Starting phenix.real_space_refine on Sat Mar 7 12:47:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7re3_24432/03_2026/7re3_24432.cif Found real_map, /net/cci-nas-00/data/ceres_data/7re3_24432/03_2026/7re3_24432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7re3_24432/03_2026/7re3_24432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7re3_24432/03_2026/7re3_24432.map" model { file = "/net/cci-nas-00/data/ceres_data/7re3_24432/03_2026/7re3_24432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7re3_24432/03_2026/7re3_24432.cif" } resolution = 3.33 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= 0.009 sd= 0.100 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: 9 Type Number sf(0) Gaussians Zn 16 6.06 5 Al 4 5.89 5 P 154 5.49 5 Mg 6 5.21 5 S 302 5.16 5 C 26795 2.51 5 N 7293 2.21 5 O 8572 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43154 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1408 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1415 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 4507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4507 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 5, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "F" Number of atoms: 4563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4563 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "H" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1405 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "P" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "T" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 789 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna3p': 36} Chain: "G" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "I" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "J" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1406 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "K" Number of atoms: 4507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4507 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 5, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "L" Number of atoms: 4563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4563 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "Q" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "U" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 789 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 71.716 107.817 125.241 1.00 48.15 S ATOM 2495 SG CYS A 306 72.969 110.339 122.628 1.00 44.53 S ATOM 2527 SG CYS A 310 69.230 109.649 123.106 1.00 42.04 S ATOM 3935 SG CYS A 487 84.164 105.204 141.355 1.00 49.55 S ATOM 5188 SG CYS A 645 86.371 107.163 138.880 1.00 53.05 S ATOM 5194 SG CYS A 646 83.512 104.900 137.678 1.00 49.44 S ATOM 10896 SG CYS E 5 64.983 101.397 206.009 1.00214.26 S ATOM 10917 SG CYS E 8 63.948 104.559 207.246 1.00216.50 S ATOM 11055 SG CYS E 26 67.501 104.495 206.541 1.00216.99 S ATOM 11076 SG CYS E 29 66.080 102.267 209.512 1.00221.11 S ATOM 11241 SG CYS E 50 89.647 92.342 201.046 1.00222.74 S ATOM 11271 SG CYS E 55 90.295 89.014 202.792 1.00227.14 S ATOM 11404 SG CYS E 72 91.723 92.243 204.282 1.00224.64 S ATOM 10978 SG CYS E 16 70.977 92.282 205.816 1.00231.46 S ATOM 10993 SG CYS E 19 67.685 90.636 206.252 1.00236.80 S ATOM 15403 SG CYS F 5 92.499 72.975 173.413 1.00112.81 S ATOM 15424 SG CYS F 8 92.298 72.641 177.001 1.00112.92 S ATOM 15562 SG CYS F 26 94.577 75.414 175.796 1.00115.34 S ATOM 15583 SG CYS F 29 95.774 72.066 175.376 1.00114.77 S ATOM 15748 SG CYS F 50 106.308 89.273 157.575 1.00122.55 S ATOM 15778 SG CYS F 55 109.082 87.894 155.120 1.00126.81 S ATOM 15911 SG CYS F 72 110.114 88.749 158.804 1.00126.94 S ATOM 15485 SG CYS F 16 99.009 73.174 164.183 1.00111.33 S ATOM 15500 SG CYS F 19 96.770 70.039 163.475 1.00112.67 S ATOM 25306 SG CYS G 301 72.176 83.415 108.855 1.00 50.96 S ATOM 25347 SG CYS G 306 73.461 80.929 111.486 1.00 48.51 S ATOM 25379 SG CYS G 310 69.712 81.524 110.963 1.00 45.17 S ATOM 26787 SG CYS G 487 84.745 86.319 92.885 1.00 49.74 S ATOM 28040 SG CYS G 645 86.972 84.420 95.390 1.00 53.15 S ATOM 28046 SG CYS G 646 84.042 86.611 96.554 1.00 50.84 S ATOM 32331 SG CYS K 5 66.246 89.554 28.003 1.00243.70 S ATOM 32352 SG CYS K 8 65.305 86.366 26.758 1.00245.07 S ATOM 32490 SG CYS K 26 68.847 86.520 27.505 1.00242.75 S ATOM 32511 SG CYS K 29 67.405 88.708 24.514 1.00249.13 S ATOM 32676 SG CYS K 50 90.613 99.235 33.243 1.00236.04 S ATOM 32706 SG CYS K 55 91.198 102.576 31.499 1.00235.61 S ATOM 32839 SG CYS K 72 92.724 99.382 30.031 1.00234.50 S ATOM 32413 SG CYS K 16 72.005 98.818 28.251 1.00257.69 S ATOM 32428 SG CYS K 19 68.678 100.380 27.774 1.00268.30 S ATOM 36838 SG CYS L 5 92.646 118.705 60.875 1.00118.72 S ATOM 36859 SG CYS L 8 92.480 119.029 57.285 1.00119.51 S ATOM 36997 SG CYS L 26 94.813 116.316 58.521 1.00121.36 S ATOM 37018 SG CYS L 29 95.921 119.693 58.950 1.00121.71 S ATOM 37183 SG CYS L 50 106.673 102.781 76.903 1.00127.49 S ATOM 37213 SG CYS L 55 109.381 104.233 79.389 1.00133.66 S ATOM 37346 SG CYS L 72 110.478 103.399 75.718 1.00132.22 S ATOM 36920 SG CYS L 16 99.050 118.682 70.183 1.00117.47 S ATOM 36935 SG CYS L 19 96.724 121.761 70.859 1.00117.79 S Time building chain proxies: 9.53, per 1000 atoms: 0.22 Number of scatterers: 43154 At special positions: 0 Unit cell: (166.92, 192.6, 234.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 16 29.99 S 302 16.00 P 154 15.00 Al 4 13.00 Mg 6 11.99 F 12 9.00 O 8572 8.00 N 7293 7.00 C 26795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " pdb=" ZN G2000 " pdb="ZN ZN G2000 " - pdb=" ND1 HIS G 295 " pdb="ZN ZN G2000 " - pdb=" SG CYS G 310 " pdb="ZN ZN G2000 " - pdb=" SG CYS G 301 " pdb="ZN ZN G2000 " - pdb=" SG CYS G 306 " pdb=" ZN G2001 " pdb="ZN ZN G2001 " - pdb=" ND1 HIS G 642 " pdb="ZN ZN G2001 " - pdb=" SG CYS G 487 " pdb="ZN ZN G2001 " - pdb=" SG CYS G 646 " pdb="ZN ZN G2001 " - pdb=" SG CYS G 645 " pdb=" ZN K 701 " pdb="ZN ZN K 701 " - pdb=" SG CYS K 8 " pdb="ZN ZN K 701 " - pdb=" SG CYS K 5 " pdb="ZN ZN K 701 " - pdb=" SG CYS K 29 " pdb="ZN ZN K 701 " - pdb=" SG CYS K 26 " pdb=" ZN K 702 " pdb="ZN ZN K 702 " - pdb=" ND1 HIS K 75 " pdb="ZN ZN K 702 " - pdb=" SG CYS K 72 " pdb="ZN ZN K 702 " - pdb=" SG CYS K 55 " pdb="ZN ZN K 702 " - pdb=" SG CYS K 50 " pdb=" ZN K 703 " pdb="ZN ZN K 703 " - pdb=" NE2 HIS K 33 " pdb="ZN ZN K 703 " - pdb=" ND1 HIS K 39 " pdb="ZN ZN K 703 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 703 " - pdb=" SG CYS K 16 " pdb=" ZN L1000 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 8 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 26 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 29 " pdb="ZN ZN L1000 " - pdb=" SG CYS L 5 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 75 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 55 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 72 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 50 " pdb=" ZN L1002 " pdb="ZN ZN L1002 " - pdb=" NE2 HIS L 33 " pdb="ZN ZN L1002 " - pdb=" ND1 HIS L 39 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 19 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 16 " Number of angles added : 52 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9748 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 62 sheets defined 42.7% alpha, 11.6% beta 68 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 4.90 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.759A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 169 through 177 removed outlier: 3.990A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.613A pdb=" N GLN A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.695A pdb=" N GLN A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.752A pdb=" N SER A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.826A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.773A pdb=" N LEU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.814A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.610A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.598A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.592A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.662A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 4.157A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.924A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.718A pdb=" N TYR A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 687 through 710 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 767 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.620A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.971A pdb=" N LYS A 798 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 902 removed outlier: 4.097A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 915 removed outlier: 4.398A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.590A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 97 removed outlier: 3.638A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.899A pdb=" N VAL C 6 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.954A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 removed outlier: 4.047A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.643A pdb=" N CYS C 72 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU C 73 " --> pdb=" O LYS C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 69 through 73' Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 32 through 99 removed outlier: 3.939A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR D 84 " --> pdb=" O ARG D 80 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N SER D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 98 " --> pdb=" O MET D 94 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.692A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'E' and resid 27 through 37 Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.964A pdb=" N ALA E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'E' and resid 127 through 146 Processing helix chain 'E' and resid 260 through 264 removed outlier: 3.752A pdb=" N SER E 263 " --> pdb=" O ASP E 260 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER E 264 " --> pdb=" O GLU E 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 260 through 264' Processing helix chain 'E' and resid 265 through 274 Processing helix chain 'E' and resid 287 through 299 removed outlier: 3.926A pdb=" N ALA E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 325 Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 376 through 379 Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 Processing helix chain 'E' and resid 445 through 456 removed outlier: 4.150A pdb=" N ALA E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 456 " --> pdb=" O VAL E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 499 Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.519A pdb=" N TRP E 506 " --> pdb=" O ASN E 503 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG E 507 " --> pdb=" O PRO E 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 503 through 507' Processing helix chain 'E' and resid 515 through 527 removed outlier: 4.259A pdb=" N SER E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE E 525 " --> pdb=" O VAL E 521 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU E 526 " --> pdb=" O ALA E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.761A pdb=" N THR F 37 " --> pdb=" O HIS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 63 Processing helix chain 'F' and resid 102 through 111 Processing helix chain 'F' and resid 116 through 123 removed outlier: 4.377A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 147 removed outlier: 3.865A pdb=" N PHE F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'F' and resid 265 through 275 removed outlier: 3.776A pdb=" N GLN F 275 " --> pdb=" O LYS F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 3.695A pdb=" N TYR F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 324 Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 418 through 422 removed outlier: 3.518A pdb=" N PHE F 422 " --> pdb=" O PRO F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 432 removed outlier: 3.651A pdb=" N ILE F 432 " --> pdb=" O LEU F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.506A pdb=" N VAL F 456 " --> pdb=" O VAL F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 499 removed outlier: 3.869A pdb=" N ILE F 493 " --> pdb=" O ASN F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 526 removed outlier: 4.388A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU F 526 " --> pdb=" O ALA F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 536 No H-bonds generated for 'chain 'F' and resid 534 through 536' Processing helix chain 'F' and resid 557 through 566 removed outlier: 3.809A pdb=" N PHE F 561 " --> pdb=" O ASN F 557 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR F 566 " --> pdb=" O ASN F 562 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 29 Processing helix chain 'H' and resid 31 through 97 removed outlier: 3.867A pdb=" N ALA H 54 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N MET H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS H 82 " --> pdb=" O ASP H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 removed outlier: 3.511A pdb=" N ALA H 110 " --> pdb=" O ILE H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 125 Processing helix chain 'H' and resid 134 through 142 Processing helix chain 'H' and resid 176 through 180 Processing helix chain 'G' and resid 4 through 13 removed outlier: 3.759A pdb=" N LEU G 8 " --> pdb=" O ALA G 4 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 90 Processing helix chain 'G' and resid 123 through 133 Processing helix chain 'G' and resid 142 through 149 Processing helix chain 'G' and resid 155 through 159 Processing helix chain 'G' and resid 169 through 177 removed outlier: 3.990A pdb=" N ARG G 173 " --> pdb=" O PRO G 169 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN G 177 " --> pdb=" O ARG G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 200 removed outlier: 3.612A pdb=" N GLN G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA G 185 " --> pdb=" O ARG G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 210 removed outlier: 3.695A pdb=" N GLN G 210 " --> pdb=" O LEU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 242 removed outlier: 3.751A pdb=" N SER G 239 " --> pdb=" O ASP G 235 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU G 240 " --> pdb=" O SER G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 251 through 260 removed outlier: 3.825A pdb=" N SER G 255 " --> pdb=" O THR G 252 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS G 256 " --> pdb=" O ALA G 253 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL G 257 " --> pdb=" O GLU G 254 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASP G 258 " --> pdb=" O SER G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 287 Processing helix chain 'G' and resid 297 through 301 Processing helix chain 'G' and resid 303 through 318 removed outlier: 3.773A pdb=" N LEU G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS G 309 " --> pdb=" O ARG G 305 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU G 316 " --> pdb=" O ASN G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 326 removed outlier: 3.814A pdb=" N PHE G 326 " --> pdb=" O PRO G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 377 Processing helix chain 'G' and resid 377 through 385 removed outlier: 4.610A pdb=" N HIS G 381 " --> pdb=" O ASP G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 425 Processing helix chain 'G' and resid 447 through 454 removed outlier: 3.598A pdb=" N SER G 451 " --> pdb=" O ASN G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 455 through 459 Processing helix chain 'G' and resid 465 through 480 removed outlier: 4.592A pdb=" N PHE G 471 " --> pdb=" O ARG G 467 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU G 474 " --> pdb=" O LEU G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 509 removed outlier: 3.662A pdb=" N TRP G 509 " --> pdb=" O PHE G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 519 removed outlier: 4.157A pdb=" N TYR G 515 " --> pdb=" O LYS G 511 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET G 519 " --> pdb=" O TYR G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 520 through 532 Processing helix chain 'G' and resid 561 through 580 removed outlier: 3.923A pdb=" N THR G 567 " --> pdb=" O CYS G 563 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS G 574 " --> pdb=" O GLN G 570 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU G 575 " --> pdb=" O PHE G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 596 through 606 removed outlier: 3.719A pdb=" N TYR G 606 " --> pdb=" O LEU G 602 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 638 Processing helix chain 'G' and resid 647 through 662 Processing helix chain 'G' and resid 687 through 710 Processing helix chain 'G' and resid 717 through 733 Processing helix chain 'G' and resid 738 through 753 Processing helix chain 'G' and resid 767 through 774 Processing helix chain 'G' and resid 778 through 791 removed outlier: 3.620A pdb=" N ASN G 791 " --> pdb=" O TYR G 787 " (cutoff:3.500A) Processing helix chain 'G' and resid 795 through 799 removed outlier: 3.971A pdb=" N LYS G 798 " --> pdb=" O SER G 795 " (cutoff:3.500A) Processing helix chain 'G' and resid 833 through 842 Processing helix chain 'G' and resid 856 through 866 Processing helix chain 'G' and resid 867 through 872 Processing helix chain 'G' and resid 874 through 902 removed outlier: 4.097A pdb=" N VAL G 880 " --> pdb=" O GLU G 876 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE G 881 " --> pdb=" O TYR G 877 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS G 882 " --> pdb=" O ALA G 878 " (cutoff:3.500A) Processing helix chain 'G' and resid 911 through 915 removed outlier: 4.398A pdb=" N ARG G 914 " --> pdb=" O ASN G 911 " (cutoff:3.500A) Processing helix chain 'G' and resid 918 through 923 Processing helix chain 'G' and resid 924 through 926 No H-bonds generated for 'chain 'G' and resid 924 through 926' Processing helix chain 'I' and resid 2 through 20 removed outlier: 3.899A pdb=" N VAL I 6 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS I 7 " --> pdb=" O MET I 3 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS I 8 " --> pdb=" O SER I 4 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR I 9 " --> pdb=" O ASP I 5 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 41 removed outlier: 3.953A pdb=" N GLN I 31 " --> pdb=" O LYS I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 61 removed outlier: 4.047A pdb=" N ALA I 48 " --> pdb=" O ASP I 44 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL I 58 " --> pdb=" O SER I 54 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU I 59 " --> pdb=" O LEU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 73 removed outlier: 