11 % Favored : 93.78 % Rotamer: Outliers : 1.45 % Allowed : 19.19 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.16), residues: 2749 helix: 0.73 (0.19), residues: 772 sheet: -1.00 (0.23), residues: 500 loop : -1.63 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K5229 TYR 0.016 0.001 TYR T 517 PHE 0.015 0.001 PHE R 39 TRP 0.014 0.001 TRP T 599 HIS 0.005 0.001 HIS K5475 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.44 (29336) covalent geometry : angle 0.81321 / 0.57 (40924) SS BOND : bond 0.00184 / 0.09 ( 2) SS BOND : angle 2.39519 / 3.51 ( 4) hydrogen bonds : bond 0.14652 / 16.28 ( 1169) hydrogen bonds : angle 5.48609 / 7.41 ( 3005) metal coordination : bond 0.01127 / 1.13 ( 32) metal coordination : angle 3.73376 / 3.55 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 361 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.7302 (mtt) cc_final: 0.7093 (mtp) REVERT: B 25 ASN cc_start: 0.7778 (t0) cc_final: 0.7367 (t0) REVERT: R 172 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6814 (m-30) REVERT: N 28 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8291 (tt) REVERT: N 115 TYR cc_start: 0.8197 (m-80) cc_final: 0.7895 (m-80) REVERT: N 357 GLU cc_start: 0.7146 (pm20) cc_final: 0.6452 (pp20) REVERT: K 1360 MET cc_start: 0.2933 (ttp) cc_final: 0.1230 (ppp) REVERT: K 1376 MET cc_start: 0.6365 (pmm) cc_final: 0.4845 (mtm) REVERT: K 1417 MET cc_start: 0.6756 (tmm) cc_final: 0.6444 (tmm) REVERT: K 5280 MET cc_start: 0.4397 (ptp) cc_final: 0.4108 (pmm) outliers start: 35 outliers final: 14 residues processed: 388 average time/residue: 0.1998 time to fit residues: 118.2493 Evaluate side-chains 230 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 359 LYS Chi-restraints excluded: chain N residue 376 ASP Chi-restraints excluded: chain K residue 5232 ILE Chi-restraints excluded: chain K residue 5466 THR Chi-restraints excluded: chain K residue 5509 THR Chi-restraints excluded: chain T residue 572 CYS Chi-restraints excluded: chain T residue 592 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 2 GLN F 93 GLN H 109 HIS R 140 GLN ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN K5105 ASN K5176 HIS K5265 ASN K5475 HIS ** T 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 470 GLN ** T 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 91 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.115079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.076451 restraints weight = 82325.859| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.28 r_work: 0.3148 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 29370 Z= 0.184 Angle : 0.668 15.822 40961 Z= 0.369 Chirality : 0.047 0.300 4569 Planarity : 0.005 0.131 4224 Dihedral : 24.200 176.395 6272 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 3.15 % Allowed : 19.35 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: -0.94 (0.16), residues: 2749 helix: 1.09 (0.19), residues: 794 sheet: -0.74 (0.24), residues: 475 loop : -1.59 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 42 TYR 0.016 0.002 TYR K5210 PHE 0.018 0.002 PHE O 4 TRP 0.015 0.001 TRP R 59 HIS 0.007 0.001 HIS T 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (29336) covalent geometry : angle 0.65621 / 0.37 (40924) SS BOND : bond 0.00005 / 0.00 ( 2) SS BOND : angle 1.98518 / 3.21 ( 4) hydrogen bonds : bond 0.06188 / 6.95 ( 1169) hydrogen bonds : angle 4.32036 / 5.72 ( 3005) metal coordination : bond 0.01997 / 2.34 ( 32) metal coordination : angle 4.35923 / 5.96 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 226 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 51 GLU cc_start: 0.7785 (pm20) cc_final: 0.7502 (pm20) REVERT: O 59 TYR cc_start: 0.7425 (m-80) cc_final: 0.6979 (m-80) REVERT: A 120 MET cc_start: 0.8140 (mtt) cc_final: 0.7922 (mtp) REVERT: F 92 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8256 (ttp80) REVERT: H 83 TYR cc_start: 0.8479 (m-80) cc_final: 0.8116 (m-80) REVERT: R 115 ASP cc_start: 0.8125 (t0) cc_final: 0.7906 (t0) REVERT: R 157 ASP cc_start: 0.8088 (t0) cc_final: 0.7818 (t0) REVERT: N 128 MET cc_start: 0.8006 (mtm) cc_final: 0.7543 (mtm) REVERT: K 1360 MET cc_start: 0.0289 (ttp) cc_final: -0.0608 (ppp) REVERT: K 1404 TYR cc_start: 0.7127 (m-80) cc_final: 0.6738 (m-80) REVERT: K 1417 MET cc_start: 0.6882 (tmm) cc_final: 0.6480 (tmm) REVERT: K 5123 CYS cc_start: 0.5803 (m) cc_final: 0.5421 (m) REVERT: K 5174 ARG cc_start: 0.7145 (tpt170) cc_final: 0.6941 (tpt170) REVERT: K 5177 MET cc_start: 0.6979 (pmm) cc_final: 0.6230 (pmm) REVERT: K 5280 MET cc_start: 0.3934 (ptp) cc_final: 0.3471 (pmm) REVERT: K 5394 GLU cc_start: 0.9103 (tp30) cc_final: 0.8868 (tp30) REVERT: T 457 SER cc_start: 0.8258 (OUTLIER) cc_final: 0.7890 (p) REVERT: T 597 MET cc_start: 0.9145 (tpp) cc_final: 0.8934 (tpp) REVERT: P 58 ASP cc_start: 0.8029 (m-30) cc_final: 0.7437 (p0) REVERT: P 67 GLN cc_start: 0.7424 (mp10) cc_final: 0.7188 (mp10) REVERT: Q 83 PHE cc_start: 0.6782 (t80) cc_final: 0.6529 (t80) outliers start: 76 outliers final: 40 residues processed: 287 average time/residue: 0.1768 time to fit residues: 81.8594 Evaluate side-chains 243 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain R residue 121 CYS Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain N residue 376 ASP Chi-restraints excluded: chain K residue 5093 SER Chi-restraints excluded: chain K residue 5175 LEU Chi-restraints excluded: chain K residue 5208 VAL Chi-restraints excluded: chain K residue 5232 ILE Chi-restraints excluded: chain K residue 5293 LEU Chi-restraints excluded: chain K residue 5424 ILE Chi-restraints excluded: chain K residue 5427 ILE Chi-restraints excluded: chain K residue 5466 THR Chi-restraints excluded: chain K residue 5485 VAL Chi-restraints excluded: chain K residue 5509 THR Chi-restraints excluded: chain K residue 5532 CYS Chi-restraints excluded: chain T residue 377 LEU Chi-restraints excluded: chain T residue 401 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 457 SER Chi-restraints excluded: chain T