3.643A pdb=" N CYS I 72 " --> pdb=" O ASN I 69 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU I 73 " --> pdb=" O LYS I 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 69 through 73' Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 32 through 99 removed outlier: 3.939A pdb=" N ASP J 52 " --> pdb=" O GLU J 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS J 82 " --> pdb=" O ASP J 78 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL J 83 " --> pdb=" O LYS J 79 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR J 84 " --> pdb=" O ARG J 80 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N SER J 85 " --> pdb=" O ALA J 81 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU J 98 " --> pdb=" O MET J 94 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP J 99 " --> pdb=" O LEU J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 112 removed outlier: 3.692A pdb=" N ASP J 112 " --> pdb=" O ASN J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 141 Processing helix chain 'K' and resid 27 through 37 Processing helix chain 'K' and resid 102 through 112 removed outlier: 3.963A pdb=" N ALA K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 123 Processing helix chain 'K' and resid 127 through 146 Processing helix chain 'K' and resid 260 through 264 removed outlier: 3.751A pdb=" N SER K 263 " --> pdb=" O ASP K 260 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER K 264 " --> pdb=" O GLU K 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 260 through 264' Processing helix chain 'K' and resid 265 through 274 Processing helix chain 'K' and resid 287 through 299 removed outlier: 3.925A pdb=" N ALA K 292 " --> pdb=" O LYS K 288 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE K 293 " --> pdb=" O SER K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 325 Processing helix chain 'K' and resid 361 through 363 No H-bonds generated for 'chain 'K' and resid 361 through 363' Processing helix chain 'K' and resid 376 through 379 Processing helix chain 'K' and resid 380 through 391 Processing helix chain 'K' and resid 418 through 422 Processing helix chain 'K' and resid 423 through 432 Processing helix chain 'K' and resid 445 through 456 removed outlier: 4.150A pdb=" N ALA K 454 " --> pdb=" O ASP K 450 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU K 455 " --> pdb=" O THR K 451 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL K 456 " --> pdb=" O VAL K 452 " (cutoff:3.500A) Processing helix chain 'K' and resid 489 through 499 Processing helix chain 'K' and resid 503 through 507 removed outlier: 3.519A pdb=" N TRP K 506 " --> pdb=" O ASN K 503 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG K 507 " --> pdb=" O PRO K 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 503 through 507' Processing helix chain 'K' and resid 515 through 527 removed outlier: 4.258A pdb=" N SER K 523 " --> pdb=" O ASN K 519 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LYS K 524 " --> pdb=" O ALA K 520 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE K 525 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU K 526 " --> pdb=" O ALA K 522 " (cutoff:3.500A) Processing helix chain 'K' and resid 557 through 566 Processing helix chain 'L' and resid 26 through 37 removed outlier: 3.761A pdb=" N THR L 37 " --> pdb=" O HIS L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 63 Processing helix chain 'L' and resid 102 through 111 Processing helix chain 'L' and resid 116 through 123 removed outlier: 4.376A pdb=" N TYR L 120 " --> pdb=" O ASN L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 147 removed outlier: 3.864A pdb=" N PHE L 133 " --> pdb=" O ARG L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 264 No H-bonds generated for 'chain 'L' and resid 262 through 264' Processing helix chain 'L' and resid 265 through 275 removed outlier: 3.777A pdb=" N GLN L 275 " --> pdb=" O LYS L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 299 removed outlier: 3.695A pdb=" N TYR L 299 " --> pdb=" O LEU L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 324 Processing helix chain 'L' and resid 361 through 363 No H-bonds generated for 'chain 'L' and resid 361 through 363' Processing helix chain 'L' and resid 380 through 390 Processing helix chain 'L' and resid 418 through 422 removed outlier: 3.519A pdb=" N PHE L 422 " --> pdb=" O PRO L 419 " (cutoff:3.500A) Processing helix chain 'L' and resid 423 through 432 removed outlier: 3.652A pdb=" N ILE L 432 " --> pdb=" O LEU L 428 " (cutoff:3.500A) Processing helix chain 'L' and resid 445 through 456 removed outlier: 3.505A pdb=" N VAL L 456 " --> pdb=" O VAL L 452 " (cutoff:3.500A) Processing helix chain 'L' and resid 489 through 499 removed outlier: 3.870A pdb=" N ILE L 493 " --> pdb=" O ASN L 489 " (cutoff:3.500A) Processing helix chain 'L' and resid 515 through 526 removed outlier: 4.389A pdb=" N SER L 523 " --> pdb=" O ASN L 519 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS L 524 " --> pdb=" O ALA L 520 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE L 525 " --> pdb=" O VAL L 521 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU L 526 " --> pdb=" O ALA L 522 " (cutoff:3.500A) Processing helix chain 'L' and resid 534 through 536 No H-bonds generated for 'chain 'L' and resid 534 through 536' Processing helix chain 'L' and resid 557 through 566 removed outlier: 3.810A pdb=" N PHE L 561 " --> pdb=" O ASN L 557 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR L 566 " --> pdb=" O ASN L 562 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.114A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.076A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.378A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 339 removed outlier: 6.944A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.710A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 149 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 614 through 616 Processing sheet with id=AA9, first strand: chain 'A' and resid 757 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 815 through 822 Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.714A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.714A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL D 167 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB5, first strand: chain 'E' and resid 24 through 25 removed outlier: 3.551A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AB7, first strand: chain 'E' and resid 152 through 153 Processing sheet with id=AB8, first strand: chain 'E' and resid 209 through 213 removed outlier: 3.679A pdb=" N GLU E 201 " --> pdb=" O VAL E 210 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL E 226 " --> pdb=" O THR E 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 355 through 359 removed outlier: 6.819A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP E 374 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR E 307 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET E 436 " --> pdb=" O THR E 279 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 331 through 332 Processing sheet with id=AC2, first strand: chain 'E' and resid 472 through 473 removed outlier: 6.485A pdb=" N PHE E 472 " --> pdb=" O CYS E 574 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N TYR E 541 " --> pdb=" O LYS E 569 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY E 571 " --> pdb=" O TYR E 541 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR E 543 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU E 573 " --> pdb=" O TYR E 543 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE E 545 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE E 575 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR E 547 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N THR E 547 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE E 512 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 481 through 482 Processing sheet with id=AC4, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC5, first strand: chain 'F' and resid 24 through 25 removed outlier: 3.939A pdb=" N LEU F 14 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AC7, first strand: chain 'F' and resid 165 through 166 Processing sheet with id=AC8, first strand: chain 'F' and resid 162 through 163 Processing sheet with id=AC9, first strand: chain 'F' and resid 182 through 183 Processing sheet with id=AD1, first strand: chain 'F' and resid 186 through 188 Processing sheet with id=AD2, first strand: chain 'F' and resid 330 through 332 removed outlier: 6.207A pdb=" N SER F 331 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR F 359 " --> pdb=" O SER F 331 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER F 278 " --> pdb=" O TYR F 398 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLY F 400 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU F 280 " --> pdb=" O GLY F 400 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 366 through 367 removed outlier: 7.391A pdb=" N THR F 366 " --> pdb=" O ARG F 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 471 through 475 removed outlier: 3.902A pdb=" N MET F 576 " --> pdb=" O MET F 474 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASP F 542 " --> pdb=" O LYS F 569 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR F 547 " --> pdb=" O ILE F 512 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N PHE F 511 " --> pdb=" O GLN F 531 