residue 462 SER Chi-restraints excluded: chain T residue 538 HIS Chi-restraints excluded: chain T residue 588 ASP Chi-restraints excluded: chain T residue 592 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 190 optimal weight: 0.7980 chunk 12 optimal weight: 20.0000 chunk 259 optimal weight: 0.7980 chunk 224 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 213 optimal weight: 30.0000 chunk 239 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 258 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 ASN E 125 GLN ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5096 GLN K5164 GLN ** T 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 605 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 = 0.4031 r_free = 0.4031 target = 0.112707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.073250 restraints weight = 82034.263| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.26 r_work: 0.3080 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 29370 Z= 0.207 Angle : 0.665 11.982 40961 Z= 0.364 Chirality : 0.046 0.344 4569 Planarity : 0.005 0.059 4224 Dihedral : 24.733 176.187 6259 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.67 % Favored : 94.29 % Rotamer: Outliers : 3.81 % Allowed : 20.31 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: -0.81 (0.16), residues: 2749 helix: 1.19 (0.19), residues: 807 sheet: -0.58 (0.24), residues: 485 loop : -1.58 (0.15), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 54 TYR 0.021 0.002 TYR R 243 PHE 0.020 0.002 PHE T 578 TRP 0.025 0.002 TRP R 330 HIS 0.006 0.001 HIS T 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (29336) covalent geometry : angle 0.65794 / 0.36 (40924) SS BOND : bond 0.00141 / 0.07 ( 2) SS BOND : angle 1.67138 / 2.77 ( 4) hydrogen bonds : bond 0.06050 / 6.80 ( 1169) hydrogen bonds : angle 4.17748 / 5.45 ( 3005) metal coordination : bond 0.01300 / 1.22 ( 32) metal coordination : angle 3.51455 / 3.72 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 215 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8243 (mtt) cc_final: 0.8017 (mtp) REVERT: H 83 TYR cc_start: 0.8432 (m-10) cc_final: 0.8108 (m-80) REVERT: R 80 GLU cc_start: 0.8813 (tp30) cc_final: 0.8277 (tp30) REVERT: R 115 ASP cc_start: 0.8265 (t0) cc_final: 0.8034 (t0) REVERT: R 157 ASP cc_start: 0.8281 (t0) cc_final: 0.8067 (t0) REVERT: N 111 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8154 (mt) REVERT: N 128 MET cc_start: 0.8067 (mtm) cc_final: 0.7775 (mtm) REVERT: K 1360 MET cc_start: 0.0269 (OUTLIER) cc_final: -0.0603 (ppp) REVERT: K 1375 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7093 (pt) REVERT: K 1404 TYR cc_start: 0.7149 (m-80) cc_final: 0.6674 (m-80) REVERT: K 5123 CYS cc_start: 0.5769 (m) cc_final: 0.5497 (m) REVERT: K 5174 ARG cc_start: 0.7245 (tpt170) cc_final: 0.6979 (tpt170) REVERT: K 5177 MET cc_start: 0.6899 (pmm) cc_final: 0.6015 (pmm) REVERT: K 5280 MET cc_start: 0.3765 (ptp) cc_final: 0.3544 (mtm) REVERT: T 457 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7977 (p) REVERT: P 56 TYR cc_start: 0.6685 (OUTLIER) cc_final: 0.6049 (m-80) outliers start: 92 outliers final: 54 residues processed: 293 average time/residue: 0.1826 time to fit residues: 87.8723 Evaluate side-chains 249 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 190 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain R residue 121 CYS Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 376 ASP Chi-restraints excluded: chain N residue 459 LEU Chi-restraints excluded: chain K residue 1360 MET Chi-restraints excluded: chain K residue 1364 VAL Chi-restraints excluded: chain K residue 1368 SER Chi-restraints excluded: chain K residue 1375 LEU Chi-restraints excluded: chain K residue 1424 CYS Chi-restraints excluded: chain K residue 5112 VAL Chi-restraints excluded: chain K residue 5175 LEU Chi-restraints excluded: chain K residue 5208 VAL Chi-restraints excluded: chain K residue 5232 ILE Chi-restraints excluded: chain K residue 5424 ILE Chi-restraints excluded: chain K residue 5427 ILE Chi-restraints excluded: chain K residue 5466 THR Chi-restraints excluded: chain K residue 5485 VAL Chi-restraints excluded: chain K residue 5487 THR Chi-restraints excluded: chain K residue 5490 LYS Chi-restraints excluded: chain K residue 5532 CYS Chi-restraints excluded: chain T residue 401 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 457 SER Chi-restraints excluded: chain T residue 462 SER Chi-restraints excluded: chain T residue 516 SER Chi-restraints excluded: chain T residue 538 HIS Chi-restraints excluded: chain T residue 588 ASP Chi-restraints excluded: chain T residue 592 ARG Chi-restraints excluded: chain P residue 56 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 249 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 209 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 292 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 2 GLN ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 577 ASN ** T 605 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 = 0.4019 r_free = 0.4019 target = 0.111939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.073994 restraints weight = 82319.215| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.39 r_work: 0.3045 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29370 Z= 0.205 Angle : 0.649 12.228 40961 Z= 0.353 Chirality : 0.045 0.348 4569 Planarity : 0.004 0.051 4224 Dihedral : 24.844 175.178 6255 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.64 % Favored : 94.33 % Rotamer: Outliers : 3.85 % Allowed : 21.43 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: -0.82 (0.16), residues: 2749 helix: 1.20 (0.19), residues: 813 sheet: -0.53 (0.24), residues: 470 loop : -1.62 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 29 TYR 0.028 0.001 TYR K5070 PHE 0.025 0.002 PHE K5012 TRP 0.012 0.001 TRP K5535 HIS 0.007 0.001 HIS T 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (29336) covalent geometry : angle 0.64198 / 0.35 (40924) SS BOND : bond 0.00060 / 0.03 ( 2) SS BOND : angle 1.74447 / 3.04 ( 4) hydrogen bonds : bond 0.05756 / 6.44 ( 1169) hydrogen bonds : angle 4.11641 / 5.38 ( 3005) metal coordination : bond 0.00988 / 1.01 ( 32) metal coordination : angle 3.36871 / 3.51 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 199 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.6984 (ttp) cc_final: 0.6212 (tpp) REVERT: O 59 TYR cc_start: 0.7043 (m-80) cc_final: 0.6797 (m-80) REVERT: O 63 LYS cc_start: 0.7300 (mmmt) cc_final: 0.6907 (pttm) REVERT: H 71 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8364 (tm-30) REVERT: R 80 GLU cc_start: 0.8759 (tp30) cc_final: 0.8274 (tp30) REVERT: R 115 ASP cc_start: 0.8252 (t0) cc_final: 0.7974 (t0) REVERT: N 111 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8281 (mt) REVERT: N 128 MET cc_start: 0.8107 (mtm) cc_final: 0.7717 (mtm) REVERT: K 1360 MET cc_start: 0.0028 (OUTLIER) cc_final: -0.0571 (ppp) REVERT: K 1375 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7087 (pp) REVERT: K 1404 TYR cc_start: 0.7287 (m-80) cc_final: 0.6769 (m-80) REVERT: K 1552 ASP cc_start: -0.0592 (OUTLIER) cc_final: -0.1254 (m-30) REVERT: K 5123 CYS cc_start: 0.5901 (m) cc_final: 0.5660 (m) REVERT: K 5174 ARG cc_start: 0.7351 (tpt170) cc_final: 0.7073 (tpt170) REVERT: K 5177 MET cc_start: 0.6805 (pmm) cc_final: 0.6035 (pmm) REVERT: T 399 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7684 (tt) REVERT: T 457 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.7956 (p) REVERT: P 56 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.6214 (m-80) outliers start: 93 outliers final: 63 residues processed: 276 average time/residue: 0.1770 time to fit residues: 80.5150 Evaluate side-chains 258 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 188 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain R residue 121 CYS Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 162 LYS Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 355 GLU Chi-restraints excluded: chain N residue 376 ASP Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 388 SER Chi-restraints excluded: chain N residue 459 LEU Chi-restraints excluded: chain K residue 1360 MET Chi-restraints excluded: chain K residue 1375 LEU Chi-restraints excluded: chain K residue 1424 CYS Chi-restraints excluded: chain K residue 1552 ASP Chi-restraints excluded: chain K residue 5078 MET Chi-restraints excluded: chain K residue 5112 VAL Chi-restraints excluded: chain K residue 5175 LEU Chi-restraints excluded: chain K residue 5176 HIS Chi-restraints excluded: chain K residue 5208 VAL Chi-restraints excluded: chain K residue 5232 ILE Chi-restraints excluded: chain K residue 5423 VAL Chi-restraints excluded: chain K residue 5424 ILE Chi-restraints excluded: chain K residue 5427 ILE Chi-restraints excluded: chain K residue 5452 MET Chi-restraints excluded: chain K residue 5466 THR Chi-restraints excluded: chain K residue 5485 VAL Chi-restraints excluded: chain K residue 5487 THR Chi-restraints excluded: chain K residue 5490 LYS Chi-restraints excluded: chain K residue 5532 CYS Chi-restraints excluded: chain T residue 399 LEU Chi-restraints excluded: chain T residue 401 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 457 SER Chi-restraints excluded: chain T residue 462 SER Chi-restraints excluded: chain T residue 516 SER Chi-restraints excluded: chain T residue 538 HIS Chi-restraints excluded: chain T residue 588 ASP Chi-restraints excluded: chain T residue 592 ARG Chi-restraints excluded: chain T residue 607 LEU Chi-restraints excluded: chain P residue 56 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 68 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 199 optimal weight: 20.0000 chunk 295 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 2 GLN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 605 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 = 0.4019 r_free = 0.4019 target = 0.111926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.074127 restraints weight = 81942.582| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.23 r_work: 0.3059 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 29370 Z= 0.174 Angle : 0.625 11.488 40961 Z= 0.340 Chirality : 0.044 0.358 4569 Planarity : 0.004 0.050 4224 Dihedral : 24.903 174.481 6255 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 4.19 % Allowed : 21.43 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: -0.70 (0.16), residues: 2749 helix: 1.30 (0.19), residues: 816 sheet: -0.32 (0.25), residues: 459 loop : -1.59 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 42 TYR 0.027 0.001 TYR K5070 PHE 0.015 0.001 PHE O 4 TRP 0.012 0.001 TRP R 286 HIS 0.006 0.001 HIS T 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (29336) covalent geometry : angle 0.61808 / 0.34 (40924) SS BOND : bond 0.00071 / 0.04 ( 2) SS BOND : angle 1.87282 / 3.44 ( 4) hydrogen bonds : bond 0.05392 / 6.04 ( 1169) hydrogen bonds : angle 4.00866 / 5.23 ( 3005) metal coordination : bond 0.00829 / 0.83 ( 32) metal coordination : angle 3.24529 / 3.28 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 195 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.7113 (ttp) cc_final: 0.6038 (tpp) REVERT: O 63 LYS cc_start: 0.7204 (mmmt) cc_final: 0.6860 (pttm) REVERT: F 92 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8362 (ttp80) REVERT: H 52 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8582 (t) REVERT: H 71 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8356 (tm-30) REVERT: R 80 GLU cc_start: 0.8725 (tp30) cc_final: 0.8324 (tp30) REVERT: R 115 ASP cc_start: 0.8210 (t0) cc_final: 0.7926 (t0) REVERT: N 111 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8282 (mt) REVERT: N 128 MET cc_start: 0.8139 (mtm) cc_final: 0.7757 (mtm) REVERT: K 1360 MET cc_start: 0.0080 (OUTLIER) cc_final: -0.0535 (ppp) REVERT: K 1375 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7135 (pt) REVERT: K 1404 TYR cc_start: 0.7233 (m-80) cc_final: 0.6939 (m-80) REVERT: K 1417 MET cc_start: 