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 115 through 116 removed outlier: 7.138A pdb=" N GLY G 327 " --> pdb=" O TYR G 346 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR G 346 " --> pdb=" O GLY G 327 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU G 329 " --> pdb=" O THR G 344 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 146 through 149 removed outlier: 3.534A pdb=" N TYR H 149 " --> pdb=" O ALA H 152 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE H 156 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU H 189 " --> pdb=" O ILE H 156 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS H 127 " --> pdb=" O LEU G 387 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEU G 389 " --> pdb=" O LYS H 127 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET H 129 " --> pdb=" O LEU G 389 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU G 388 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL G 398 " --> pdb=" O LEU G 388 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER G 397 " --> pdb=" O VAL G 675 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL G 675 " --> pdb=" O SER G 397 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR G 540 " --> pdb=" O MET G 668 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 19 through 21 removed outlier: 5.115A pdb=" N SER G 68 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TYR G 69 " --> pdb=" O ARG G 118 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 36 through 38 Processing sheet with id=AD9, first strand: chain 'G' and resid 223 through 224 removed outlier: 7.075A pdb=" N VAL G 233 " --> pdb=" O ILE G 201 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLY G 203 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 338 through 339 removed outlier: 6.944A pdb=" N PHE G 334 " --> pdb=" O SER G 363 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 414 through 415 Processing sheet with id=AE3, first strand: chain 'G' and resid 614 through 616 Processing sheet with id=AE4, first strand: chain 'G' and resid 757 through 758 Processing sheet with id=AE5, first strand: chain 'G' and resid 815 through 822 Processing sheet with id=AE6, first strand: chain 'J' and resid 127 through 132 removed outlier: 6.714A pdb=" N LEU J 189 " --> pdb=" O ILE J 156 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE J 156 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 127 through 132 removed outlier: 6.714A pdb=" N LEU J 189 " --> pdb=" O ILE J 156 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE J 156 " --> pdb=" O LEU J 189 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL J 159 " --> pdb=" O VAL J 167 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL J 167 " --> pdb=" O VAL J 159 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 3 through 4 Processing sheet with id=AE9, first strand: chain 'K' and resid 24 through 25 removed outlier: 3.551A pdb=" N LEU K 14 " --> pdb=" O LEU K 25 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 64 through 66 Processing sheet with id=AF2, first strand: chain 'K' and resid 152 through 153 Processing sheet with id=AF3, first strand: chain 'K' and resid 209 through 213 removed outlier: 3.678A pdb=" N GLU K 201 " --> pdb=" O VAL K 210 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL K 226 " --> pdb=" O THR K 183 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 355 through 359 removed outlier: 6.820A pdb=" N VAL K 305 " --> pdb=" O VAL K 372 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASP K 374 " --> pdb=" O VAL K 305 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR K 307 " --> pdb=" O ASP K 374 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER K 278 " --> pdb=" O TYR K 398 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET K 436 " --> pdb=" O THR K 279 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 331 through 332 Processing sheet with id=AF6, first strand: chain 'K' and resid 472 through 473 removed outlier: 6.486A pdb=" N PHE K 472 " --> pdb=" O CYS K 574 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N TYR K 541 " --> pdb=" O LYS K 569 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLY K 571 " --> pdb=" O TYR K 541 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR K 543 " --> pdb=" O GLY K 571 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU K 573 " --> pdb=" O TYR K 543 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE K 545 " --> pdb=" O LEU K 573 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE K 575 " --> pdb=" O ILE K 545 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR K 547 " --> pdb=" O ILE K 575 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL K 510 " --> pdb=" O ILE K 545 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N THR K 547 " --> pdb=" O VAL K 510 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE K 512 " --> pdb=" O THR K 547 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE K 511 " --> pdb=" O GLN K 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'K' and resid 481 through 482 Processing sheet with id=AF8, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AF9, first strand: chain 'L' and resid 24 through 25 removed outlier: 3.938A pdb=" N LEU L 14 " --> pdb=" O LEU L 25 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 64 through 66 Processing sheet with id=AG2, first strand: chain 'L' and resid 165 through 166 Processing sheet with id=AG3, first strand: chain 'L' and resid 162 through 163 Processing sheet with id=AG4, first strand: chain 'L' and resid 182 through 183 Processing sheet with id=AG5, first strand: chain 'L' and resid 186 through 188 Processing sheet with id=AG6, first strand: chain 'L' and resid 330 through 332 removed outlier: 6.208A pdb=" N SER L 331 " --> pdb=" O PHE L 357 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR L 359 " --> pdb=" O SER L 331 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER L 278 " --> pdb=" O TYR L 398 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLY L 400 " --> pdb=" O SER L 278 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU L 280 " --> pdb=" O GLY L 400 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 366 through 367 removed outlier: 7.391A pdb=" N THR L 366 " --> pdb=" O ARG L 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'L' and resid 471 through 475 removed outlier: 3.902A pdb=" N MET L 576 " --> pdb=" O MET L 474 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASP L 542 " --> pdb=" O LYS L 569 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR L 547 " --> pdb=" O ILE L 512 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N PHE L 511 " --> pdb=" O GLN L 531 " (cutoff:3.500A) 1665 hydrogen bonds defined for protein. 4650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 168 hydrogen bonds 336 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 11.08 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9891 1.33 - 1.46: 11051 1.46 - 1.58: 22628 1.58 - 1.70: 348 1.70 - 1.83: 440 Bond restraints: 44358 Sorted by residual: bond pdb=" F2 AF3 L1005 " pdb="AL AF3 L1005 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" F1 AF3 K 706 " pdb="AL AF3 K 706 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" F3 AF3 L1005 " pdb="AL AF3 L1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" F2 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" F1 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.65e+01 ... (remaining 44353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.15: 60818 7.15 - 14.31: 143 14.31 - 21.46: 16 21.46 - 28.61: 4 28.61 - 35.76: 2 Bond angle restraints: 60983 Sorted by residual: angle pdb=" CB MET D 55 " pdb=" CG MET D 55 " pdb=" SD MET D 55 " ideal model delta sigma weight residual 112.70 148.46 -35.76 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CB MET J 55 " pdb=" CG MET J 55 " pdb=" SD MET J 55 " ideal model delta sigma weight residual 112.70 148.42 -35.72 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CA GLU C 50 " pdb=" CB GLU C 50 " pdb=" CG GLU C 50 " ideal model delta sigma weight residual 114.10 130.71 -16.61 2.00e+00 2.50e-01 6.90e+01 angle pdb=" CA GLU I 50 " pdb=" CB GLU I 50 " pdb=" CG GLU I 50 " ideal model delta sigma weight residual 114.10 130.67 -16.57 2.00e+00 2.50e-01 6.86e+01 angle pdb=" CA GLU C 74 " pdb=" CB GLU C 74 " pdb=" CG GLU C 74 " ideal model delta sigma weight residual 114.10 130.59 -16.49 2.00e+00 2.50e-01 6.80e+01 ... (remaining 60978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.50: 25614 33.50 - 67.00: 1101 67.00 - 100.50: 95 100.50 - 134.01: 27 134.01 - 167.51: 2 Dihedral angle restraints: 26839 sinusoidal: 11729 harmonic: 15110 Sorted by residual: dihedral pdb=" CA LYS L 189 " pdb=" C LYS L 189 " pdb=" N ASN L 190 " pdb=" CA ASN L 190 " ideal model delta harmonic sigma weight residual -180.00 -78.48 -101.52 0 5.00e+00 4.00e-02 4.12e+02 dihedral pdb=" CA LYS F 189 " pdb=" C LYS F 189 " pdb=" N ASN F 190 " pdb=" CA ASN F 190 " ideal model delta harmonic sigma weight residual -180.00 -78.49 -101.51 0 5.00e+00 4.00e-02 4.12e+02 dihedral pdb=" CA GLN D 158 " pdb=" C GLN D 158 " pdb=" N VAL D 159 " pdb=" CA VAL D 159 " ideal model delta harmonic sigma weight residual 180.00 133.51 46.49 0 5.00e+00 4.00e-02 8.65e+01 ... (remaining 26836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 6228 0.074 - 0.148: 781 0.148 - 0.222: 55 0.222 - 0.296: 22 0.296 - 0.370: 6 Chirality restraints: 7092 Sorted by residual: chirality