0.6198 (tmm) cc_final: 0.5878 (tmm) REVERT: K 5123 CYS cc_start: 0.5825 (m) cc_final: 0.5608 (m) REVERT: K 5174 ARG cc_start: 0.7345 (tpt170) cc_final: 0.7068 (tpt170) REVERT: K 5177 MET cc_start: 0.6788 (pmm) cc_final: 0.6057 (pmm) REVERT: T 387 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6044 (m-30) REVERT: T 399 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7729 (tt) REVERT: T 457 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.8067 (p) REVERT: P 56 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.6183 (m-80) outliers start: 101 outliers final: 67 residues processed: 278 average time/residue: 0.1851 time to fit residues: 84.1153 Evaluate side-chains 264 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 188 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain R residue 86 HIS Chi-restraints excluded: chain R residue 121 CYS Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 162 LYS Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 376 ASP Chi-restraints excluded: chain N residue 388 SER Chi-restraints excluded: chain K residue 1360 MET Chi-restraints excluded: chain K residue 1368 SER Chi-restraints excluded: chain K residue 1375 LEU Chi-restraints excluded: chain K residue 5112 VAL Chi-restraints excluded: chain K residue 5176 HIS Chi-restraints excluded: chain K residue 5208 VAL Chi-restraints excluded: chain K residue 5232 ILE Chi-restraints excluded: chain K residue 5259 SER Chi-restraints excluded: chain K residue 5293 LEU Chi-restraints excluded: chain K residue 5424 ILE Chi-restraints excluded: chain K residue 5427 ILE Chi-restraints excluded: chain K residue 5452 MET Chi-restraints excluded: chain K residue 5466 THR Chi-restraints excluded: chain K residue 5485 VAL Chi-restraints excluded: chain K residue 5487 THR Chi-restraints excluded: chain K residue 5490 LYS Chi-restraints excluded: chain K residue 5509 THR Chi-restraints excluded: chain K residue 5532 CYS Chi-restraints excluded: chain T residue 376 CYS Chi-restraints excluded: chain T residue 387 ASP Chi-restraints excluded: chain T residue 399 LEU Chi-restraints excluded: chain T residue 401 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 430 MET Chi-restraints excluded: chain T residue 457 SER Chi-restraints excluded: chain T residue 462 SER Chi-restraints excluded: chain T residue 516 SER Chi-restraints excluded: chain T residue 538 HIS Chi-restraints excluded: chain T residue 588 ASP Chi-restraints excluded: chain T residue 592 ARG Chi-restraints excluded: chain T residue 607 LEU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 56 TYR Chi-restraints excluded: chain Q residue 69 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 250 optimal weight: 0.7980 chunk 278 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 213 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 2 GLN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 ASN ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 468 HIS ** K5051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 605 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 = 0.4031 r_free = 0.4031 target = 0.112639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.074983 restraints weight = 82223.114| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.34 r_work: 0.3074 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29370 Z= 0.137 Angle : 0.596 10.649 40961 Z= 0.326 Chirality : 0.044 0.359 4569 Planarity : 0.004 0.049 4224 Dihedral : 24.882 175.012 6255 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.31 % Favored : 94.65 % Rotamer: Outliers : 3.77 % Allowed : 22.46 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: -0.54 (0.16), residues: 2749 helix: 1.45 (0.19), residues: 815 sheet: -0.26 (0.24), residues: 469 loop : -1.50 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K5174 TYR 0.027 0.001 TYR K5070 PHE 0.015 0.001 PHE T 423 TRP 0.024 0.001 TRP R 330 HIS 0.006 0.001 HIS T 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (29336) covalent geometry : angle 0.58967 / 0.33 (40924) SS BOND : bond 0.00062 / 0.03 ( 2) SS BOND : angle 1.66064 / 2.95 ( 4) hydrogen bonds : bond 0.04897 / 5.51 ( 1169) hydrogen bonds : angle 3.89702 / 5.07 ( 3005) metal coordination : bond 0.00667 / 0.67 ( 32) metal coordination : angle 2.98487 / 3.08 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 198 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.7241 (ttp) cc_final: 0.6440 (tpp) REVERT: O 63 LYS cc_start: 0.7400 (mmmt) cc_final: 0.7107 (pttm) REVERT: F 92 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8373 (ttp80) REVERT: H 71 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8346 (tm-30) REVERT: R 80 GLU cc_start: 0.8708 (tp30) cc_final: 0.8305 (tp30) REVERT: R 115 ASP cc_start: 0.8160 (t0) cc_final: 0.7876 (t0) REVERT: N 111 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8273 (mt) REVERT: N 128 MET cc_start: 0.8111 (mtm) cc_final: 0.7847 (mtm) REVERT: K 1360 MET cc_start: 0.0102 (ttp) cc_final: -0.0542 (ppp) REVERT: K 1404 TYR cc_start: 0.6871 (m-80) cc_final: 0.6541 (m-80) REVERT: K 1552 ASP cc_start: -0.0596 (OUTLIER) cc_final: -0.1166 (m-30) REVERT: K 5123 CYS cc_start: 0.5821 (m) cc_final: 0.5614 (m) REVERT: K 5174 ARG cc_start: 0.7332 (tpt170) cc_final: 0.7061 (tpt170) REVERT: K 5177 MET cc_start: 0.6652 (pmm) cc_final: 0.5981 (pmm) REVERT: T 387 ASP cc_start: 0.6751 (OUTLIER) cc_final: 0.5984 (m-30) REVERT: T 399 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7722 (tt) REVERT: T 457 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.8082 (p) REVERT: P 56 TYR cc_start: 0.6721 (OUTLIER) cc_final: 0.6053 (m-80) REVERT: Q 56 TYR cc_start: 0.6787 (t80) cc_final: 0.6555 (t80) outliers start: 91 outliers final: 65 residues processed: 273 average time/residue: 0.1863 time to fit residues: 82.9167 Evaluate side-chains 260 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 188 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain R residue 86 HIS Chi-restraints excluded: chain R residue 