pdb=" C17 1N7 K 707 " pdb=" C16 1N7 K 707 " pdb=" C18 1N7 K 707 " pdb=" O3 1N7 K 707 " both_signs ideal model delta sigma weight residual False 2.40 2.77 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C17 1N7 E 707 " pdb=" C16 1N7 E 707 " pdb=" C18 1N7 E 707 " pdb=" O3 1N7 E 707 " both_signs ideal model delta sigma weight residual False 2.40 2.77 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CB ILE F 258 " pdb=" CA ILE F 258 " pdb=" CG1 ILE F 258 " pdb=" CG2 ILE F 258 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 7089 not shown) Planarity restraints: 7223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 178 " -0.550 9.50e-02 1.11e+02 2.47e-01 3.95e+01 pdb=" NE ARG F 178 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG F 178 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG F 178 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG F 178 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 178 " 0.551 9.50e-02 1.11e+02 2.47e-01 3.94e+01 pdb=" NE ARG L 178 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG L 178 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG L 178 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG L 178 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 55 " -0.442 9.50e-02 1.11e+02 1.99e-01 2.86e+01 pdb=" NE ARG G 55 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG G 55 " -0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG G 55 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG G 55 " -0.003 2.00e-02 2.50e+03 ... (remaining 7220 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 703 2.63 - 3.20: 38201 3.20 - 3.77: 69753 3.77 - 4.33: 94166 4.33 - 4.90: 149497 Nonbonded interactions: 352320 Sorted by model distance: nonbonded pdb="MG MG K 705 " pdb=" F1 AF3 K 706 " model vdw 2.063 2.120 nonbonded pdb="MG MG E 705 " pdb=" F1 AF3 E 706 " model vdw 2.064 2.120 nonbonded pdb=" O ASP F 344 " pdb=" NE2 GLN G 81 " model vdw 2.103 3.120 nonbonded pdb=" O1B ADP E 704 " pdb="MG MG E 705 " model vdw 2.119 2.170 nonbonded pdb=" O2B ADP K 704 " pdb="MG MG K 705 " model vdw 2.119 2.170 ... (remaining 352315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = (chain 'B' and (resid 7 through 22 or (resid 23 through 25 and (name N or name C \ A or name C or name O or name CB )) or resid 26 through 49 or (resid 50 through \ 54 and (name N or name CA or name C or name O or name CB )) or resid 55 through \ 191)) selection = (chain 'D' and (resid 7 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and (n \ ame N or name CA or name C or name O or name CB )) or resid 40 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 or ( \ resid 50 through 54 and (name N or name CA or name C or name O or name CB )) or \ resid 55 through 191)) selection = (chain 'H' and (resid 7 through 22 or (resid 23 through 25 and (name N or name C \ A or name C or name O or name CB )) or resid 26 through 49 or (resid 50 through \ 54 and (name N or name CA or name C or name O or name CB )) or resid 55 through \ 191)) selection = (chain 'J' and (resid 7 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and (n \ ame N or name CA or name C or name O or name CB )) or resid 40 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thro \ ugh 51 or (resid 52 through 54 and (name N or name CA or name C or name O or nam \ e CB )) or resid 55 through 191)) } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = (chain 'E' and resid 1 through 706) selection = (chain 'F' and (resid 1 through 145 or (resid 146 and (name N or name CA or name \ C or name O or name CB )) or resid 147 through 148 or (resid 149 and (name N or \ name CA or name C or name O or name CB )) or resid 150 through 172 or (resid 17 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 174 through \ 177 or (resid 178 through 179 and (name N or name CA or name C or name O or name \ CB )) or resid 180 through 185 or (resid 186 and (name N or name CA or name C o \ r name O or name CB )) or resid 187 through 222 or (resid 223 through 225 and (n \ ame N or name CA or name C or name O or name CB )) or resid 226 or (resid 227 an \ d (name N or name CA or name C or name O or name CB )) or resid 228 through 229 \ or (resid 230 and (name N or name CA or name C or name O or name CB )) or resid \ 231 through 1005)) selection = (chain 'K' and resid 1 through 706) selection = (chain 'L' and (resid 1 through 145 or (resid 146 and (name N or name CA or name \ C or name O or name CB )) or resid 147 through 148 or (resid 149 and (name N or \ name CA or name C or name O or name CB )) or resid 150 through 172 or (resid 17 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 174 through \ 177 or (resid 178 through 179 and (name N or name CA or name C or name O or name \ CB )) or resid 180 through 185 or (resid 186 and (name N or name CA or name C o \ r name O or name CB )) or resid 187 through 222 or (resid 223 through 225 and (n \ ame N or name CA or name C or name O or name CB )) or resid 226 or (resid 227 an \ d (name N or name CA or name C or name O or name CB )) or resid 228 through 229 \ or (resid 230 and (name N or name CA or name C or name O or name CB )) or resid \ 231 through 1005)) } ncs_group { reference = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'T' selection = chain 'U' } 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 47.020 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 0.164 44422 Z= 0.284 Angle : 1.063 35.764 61035 Z= 0.555 Chirality : 0.051 0.370 7092 Planarity : 0.008 0.247 7223 Dihedral : 17.695 167.506 17091 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 6.67 % Allowed : 1.69 % Favored : 91.63 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.70 (0.11), residues: 5082 helix: -0.51 (0.12), residues: 1906 sheet: -0.91 (0.23), residues: 546 loop : -1.64 (0.11), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG A 55 TYR 0.033 0.002 TYR D 138 PHE 0.024 0.002 PHE D 147 TRP 0.019 0.002 TRP A 268 HIS 0.017 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00581 (44358) covalent geometry : angle 1.05170 (60983) hydrogen bonds : bond 0.17395 ( 1813) hydrogen bonds : angle 7.11563 ( 4986) metal coordination : bond 0.01074 ( 64) metal coordination : angle 5.45447 ( 52) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 292 poor density : 453 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7602 (mtp85) REVERT: A 124 MET cc_start: 0.8067 (mmm) cc_final: 0.7850 (mmp) REVERT: A 545 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8503 (mmmm) REVERT: A 847 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8095 (mm) REVERT: B 149 TYR cc_start: 0.8538 (t80) cc_final: 0.8301 (t80) REVERT: C 60 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7637 (mt) REVERT: D 65 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7690 (mm-40) REVERT: D 69 GLN cc_start: 0.8673 (mm110) cc_final: 0.8344 (mm-40) REVERT: D 70 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7969 (tmm) REVERT: D 158 GLN cc_start: 0.5826 (OUTLIER) cc_final: 0.4994 (mm-40) REVERT: D 168 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.6953 (pp30) REVERT: E 185 TYR cc_start: 0.4452 (m-10) cc_final: 0.4243 (m-10) REVERT: E 438 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6795 (tt) REVERT: E 459 ASN cc_start: 0.7975 (m110) cc_final: 0.7081 (p0) REVERT: E 497 ARG cc_start: 0.3523 (OUTLIER) cc_final: 0.3221 (ttm170) REVERT: F 582 TYR cc_start: 0.5037 (OUTLIER) cc_final: 0.4680 (m-80) REVERT: H 64 ASP cc_start: 0.7348 (p0) cc_final: 0.6717 (p0) REVERT: G 900 LEU cc_start: 0.8698 (tp) cc_final: 0.8333 (tt) REVERT: G 913 SER cc_start: 0.7544 (OUTLIER) cc_final: 0.7146 (m) REVERT: J 69 GLN cc_start: 0.9232 (mm110) cc_final: 0.9031 (mm110) REVERT: J 161 ASP cc_start: 0.7004 (p0) cc_final: 0.6625 (p0) REVERT: K 68 MET cc_start: 0.5086 (ppp) cc_final: 0.4265 (ppp) REVERT: K 378 MET cc_start: 0.5648 (OUTLIER) cc_final: 0.4293 (tpt) REVERT: K 482 HIS cc_start: 0.3708 (t-170) cc_final: 0.3031 (m-70) REVERT: K 486 SER cc_start: -0.0581 (OUTLIER) cc_final: -0.0827 (t) REVERT: L 122 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8594 (pp) REVERT: L 254 PRO cc_start: 0.6500 (Cg_exo) cc_final: 0.6237 (Cg_endo) REVERT: L 576 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.6376 (ptp) REVERT: L 582 TYR cc_start: 0.4180 (OUTLIER) cc_final: 0.3846 (m-80) outliers start: 292 outliers final: 28 residues processed: 621 average time/residue: 0.2523 time to fit residues: 259.0967 Evaluate side-chains 329 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 284 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain G residue 681 SER Chi-restraints excluded: chain G residue 913 SER Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain K residue 378 MET Chi-restraints excluded: chain K residue 486 SER Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 212 ARG Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 576 MET Chi-restraints excluded: chain L residue 582 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 394 optimal weight: 0.4980 chunk 430 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 8.9990 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 30.0000 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 chunk 516 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 177 ASN A 210 GLN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN ** E 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS G 177 ASN G 210 GLN G 911 ASN ** K 