121 CYS Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 162 LYS Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 299 LEU Chi-restraints excluded: chain N residue 376 ASP Chi-restraints excluded: chain N residue 388 SER Chi-restraints excluded: chain N residue 459 LEU Chi-restraints excluded: chain K residue 1424 CYS Chi-restraints excluded: chain K residue 1552 ASP Chi-restraints excluded: chain K residue 5029 MET Chi-restraints excluded: chain K residue 5112 VAL Chi-restraints excluded: chain K residue 5176 HIS Chi-restraints excluded: chain K residue 5208 VAL Chi-restraints excluded: chain K residue 5232 ILE Chi-restraints excluded: chain K residue 5259 SER Chi-restraints excluded: chain K residue 5293 LEU Chi-restraints excluded: chain K residue 5423 VAL Chi-restraints excluded: chain K residue 5424 ILE Chi-restraints excluded: chain K residue 5427 ILE Chi-restraints excluded: chain K residue 5452 MET Chi-restraints excluded: chain K residue 5466 THR Chi-restraints excluded: chain K residue 5485 VAL Chi-restraints excluded: chain K residue 5490 LYS Chi-restraints excluded: chain K residue 5509 THR Chi-restraints excluded: chain K residue 5532 CYS Chi-restraints excluded: chain T residue 387 ASP Chi-restraints excluded: chain T residue 399 LEU Chi-restraints excluded: chain T residue 401 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 430 MET Chi-restraints excluded: chain T residue 457 SER Chi-restraints excluded: chain T residue 462 SER Chi-restraints excluded: chain T residue 516 SER Chi-restraints excluded: chain T residue 536 THR Chi-restraints excluded: chain T residue 538 HIS Chi-restraints excluded: chain T residue 577 ASN Chi-restraints excluded: chain T residue 588 ASP Chi-restraints excluded: chain T residue 592 ARG Chi-restraints excluded: chain T residue 607 LEU Chi-restraints excluded: chain P residue 56 TYR Chi-restraints excluded: chain Q residue 54 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 83 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 14 optimal weight: 40.0000 chunk 81 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 245 optimal weight: 0.0870 chunk 215 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 201 optimal weight: 30.0000 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 2 GLN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 ASN R 265 ASN ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5061 ASN K5096 GLN ** K5164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 605 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 = 0.4031 r_free = 0.4031 target = 0.112683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.075960 restraints weight = 81884.564| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.25 r_work: 0.3078 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29370 Z= 0.135 Angle : 0.595 10.140 40961 Z= 0.324 Chirality : 0.043 0.355 4569 Planarity : 0.004 0.050 4224 Dihedral : 24.872 175.465 6255 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 3.77 % Allowed : 22.50 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: -0.42 (0.16), residues: 2749 helix: 1.57 (0.19), residues: 809 sheet: -0.18 (0.24), residues: 469 loop : -1.44 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K5108 TYR 0.027 0.001 TYR K5070 PHE 0.014 0.001 PHE O 4 TRP 0.020 0.001 TRP R 330 HIS 0.005 0.001 HIS T 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (29336) covalent geometry : angle 0.58909 / 0.32 (40924) SS BOND : bond 0.00062 / 0.03 ( 2) SS BOND : angle 1.69363 / 3.05 ( 4) hydrogen bonds : bond 0.04740 / 5.33 ( 1169) hydrogen bonds : angle 3.83578 / 4.98 ( 3005) metal coordination : bond 0.00659 / 0.66 ( 32) metal coordination : angle 2.95155 / 3.09 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 196 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.7336 (ttp) cc_final: 0.6571 (tpp) REVERT: O 63 LYS cc_start: 0.7475 (mmmt) cc_final: 0.7256 (pttm) REVERT: A 105 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8082 (tm-30) REVERT: C 41 GLU cc_start: 0.8175 (mp0) cc_final: 0.7859 (mp0) REVERT: C 58 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8953 (mt) REVERT: F 92 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8367 (ttp80) REVERT: G 58 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8870 (mt) REVERT: R 80 GLU cc_start: 0.8720 (tp30) cc_final: 0.8323 (tp30) REVERT: R 115 ASP cc_start: 0.8165 (t0) cc_final: 0.7871 (t0) REVERT: N 111 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8260 (mt) REVERT: N 128 MET cc_start: 0.8154 (mtm) cc_final: 0.7877 (mtm) REVERT: K 1360 MET cc_start: 0.0074 (ttp) cc_final: -0.0570 (ppp) REVERT: K 1375 LEU cc_start: 0.8072 (tp) cc_final: 0.7518 (pt) REVERT: K 1404 TYR cc_start: 0.6897 (m-80) cc_final: 0.6593 (m-80) REVERT: K 1552 ASP cc_start: -0.0468 (OUTLIER) cc_final: -0.1118 (m-30) REVERT: K 5174 ARG cc_start: 0.7328 (tpt170) cc_final: 0.7056 (tpt170) REVERT: K 5177 MET cc_start: 0.6583 (pmm) cc_final: 0.5966 (pmm) REVERT: K 5280 MET cc_start: 0.3677 (mtm) cc_final: 0.3452 (mtm) REVERT: T 387 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.5904 (m-30) REVERT: T 399 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7741 (tt) REVERT: T 457 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.8073 (p) REVERT: P 56 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6165 (m-80) REVERT: Q 56 TYR cc_start: 0.6806 (t80) cc_final: 0.6580 (t80) outliers start: 91 outliers final: 67 residues processed: 269 average time/residue: 0.1848 time to fit residues: 81.5571 Evaluate side-chains 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 191 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain R residue 86 HIS Chi-restraints excluded: chain R residue 121 CYS Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 162 LYS Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 299 LEU Chi-restraints excluded: chain N residue 376 ASP Chi-restraints excluded: chain N residue 388 SER Chi-restraints excluded: chain N residue 459 LEU