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 243 GLN K 311 HIS K 464 HIS ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 354 GLN L 554 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.122370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.076061 restraints weight = 126564.872| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.02 r_work: 0.3171 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 44422 Z= 0.170 Angle : 0.671 12.689 61035 Z= 0.340 Chirality : 0.042 0.229 7092 Planarity : 0.004 0.054 7223 Dihedral : 14.267 167.807 8060 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.41 % Favored : 94.55 % Rotamer: Outliers : 2.08 % Allowed : 7.84 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.25 (0.11), residues: 5082 helix: -0.05 (0.12), residues: 1992 sheet: -0.76 (0.22), residues: 550 loop : -1.46 (0.12), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 15 TYR 0.019 0.001 TYR A 32 PHE 0.024 0.001 PHE J 49 TRP 0.020 0.001 TRP L 506 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00373 (44358) covalent geometry : angle 0.65374 (60983) hydrogen bonds : bond 0.04295 ( 1813) hydrogen bonds : angle 4.84654 ( 4986) metal coordination : bond 0.01000 ( 64) metal coordination : angle 5.14799 ( 52) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 301 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8592 (mtpt) REVERT: A 615 MET cc_start: 0.8891 (ttm) cc_final: 0.8645 (ttm) REVERT: B 94 MET cc_start: 0.8744 (mtp) cc_final: 0.8512 (mtm) REVERT: C 52 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8149 (tpt) REVERT: C 62 MET cc_start: 0.8718 (mmm) cc_final: 0.8140 (mtt) REVERT: D 55 MET cc_start: 0.8259 (ppp) cc_final: 0.8043 (tmm) REVERT: D 69 GLN cc_start: 0.8839 (mm110) cc_final: 0.8413 (mm-40) REVERT: D 158 GLN cc_start: 0.6575 (OUTLIER) cc_final: 0.6192 (tm-30) REVERT: H 60 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7882 (tm-30) REVERT: H 64 ASP cc_start: 0.7286 (p0) cc_final: 0.6993 (p0) REVERT: G 855 MET cc_start: 0.8230 (mmt) cc_final: 0.8024 (mmt) REVERT: G 865 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8646 (m-30) REVERT: G 900 LEU cc_start: 0.8975 (tp) cc_final: 0.8771 (tt) REVERT: G 902 MET cc_start: 0.7509 (tmm) cc_final: 0.7162 (tmm) REVERT: G 906 MET cc_start: 0.8053 (tpp) cc_final: 0.7764 (tpp) REVERT: I 62 MET cc_start: 0.9021 (mmm) cc_final: 0.8816 (mmm) REVERT: J 55 MET cc_start: 0.9295 (ppp) cc_final: 0.9091 (ppp) REVERT: J 60 GLU cc_start: 0.7433 (mp0) cc_final: 0.7223 (mp0) REVERT: J 70 MET cc_start: 0.8647 (tpp) cc_final: 0.8180 (mmt) REVERT: K 68 MET cc_start: 0.4871 (ppp) cc_final: 0.3917 (ppp) REVERT: K 466 ASP cc_start: 0.5198 (p0) cc_final: 0.4969 (m-30) REVERT: K 482 HIS cc_start: 0.4161 (t-170) cc_final: 0.3594 (m170) REVERT: K 486 SER cc_start: -0.0466 (OUTLIER) cc_final: -0.0903 (t) REVERT: L 219 LEU cc_start: 0.6960 (mp) cc_final: 0.6674 (mp) REVERT: L 304 ILE cc_start: 0.7329 (mp) cc_final: 0.6807 (mp) REVERT: L 436 MET cc_start: 0.4027 (ttt) cc_final: 0.1911 (mpp) REVERT: L 580 ASP cc_start: 0.7215 (m-30) cc_final: 0.6974 (p0) outliers start: 91 outliers final: 46 residues processed: 371 average time/residue: 0.2301 time to fit residues: 147.4856 Evaluate side-chains 299 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 523 SER Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain G residue 865 ASP Chi-restraints excluded: chain G residue 877 TYR Chi-restraints excluded: chain G residue 885 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain K residue 486 SER Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 545 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 248 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 244 optimal weight: 0.6980 chunk 338 optimal weight: 7.9990 chunk 403 optimal weight: 0.9980 chunk 514 optimal weight: 20.0000 chunk 285 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 484 optimal weight: 5.9990 chunk 112 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 791 ASN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 164 HIS ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 ASN F 354 GLN ** G 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN G 911 ASN J 158 GLN ** K 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.121326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.074864 restraints weight = 125760.240| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.07 r_work: 0.3149 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 44422 Z= 0.155 Angle : 0.613 12.470 61035 Z= 0.308 Chirality : 0.041 0.247 7092 Planarity : 0.004 0.046 7223 Dihedral : 13.539 172.134 7991 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.45 % Favored : 94.51 % Rotamer: Outliers : 1.90 % Allowed : 9.90 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.93 (0.12), residues: 5082 helix: 0.29 (0.12), residues: 1982 sheet: -0.84 (0.21), residues: 576 loop : -1.28 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 212 TYR 0.022 0.001 TYR E 211 PHE 0.018 0.001 PHE F 182 TRP 0.016 0.001 TRP L 506 HIS 0.018 0.001 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00346 (44358) covalent geometry : angle 0.59756 (60983) hydrogen bonds : bond 0.03909 ( 1813) hydrogen bonds : angle 4.46686 ( 4986) metal coordination : bond 0.00975 ( 64) metal coordination : angle 4.71878 ( 52) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 257 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 615 MET cc_start: 0.9081 (ttm) cc_final: 0.8846 (ttm) REVERT: A 899 MET cc_start: 0.8624 (ttm) cc_final: 0.8413 (ttm) REVERT: C 38 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8690 (m-30) REVERT: C 62 MET cc_start: 0.8810 (mmm) cc_final: 0.8208 (mtt) REVERT: D 67 MET cc_start: 0.8700 (ttm) cc_final: 0.8433 (ttm) REVERT: D 70 MET cc_start: 0.8668 (tmm) cc_final: 0.8420 (tmm) REVERT: D 73 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8207 (pt0) REVERT: D 158 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6307 (tm-30) REVERT: F 378 MET cc_start: 0.6820 (tmm) cc_final: 0.6111 (tpp) REVERT: F 474 MET cc_start: 0.7487 (mtt) cc_final: 0.7195 (mtm) REVERT: F 545 ILE cc_start: 0.7613 (mm) cc_final: 0.7025 (pt) REVERT: G 83 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8445 (mm-30) REVERT: G 855 MET cc_start: 0.8444 (mmt) cc_final: 0.8212 (mmt) REVERT: G 865 ASP cc_start: 0.9126 (OUTLIER) cc_final: 0.8816 (m-30) REVERT: G 900 LEU cc_start: 0.8998 (tp) cc_final: 0.8737 (tt) REVERT: I 70 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8610 (mttt) REVERT: J 70 MET cc_start: 0.8678 (tpp) cc_final: 0.8215 (mmt) REVERT: K 68 MET cc_start: 0.4655 (ppp) cc_final: 0.3630 (ppp) REVERT: K 482 HIS cc_start: 0.4238 (t-170) cc_final: 0.3675 (m170) REVERT: K 486 SER cc_start: -0.0158 (OUTLIER) cc_final: -0.0513 (t) outliers start: 83 outliers final: 51 residues processed: 326 average time/residue: 0.2221 time to fit residues: 126.1444 Evaluate side-chains 289 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 234 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain G residue 681 SER Chi-restraints excluded: chain G residue 865 ASP Chi-restraints excluded: chain G residue 877 TYR Chi-restraints excluded: chain G residue 911 ASN Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain K residue 486 SER Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 370 ILE Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 545 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 471 optimal weight: 7.9990 chunk 350 optimal weight: 5.9990 chunk 431 optimal weight: 30.0000 chunk 449 optimal weight: 3.9990 chunk 394 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 186 optimal weight: 50.0000 chunk 365 optimal weight: 6.9990 chunk 178 optimal weight: 40.0000 chunk 255 optimal weight: 50.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 HIS F 354 GLN G 75 HIS G 357 GLN G 381 HIS G 497 ASN ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 ASN L 518 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.118994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.072061 restraints weight = 125003.020| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.07 r_work: 0.3086 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 44422 Z= 0.224 Angle : 0.660 12.675 61035 Z= 0.332 Chirality : 0.042 0.240 7092 Planarity : 0.004 0.053 7223 Dihedral : 13.227 173.872 7976 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.96 % Favored : 94.00 % Rotamer: Outliers : 2.06 % Allowed : 11.34 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.88 (0.12), residues: 5082 helix: 0.34 (0.12), residues: 1976 sheet: -0.77 (0.21), residues: 574 loop : -1.27 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 579 TYR 0.021 0.002 TYR L 217 PHE 0.019 0.002 PHE L 182 TRP 0.015 0.001 TRP L 506 HIS 0.040 0.002 HIS E 164 Details of bonding type rmsd covalent geometry : bond 0.00507 (44358) covalent geometry : angle 0.64342 (60983) hydrogen bonds : bond 0.04072 ( 1813) hydrogen bonds : angle 4.38779 ( 4986) metal coordination : bond 0.01044 ( 64) metal coordination : angle 5.02309 ( 52) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 259 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 551 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8487 (pttp) REVERT: A 615 MET cc_start: 0.8888 (ttm) cc_final: 0.8685 (ttm) REVERT: A 847 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8782 (tp) REVERT: A 899 MET cc_start: 0.8502 (ttm) cc_final: 0.8290 (ttm) REVERT: B 171 