Chi-restraints excluded: chain K residue 1552 ASP Chi-restraints excluded: chain K residue 5029 MET Chi-restraints excluded: chain K residue 5112 VAL Chi-restraints excluded: chain K residue 5176 HIS Chi-restraints excluded: chain K residue 5208 VAL Chi-restraints excluded: chain K residue 5232 ILE Chi-restraints excluded: chain K residue 5259 SER Chi-restraints excluded: chain K residue 5293 LEU Chi-restraints excluded: chain K residue 5424 ILE Chi-restraints excluded: chain K residue 5427 ILE Chi-restraints excluded: chain K residue 5452 MET Chi-restraints excluded: chain K residue 5466 THR Chi-restraints excluded: chain K residue 5485 VAL Chi-restraints excluded: chain K residue 5487 THR Chi-restraints excluded: chain K residue 5532 CYS Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 376 CYS Chi-restraints excluded: chain T residue 387 ASP Chi-restraints excluded: chain T residue 399 LEU Chi-restraints excluded: chain T residue 401 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 430 MET Chi-restraints excluded: chain T residue 457 SER Chi-restraints excluded: chain T residue 462 SER Chi-restraints excluded: chain T residue 495 ASP Chi-restraints excluded: chain T residue 516 SER Chi-restraints excluded: chain T residue 536 THR Chi-restraints excluded: chain T residue 538 HIS Chi-restraints excluded: chain T residue 577 ASN Chi-restraints excluded: chain T residue 588 ASP Chi-restraints excluded: chain T residue 592 ARG Chi-restraints excluded: chain T residue 607 LEU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 56 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 211 optimal weight: 20.0000 chunk 38 optimal weight: 0.0060 chunk 52 optimal weight: 0.1980 chunk 186 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 13 optimal weight: 40.0000 chunk 113 optimal weight: 2.9990 chunk 41 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 overall best weight: 3.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 2 GLN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 491 ASN ** T 605 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 = 0.3979 r_free = 0.3979 target = 0.109617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.071378 restraints weight = 81892.488| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.38 r_work: 0.2985 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 29370 Z= 0.292 Angle : 0.758 13.517 40961 Z= 0.401 Chirality : 0.049 0.315 4569 Planarity : 0.005 0.048 4224 Dihedral : 25.244 173.213 6255 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.80 % Favored : 93.16 % Rotamer: Outliers : 4.14 % Allowed : 22.88 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: -0.91 (0.16), residues: 2749 helix: 0.91 (0.18), residues: 815 sheet: -0.44 (0.24), residues: 467 loop : -1.58 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 29 TYR 0.030 0.002 TYR K5070 PHE 0.021 0.002 PHE N 213 TRP 0.023 0.002 TRP R 330 HIS 0.009 0.002 HIS T 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.29 (29336) covalent geometry : angle 0.74978 / 0.40 (40924) SS BOND : bond 0.00128 / 0.06 ( 2) SS BOND : angle 1.67869 / 3.01 ( 4) hydrogen bonds : bond 0.07057 / 7.81 ( 1169) hydrogen bonds : angle 4.36137 / 5.69 ( 3005) metal coordination : bond 0.01179 / 1.15 ( 32) metal coordination : angle 3.89983 / 3.92 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 189 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.7439 (ttp) cc_final: 0.6373 (tpp) REVERT: O 51 GLU cc_start: 0.7312 (pm20) cc_final: 0.7014 (pm20) REVERT: O 63 LYS cc_start: 0.7408 (mmmt) cc_final: 0.7130 (pttm) REVERT: C 41 GLU cc_start: 0.8175 (mp0) cc_final: 0.7869 (mp0) REVERT: C 94 ASN cc_start: 0.9400 (OUTLIER) cc_final: 0.9129 (t0) REVERT: R 80 GLU cc_start: 0.8673 (tp30) cc_final: 0.8368 (tp30) REVERT: R 115 ASP cc_start: 0.8250 (t0) cc_final: 0.7987 (t0) REVERT: N 128 MET cc_start: 0.8232 (mtm) cc_final: 0.7957 (mtm) REVERT: K 1360 MET cc_start: -0.0095 (OUTLIER) cc_final: -0.0800 (ppp) REVERT: K 1375 LEU cc_start: 0.8083 (tp) cc_final: 0.7560 (pt) REVERT: K 1404 TYR cc_start: 0.7198 (m-80) cc_final: 0.6847 (m-80) REVERT: K 5177 MET cc_start: 0.6932 (pmm) cc_final: 0.6271 (pmm) REVERT: T 399 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7682 (tt) REVERT: T 454 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7164 (p0) REVERT: T 457 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8220 (p) REVERT: T 459 SER cc_start: 0.8646 (t) cc_final: 0.8368 (t) REVERT: P 56 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.6292 (m-80) outliers start: 100 outliers final: 74 residues processed: 273 average time/residue: 0.1891 time to fit residues: 83.5198 Evaluate side-chains 262 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 182 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain R residue 121 CYS Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 162 LYS Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain N residue 204 ILE Chi-restraints excluded: chain N residue 299 LEU Chi-restraints excluded: chain N residue 376 ASP Chi-restraints excluded: chain N residue 388 SER Chi-restraints excluded: chain N residue 459 LEU Chi-restraints excluded: chain K residue 1360 MET Chi-restraints excluded: chain K residue 5029 MET Chi-restraints excluded: chain K residue 5112 VAL Chi-restraints excluded: chain K residue 5176 HIS Chi-restraints excluded: chain K residue 5208 VAL Chi-restraints excluded: chain K residue 5232 ILE Chi-restraints excluded: chain K residue 5259 SER Chi-restraints excluded: chain K residue 5293 LEU Chi-restraints excluded: chain K residue 5423 VAL Chi-restraints excluded: chain K residue 5424 ILE Chi-restraints excluded: chain K residue 5427 ILE Chi-restraints excluded: chain K residue 5452 MET Chi-restraints excluded: chain K residue 5466 THR Chi-restraints excluded: chain K residue 5485 VAL Chi-restraints excluded: chain K residue 5487 THR Chi-restraints excluded: chain K residue 5490 LYS Chi-restraints excluded: chain K residue 5532 CYS Chi-restraints excluded: chain T residue 376 CYS Chi-restraints excluded: chain T residue 399 LEU Chi-restraints excluded: chain T residue 401 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 457 SER Chi-restraints excluded: chain T residue 462 SER Chi-restraints excluded: chain T residue 516 SER Chi-restraints excluded: chain T residue 536 THR Chi-restraints excluded: chain T residue 538 HIS Chi-restraints excluded: chain T residue 577 ASN Chi-restraints excluded: chain T residue 588 ASP Chi-restraints excluded: chain T residue 607 LEU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 56 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 220 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 138 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 275 optimal weight: 0.8980 chunk 214 optimal weight: 8.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 351 HIS ** T 605 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 = 0.3997 r_free = 0.3997 target = 0.110682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.072706 restraints weight = 82157.620| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.36 r_work: 0.3021 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29370 Z= 0.193 Angle : 0.664 12.388 40961 Z= 0.356 Chirality : 0.045 0.366 4569 Planarity : 0.004 0.049 4224 Dihedral : 25.138 171.874 6251 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.43 % Rotamer: Outliers : 3.65 % Allowed : 23.37 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: -0.72 (0.16), residues: 2749 helix: 1.15 (0.19), residues: 818 sheet: -0.33 (0.24), residues: 463 loop : -1.53 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 592 TYR 0.027 0.001 TYR K5070 PHE 0.014 0.001 PHE O 4 TRP 0.014 0.001 TRP R 286 HIS 0.006 0.001 HIS T 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (29336) covalent geometry : angle 0.65676 / 0.36 (40924) SS BOND : bond 0.00501 / 0.25 ( 2) SS BOND : angle 2.06163 / 3.98 ( 4) hydrogen bonds : bond 0.05689 / 6.34 ( 1169) hydrogen bonds : angle 4.11334 / 5.36 ( 3005) metal coordination : bond 0.00903 / 0.88 ( 32) metal coordination : angle 3.39079 / 3.36 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 194 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.7508 (ttp) cc_final: 0.6566 (tpp) REVERT: O 63 LYS cc_start: 0.7541 (mmmt) cc_final: 0.7320 (pttm) REVERT: A 105 GLU cc_start: 0.8254 (tm-30) cc_final: 0.8020 (tm-30) REVERT: C 41 GLU cc_start: 0.8199 (mp0) cc_final: 0.7862 (mp0) REVERT: D 33 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6170 (mtp180) REVERT: R 80 GLU cc_start: 0.8672 (tp30) cc_final: 0.8328 (tp30) REVERT: R 115 ASP cc_start: 0.8224 (t0) cc_final: 0.7974 (t0) REVERT: N 128 MET cc_start: 0.8216 (mtm) cc_final: 0.7943 (mtm) REVERT: K 1360 MET cc_start: -0.0138 (ttp) cc_final: -0.0836 (ppp) REVERT: K 1375 LEU cc_start: 0.8044 (tp) cc_final: 0.7598 (pt) REVERT: K 1404 TYR cc_start: 0.7052 (m-80) cc_final: 0.6720 (m-80) REVERT: K 5177 MET cc_start: 0.6788 (pmm) cc_final: 0.6169 (pmm) REVERT: T 399 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7740 (tt) REVERT: T 457 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8173 (p) REVERT: P 56 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6273 (m-80) outliers start: 88 outliers final: 73 residues processed: 264 average time/residue: 0.1913 time to fit residues: 81.9642 Evaluate side-chains 261 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 184 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain R residue 121 CYS Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 162 LYS Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain N residue 204 ILE Chi-restraints excluded: chain N residue 299 LEU Chi-restraints excluded: chain N residue 355 GLU Chi-restraints excluded: chain N residue 376 ASP Chi-restraints excluded: chain N residue 388 SER Chi-restraints excluded: chain N residue 459 LEU Chi-restraints excluded: chain K residue 1368 SER Chi-restraints excluded: chain K residue 5029 MET Chi-restraints excluded: chain K residue 5112 VAL Chi-restraints excluded: chain K residue 5176 HIS Chi-restraints excluded: chain K residue 5232 ILE Chi-restraints excluded: chain K residue 5259 SER Chi-restraints excluded: chain K residue 5293 LEU Chi-restraints excluded: chain K residue 5423 VAL Chi-restraints excluded: chain K residue 5424 ILE Chi-restraints excluded: chain K residue 5427 ILE Chi-restraints excluded: chain K residue 5452 MET Chi-restraints excluded: chain K residue 5466 THR Chi-restraints excluded: chain K residue 5485 VAL Chi-restraints excluded: chain K residue 5487 THR Chi-restraints excluded: chain K residue 5532 CYS Chi-restraints excluded: chain T residue 376 CYS Chi-restraints excluded: chain T residue 399 LEU Chi-restraints excluded: chain T residue 401 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 430 MET Chi-restraints excluded: chain T residue 457 SER Chi-restraints excluded: chain T residue 462 SER Chi-restraints excluded: chain T residue 492 LEU Chi-restraints excluded: chain T residue 516 SER Chi-restraints excluded: chain T residue 536 THR Chi-restraints excluded: chain T residue 538 HIS Chi-restraints excluded: chain T residue 577 ASN Chi-restraints excluded: chain T residue 588 ASP Chi-restraints excluded: chain T residue 607 LEU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 56 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 64 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 203 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 218 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 295 optimal weight: 0.