GLU cc_start: 0.8788 (tp30) cc_final: 0.8276 (mm-30) REVERT: C 38 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8458 (m-30) REVERT: C 62 MET cc_start: 0.8747 (mmm) cc_final: 0.8267 (mtm) REVERT: D 70 MET cc_start: 0.8576 (tmm) cc_final: 0.8218 (tmm) REVERT: D 158 GLN cc_start: 0.6800 (OUTLIER) cc_final: 0.6454 (tm-30) REVERT: E 215 THR cc_start: 0.2798 (OUTLIER) cc_final: 0.2581 (p) REVERT: F 68 MET cc_start: 0.7911 (tpp) cc_final: 0.7552 (tpt) REVERT: F 197 GLU cc_start: 0.7559 (mp0) cc_final: 0.7062 (mp0) REVERT: F 378 MET cc_start: 0.6755 (tmm) cc_final: 0.6278 (tpp) REVERT: F 474 MET cc_start: 0.7315 (mtt) cc_final: 0.7084 (mtm) REVERT: F 545 ILE cc_start: 0.7604 (mm) cc_final: 0.7003 (pt) REVERT: F 560 ARG cc_start: 0.6379 (OUTLIER) cc_final: 0.5818 (ttm110) REVERT: F 572 ILE cc_start: 0.4105 (OUTLIER) cc_final: 0.3801 (tt) REVERT: F 576 MET cc_start: 0.2921 (mpp) cc_final: 0.2636 (mpp) REVERT: H 19 GLN cc_start: 0.7707 (pp30) cc_final: 0.7191 (pp30) REVERT: G 83 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8150 (mm-30) REVERT: G 900 LEU cc_start: 0.8977 (tp) cc_final: 0.8663 (tt) REVERT: I 52 MET cc_start: 0.9378 (tpp) cc_final: 0.9154 (tpp) REVERT: J 55 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8984 (tmm) REVERT: J 70 MET cc_start: 0.8677 (tpp) cc_final: 0.8139 (mmt) REVERT: J 138 TYR cc_start: 0.8627 (t80) cc_final: 0.8416 (t80) REVERT: K 68 MET cc_start: 0.4575 (ppp) cc_final: 0.3769 (ppp) REVERT: K 482 HIS cc_start: 0.4406 (t-170) cc_final: 0.3694 (m170) REVERT: L 436 MET cc_start: 0.3751 (ttm) cc_final: 0.2739 (mpp) REVERT: L 466 ASP cc_start: 0.6673 (t0) cc_final: 0.6039 (p0) outliers start: 90 outliers final: 57 residues processed: 331 average time/residue: 0.2198 time to fit residues: 126.4181 Evaluate side-chains 295 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 230 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 560 ARG Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain G residue 885 LEU Chi-restraints excluded: chain G residue 902 MET Chi-restraints excluded: chain G residue 905 VAL Chi-restraints excluded: chain G residue 912 THR Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 119 ILE Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 545 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 475 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 308 optimal weight: 0.0570 chunk 417 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 344 optimal weight: 3.9990 chunk 6 optimal weight: 0.0470 chunk 429 optimal weight: 30.0000 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN A 752 HIS E 164 HIS ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN G 177 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.120026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.073016 restraints weight = 125148.147| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.13 r_work: 0.3094 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 44422 Z= 0.114 Angle : 0.577 12.377 61035 Z= 0.288 Chirality : 0.040 0.226 7092 Planarity : 0.003 0.042 7223 Dihedral : 13.050 179.836 7973 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 1.74 % Allowed : 12.98 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.63 (0.12), residues: 5082 helix: 0.57 (0.12), residues: 1966 sheet: -0.65 (0.22), residues: 558 loop : -1.12 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 111 TYR 0.016 0.001 TYR A 788 PHE 0.015 0.001 PHE F 182 TRP 0.015 0.001 TRP F 506 HIS 0.006 0.001 HIS E 164 Details of bonding type rmsd covalent geometry : bond 0.00247 (44358) covalent geometry : angle 0.56464 (60983) hydrogen bonds : bond 0.03413 ( 1813) hydrogen bonds : angle 4.14503 ( 4986) metal coordination : bond 0.00805 ( 64) metal coordination : angle 4.06415 ( 52) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 258 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 551 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8372 (pttp) REVERT: A 615 MET cc_start: 0.9119 (ttm) cc_final: 0.8883 (ttm) REVERT: C 38 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: C 62 MET cc_start: 0.8795 (mmm) cc_final: 0.8358 (mtm) REVERT: D 22 TYR cc_start: 0.4898 (t80) cc_final: 0.4078 (t80) REVERT: D 70 MET cc_start: 0.8559 (tmm) cc_final: 0.8218 (tmm) REVERT: D 77 GLU cc_start: 0.8495 (pp20) cc_final: 0.8234 (pp20) REVERT: D 158 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6313 (tm-30) REVERT: E 164 HIS cc_start: 0.0694 (OUTLIER) cc_final: 0.0335 (m90) REVERT: F 197 GLU cc_start: 0.7858 (mp0) cc_final: 0.7398 (mp0) REVERT: F 378 MET cc_start: 0.6710 (tmm) cc_final: 0.6313 (tpp) REVERT: F 474 MET cc_start: 0.7435 (mtt) cc_final: 0.7214 (mtm) REVERT: F 545 ILE cc_start: 0.7605 (mm) cc_final: 0.7001 (pt) REVERT: G 83 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8099 (mm-30) REVERT: G 371 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8539 (mm) REVERT: G 380 MET cc_start: 0.8570 (mmm) cc_final: 0.8337 (tpt) REVERT: G 626 MET cc_start: 0.9165 (ttm) cc_final: 0.8922 (ttm) REVERT: G 900 LEU cc_start: 0.8970 (tp) cc_final: 0.8690 (tt) REVERT: J 55 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8978 (tmm) REVERT: J 70 MET cc_start: 0.8736 (tpp) cc_final: 0.8252 (mmt) REVERT: J 77 GLU cc_start: 0.8849 (pm20) cc_final: 0.8608 (pm20) REVERT: J 129 MET cc_start: 0.8274 (mtm) cc_final: 0.8039 (mtt) REVERT: K 68 MET cc_start: 0.4357 (ppp) cc_final: 0.3487 (ppp) REVERT: L 429 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6728 (ppp) REVERT: L 436 MET cc_start: 0.3974 (ttm) cc_final: 0.2597 (mpp) REVERT: L 466 ASP cc_start: 0.6774 (t0) cc_final: 0.6071 (p0) outliers start: 76 outliers final: 47 residues processed: 320 average time/residue: 0.2233 time to fit residues: 123.5769 Evaluate side-chains 283 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 371 LEU Chi-restraints excluded: chain G residue 613 HIS Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain G residue 681 SER Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 429 MET Chi-restraints excluded: chain L residue 545 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 222 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 442 optimal weight: 1.9990 chunk 278 optimal weight: 0.0980 chunk 420 optimal weight: 9.9990 chunk 177 optimal weight: 30.0000 chunk 338 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 351 optimal weight: 6.9990 chunk 440 optimal weight: 30.0000 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 164 HIS ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS F 354 GLN G 177 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** 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 = 0.4188 r_free = 0.4188 target = 0.119253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.072500 restraints weight = 125709.705| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.12 r_work: 0.3071 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44422 Z= 0.142 Angle : 0.586 12.377 61035 Z= 0.292 Chirality : 0.040 0.229 7092 Planarity : 0.003 0.045 7223 Dihedral : 12.872 168.380 7971 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.45 % Favored : 94.51 % Rotamer: Outliers : 2.17 % Allowed : 13.28 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.53 (0.12), residues: 5082 helix: 0.66 (0.12), residues: 1964 sheet: -0.49 (0.22), residues: 552 loop : -1.10 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 467 TYR 0.015 0.001 TYR F 298 PHE 0.016 0.001 PHE F 182 TRP 0.014 0.001 TRP J 182 HIS 0.025 0.001 HIS E 164 Details of bonding type rmsd covalent geometry : bond 0.00318 (44358) covalent geometry : angle 0.57164 (60983) hydrogen bonds : bond 0.03451 ( 1813) hydrogen bonds : angle 4.10004 ( 4986) metal coordination : bond 0.00814 ( 64) metal coordination : angle 4.48719 ( 52) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 239 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 551 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8335 (pttp) REVERT: A 615 MET cc_start: 0.9109 (ttm) cc_final: 0.8884 (ttm) REVERT: A 814 SER cc_start: 0.9457 (m) cc_final: 0.9082 (t) REVERT: B 62 MET cc_start: 0.7764 (tmm) cc_final: 0.7195 (tmm) REVERT: B 65 GLN cc_start: 0.8963 (mm110) cc_final: 0.8404 (tm-30) REVERT: C 38 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8485 (m-30) REVERT: C 62 MET cc_start: 0.8814 (mmm) cc_final: 0.8395 (mtm) REVERT: D 22 TYR cc_start: 0.5009 (t80) cc_final: 0.4356 (t80) REVERT: D 70 MET cc_start: 0.8648 (tmm) cc_final: 0.8141 (tmm) REVERT: D 73 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7990 (tm-30) REVERT: D 77 GLU cc_start: 0.8518 (pp20) cc_final: 0.8263 (pp20) REVERT: D 158 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6288 (tm-30) REVERT: E 164 HIS cc_start: 0.0303 (OUTLIER) cc_final: 0.0068 (m90) REVERT: F 197 GLU cc_start: 0.7851 (mp0) cc_final: 0.7288 (mp0) REVERT: F 378 MET cc_start: 0.6757 (tmm) cc_final: 0.6311 (mmm) REVERT: F 405 LEU cc_start: 0.4228 (OUTLIER) cc_final: 0.3714 (mm) REVERT: F 526 LEU cc_start: 0.5221 (OUTLIER) cc_final: 0.4626 (tp) REVERT: F 545 ILE cc_start: 0.7611 (mm) cc_final: 0.7064 (pt) REVERT: G 83 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8230 (mm-30) REVERT: G 371 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8559 (mm) REVERT: G 380 MET cc_start: 0.8598 (mmm) cc_final: 0.8314 (tpt) REVERT: G 900 LEU cc_start: 0.8968 (tp) cc_final: 0.8670 (tt) REVERT: I 70 LYS cc_start: 0.9187 (mmmt) cc_final: 0.8759 (mttt) REVERT: J 55 