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5105 ASN ** K5164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5459 HIS ** T 605 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 = 0.3996 r_free = 0.3996 target = 0.110553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.072678 restraints weight = 81418.002| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.38 r_work: 0.3019 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 29370 Z= 0.209 Angle : 0.676 11.946 40961 Z= 0.362 Chirality : 0.045 0.314 4569 Planarity : 0.004 0.048 4224 Dihedral : 25.156 172.072 6251 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.55 % Favored : 93.42 % Rotamer: Outliers : 3.40 % Allowed : 23.33 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: -0.72 (0.16), residues: 2749 helix: 1.17 (0.19), residues: 818 sheet: -0.32 (0.24), residues: 463 loop : -1.55 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K5174 TYR 0.029 0.001 TYR K5070 PHE 0.014 0.001 PHE N 213 TRP 0.022 0.002 TRP R 330 HIS 0.006 0.001 HIS T 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (29336) covalent geometry : angle 0.66901 / 0.36 (40924) SS BOND : bond 0.00086 / 0.04 ( 2) SS BOND : angle 2.03482 / 3.91 ( 4) hydrogen bonds : bond 0.05734 / 6.38 ( 1169) hydrogen bonds : angle 4.12972 / 5.37 ( 3005) metal coordination : bond 0.00918 / 0.90 ( 32) metal coordination : angle 3.34539 / 3.39 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5498 Ramachandran restraints generated. 2749 Oldfield, 0 Emsley, 2749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 193 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.7496 (ttp) cc_final: 0.6580 (tpp) REVERT: O 63 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7411 (pttm) REVERT: C 41 GLU cc_start: 0.8177 (mp0) cc_final: 0.7818 (mp0) REVERT: D 33 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6254 (mtp180) REVERT: R 80 GLU cc_start: 0.8623 (tp30) cc_final: 0.8374 (tp30) REVERT: R 115 ASP cc_start: 0.8238 (t0) cc_final: 0.7968 (t0) REVERT: N 128 MET cc_start: 0.8203 (mtm) cc_final: 0.7953 (mtm) REVERT: K 1360 MET cc_start: -0.0183 (OUTLIER) cc_final: -0.0820 (ppp) REVERT: K 1375 LEU cc_start: 0.8073 (tp) cc_final: 0.7584 (pt) REVERT: K 1376 MET cc_start: 0.6181 (mtm) cc_final: 0.5974 (mtm) REVERT: K 1404 TYR cc_start: 0.7165 (m-80) cc_final: 0.6813 (m-80) REVERT: K 5177 MET cc_start: 0.6838 (pmm) cc_final: 0.6221 (pmm) REVERT: T 399 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7768 (tt) REVERT: T 457 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8082 (p) REVERT: T 459 SER cc_start: 0.8656 (t) cc_final: 0.8395 (t) REVERT: P 56 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.6299 (m-80) outliers start: 82 outliers final: 73 residues processed: 259 average time/residue: 0.1899 time to fit residues: 79.6353 Evaluate side-chains 264 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 186 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain R residue 121 CYS Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 162 LYS Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain N residue 204 ILE Chi-restraints excluded: chain N residue 299 LEU Chi-restraints excluded: chain N residue 376 ASP Chi-restraints excluded: chain N residue 388 SER Chi-restraints excluded: chain N residue 459 LEU Chi-restraints excluded: chain K residue 1360 MET Chi-restraints excluded: chain K residue 1368 SER Chi-restraints excluded: chain K residue 5029 MET Chi-restraints excluded: chain K residue 5112 VAL Chi-restraints excluded: chain K residue 5176 HIS Chi-restraints excluded: chain K residue 5208 VAL Chi-restraints excluded: chain K residue 5232 ILE Chi-restraints excluded: chain K residue 5259 SER Chi-restraints excluded: chain K residue 5293 LEU Chi-restraints excluded: chain K residue 5423 VAL Chi-restraints excluded: chain K residue 5424 ILE Chi-restraints excluded: chain K residue 5427 ILE Chi-restraints excluded: chain K residue 5452 MET Chi-restraints excluded: chain K residue 5466 THR Chi-restraints excluded: chain K residue 5485 VAL Chi-restraints excluded: chain K residue 5487 THR Chi-restraints excluded: chain K residue 5532 CYS Chi-restraints excluded: chain T residue 376 CYS Chi-restraints excluded: chain T residue 399 LEU Chi-restraints excluded: chain T residue 401 VAL Chi-restraints excluded: chain T residue 416 VAL Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 457 SER Chi-restraints excluded: chain T residue 462 SER Chi-restraints excluded: chain T residue 492 LEU Chi-restraints excluded: chain T residue 516 SER Chi-restraints excluded: chain T residue 536 THR Chi-restraints excluded: chain T residue 538 HIS Chi-restraints excluded: chain T residue 577 ASN Chi-restraints excluded: chain T residue 588 ASP Chi-restraints excluded: chain T residue 607 LEU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 56 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 2 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 180 optimal weight: 0.3980 chunk 159 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 198 optimal weight: 20.0000 chunk 255 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.112240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.074807 restraints weight = 81940.782| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.38 r_work: 0.3075 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29370 Z= 0.129 Angle : 0.622 10.852 40961 Z= 0.336 Chirality : 0.043 0.323 4569 Planarity : 0.004 0.048 4224 Dihedral : 25.011 173.353 6251 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.16 % Rotamer: Outliers : 2.74 % Allowed : 23.95 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2749 helix: 1.44 (0.19), residues: 815 sheet: -0.12 (0.24), residues: 463 loop : -1.46 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 374 TYR 0.027 0.001 TYR R 243 PHE 0.014 0.001 PHE K5125 TRP 0.025 0.001 TRP R 330 HIS 0.005 0.001 HIS T 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 (29336) covalent geometry : angle 0.61686 / 0.34 (40924) SS BOND : bond 0.00124 / 0.06 ( 2) SS BOND : angle 2.09179 / 3.99 ( 4) hydrogen bonds : bond 0.04584 / 5.16 ( 1169) hydrogen bonds : angle 3.86533 / 5.00 ( 3005) metal coordination : bond 0.00782 / 0.76 ( 32) metal coordination : angle 2.92054 / 2.91 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7696.73 seconds wall clock time: 132 minutes 43.54 seconds (7963.54 seconds total)