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8966 (tmm) REVERT: J 70 MET cc_start: 0.8716 (tpp) cc_final: 0.8198 (mmt) REVERT: J 77 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8601 (pm20) REVERT: J 129 MET cc_start: 0.8276 (mtm) cc_final: 0.8059 (mtt) REVERT: K 68 MET cc_start: 0.4511 (ppp) cc_final: 0.3632 (ppp) REVERT: K 157 VAL cc_start: 0.2164 (OUTLIER) cc_final: 0.1963 (t) REVERT: L 436 MET cc_start: 0.4129 (ttm) cc_final: 0.2409 (mpp) REVERT: L 466 ASP cc_start: 0.6775 (t0) cc_final: 0.6144 (p0) outliers start: 95 outliers final: 62 residues processed: 315 average time/residue: 0.2048 time to fit residues: 113.7794 Evaluate side-chains 295 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 223 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 371 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 613 HIS Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain G residue 905 VAL Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 397 VAL Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 545 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 42 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 432 optimal weight: 40.0000 chunk 484 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 90 optimal weight: 0.0980 chunk 456 optimal weight: 30.0000 chunk 258 optimal weight: 5.9990 chunk 488 optimal weight: 30.0000 chunk 264 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 GLN G 177 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 470 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.119005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.071856 restraints weight = 123356.194| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.13 r_work: 0.3045 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 44422 Z= 0.159 Angle : 0.597 15.106 61035 Z= 0.299 Chirality : 0.040 0.245 7092 Planarity : 0.003 0.045 7223 Dihedral : 12.746 138.499 7971 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 2.19 % Allowed : 13.74 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.12), residues: 5082 helix: 0.70 (0.12), residues: 1984 sheet: -0.48 (0.22), residues: 556 loop : -1.09 (0.12), residues: 2542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 15 TYR 0.018 0.001 TYR F 217 PHE 0.017 0.001 PHE F 182 TRP 0.014 0.001 TRP L 506 HIS 0.040 0.001 HIS E 164 Details of bonding type rmsd covalent geometry : bond 0.00357 (44358) covalent geometry : angle 0.58133 (60983) hydrogen bonds : bond 0.03498 ( 1813) hydrogen bonds : angle 4.09717 ( 4986) metal coordination : bond 0.00833 ( 64) metal coordination : angle 4.64728 ( 52) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 248 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8181 (m-30) cc_final: 0.7768 (t0) REVERT: A 551 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8239 (pttp) REVERT: A 615 MET cc_start: 0.9204 (ttm) cc_final: 0.8981 (ttm) REVERT: A 814 SER cc_start: 0.9508 (m) cc_final: 0.9152 (t) REVERT: A 847 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8795 (tp) REVERT: B 62 MET cc_start: 0.7808 (tmm) cc_final: 0.7252 (tmm) REVERT: B 65 GLN cc_start: 0.8997 (mm110) cc_final: 0.8479 (tm-30) REVERT: B 174 MET cc_start: 0.8980 (tpt) cc_final: 0.8464 (tpp) REVERT: C 38 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: C 62 MET cc_start: 0.8738 (mmm) cc_final: 0.8381 (mtm) REVERT: D 22 TYR cc_start: 0.4967 (t80) cc_final: 0.4343 (t80) REVERT: D 67 MET cc_start: 0.8917 (ttm) cc_final: 0.8508 (mtp) REVERT: D 70 MET cc_start: 0.8688 (tmm) cc_final: 0.8114 (tmm) REVERT: D 73 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8113 (tm-30) REVERT: D 77 GLU cc_start: 0.8581 (pp20) cc_final: 0.8298 (pp20) REVERT: D 158 GLN cc_start: 0.6734 (OUTLIER) cc_final: 0.5963 (tm-30) REVERT: F 197 GLU cc_start: 0.8077 (mp0) cc_final: 0.7535 (mp0) REVERT: F 378 MET cc_start: 0.6824 (tmm) cc_final: 0.6516 (tmm) REVERT: F 474 MET cc_start: 0.7312 (mtt) cc_final: 0.7043 (mtm) REVERT: F 526 LEU cc_start: 0.5294 (OUTLIER) cc_final: 0.4704 (tp) REVERT: F 545 ILE cc_start: 0.7660 (mm) cc_final: 0.7035 (pt) REVERT: G 83 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8300 (mm-30) REVERT: G 371 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8433 (mm) REVERT: G 380 MET cc_start: 0.8592 (mmm) cc_final: 0.8337 (tpt) REVERT: G 900 LEU cc_start: 0.8985 (tp) cc_final: 0.8689 (tt) REVERT: I 31 GLN cc_start: 0.8363 (pm20) cc_final: 0.8136 (pm20) REVERT: I 52 MET cc_start: 0.9325 (tpp) cc_final: 0.9118 (tpp) REVERT: I 70 LYS cc_start: 0.9214 (mmmt) cc_final: 0.8762 (mttt) REVERT: J 52 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8519 (p0) REVERT: J 55 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.9010 (tmm) REVERT: J 70 MET cc_start: 0.8579 (tpp) cc_final: 0.8159 (mmt) REVERT: J 77 GLU cc_start: 0.8815 (pm20) cc_final: 0.8585 (pm20) REVERT: J 87 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8176 (ppp) REVERT: J 138 TYR cc_start: 0.8653 (t80) cc_final: 0.8443 (t80) REVERT: K 68 MET cc_start: 0.4472 (ppp) cc_final: 0.3588 (ppp) REVERT: K 157 VAL cc_start: 0.2581 (OUTLIER) cc_final: 0.2332 (t) REVERT: K 482 HIS cc_start: 0.4552 (t-170) cc_final: 0.3983 (m170) REVERT: L 375 GLU cc_start: 0.7566 (tp30) cc_final: 0.7102 (tp30) REVERT: L 466 ASP cc_start: 0.6842 (t0) cc_final: 0.6215 (p0) outliers start: 96 outliers final: 68 residues processed: 325 average time/residue: 0.2061 time to fit residues: 117.4107 Evaluate side-chains 311 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 233 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 157 GLN Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 371 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 613 HIS Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain G residue 885 LEU Chi-restraints excluded: chain G residue 905 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 119 ILE Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 397 VAL Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 545 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 517 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 chunk 312 optimal weight: 7.9990 chunk 422 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 228 optimal weight: 0.3980 chunk 391 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 166 optimal weight: 30.0000 chunk 406 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 GLN G 177 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** 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 = 0.4150 r_free = 0.4150 target = 0.117217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.070573 restraints weight = 123787.177| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.05 r_work: 0.3011 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 44422 Z= 0.235 Angle : 0.654 16.500 61035 Z= 0.328 Chirality : 0.043 0.338 7092 Planarity : 0.004 0.059 7223 Dihedral : 12.835 129.935 7969 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.14 % Favored : 93.82 % Rotamer: Outliers : 2.22 % Allowed : 14.01 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.62 (0.12), residues: 5082 helix: 0.52 (0.12), residues: 2004 sheet: -0.59 (0.22), residues: 572 loop : -1.11 (0.13), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 186 TYR 0.017 0.002 TYR L 224 PHE 0.020 0.002 PHE F 81 TRP 0.015 0.001 TRP G 916 HIS 0.010 0.001 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00535 (44358) covalent geometry : angle 0.63857 (60983) hydrogen bonds : bond 0.03982 ( 1813) hydrogen bonds : angle 4.26329 ( 4986) metal coordination : bond 0.00978 ( 64) metal coordination : angle 4.90696 ( 52) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 242 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8226 (m-30) cc_final: 0.7817 (t0) REVERT: A 551 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8270 (pttp) REVERT: A 555 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8128 (ptp-110) REVERT: A 615 MET cc_start: 0.9178 (ttm) cc_final: 0.8946 (ttm) REVERT: A 847 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8785 (tp) REVERT: A 899 MET cc_start: 0.8258 (ttm) cc_final: 0.8056 (ttm) REVERT: A 911 ASN cc_start: 0.8212 (t0) cc_final: 0.7848 (m-40) REVERT: B 174 MET cc_start: 0.9007 (tpt) cc_final: 0.8501 (tpp) REVERT: C 38 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8196 (m-30) REVERT: D 22 TYR cc_start: 0.4944 (t80) cc_final: 0.4443 (t80) REVERT: D 67 MET cc_start: 0.8991 (ttm) cc_final: 0.8545 (mtp) REVERT: D 70 MET cc_start: 0.8675 (tmm) cc_final: 0.8081 (tmm) REVERT: D 73 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8240 (tm-30) REVERT: D 77 GLU cc_start: 0.8573 (pp20) cc_final: 0.8313 (pp20) REVERT: D 158 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.6131 (tm-30) REVERT: E 167 TRP cc_start: 0.3120 (m100) cc_final: 0.2860 (m-10) REVERT: F 197 GLU cc_start: 0.7885 (mp0) cc_final: 0.7141 (mp0) REVERT: F 378 MET cc_start: 0.6948 (tmm) cc_final: 0.6660 (tmm) REVERT: F 474 MET cc_start: 0.7202 (mtt) cc_final: 0.6930 (mtm) REVERT: F 526 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.4962 (tp) REVERT: F 545 ILE cc_start: 0.7803 (mm) cc_final: 0.7291 (pt) REVERT: G 83 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8317 (mm-30) REVERT: G 371 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8532 (mm) REVERT: G 380 MET cc_start: 0.8699 (mmm) cc_final: 0.8416 (tpt) REVERT: G 761 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: G 900 LEU cc_start: 0.9016 (tp) cc_final: 0.8762 (tt) REVERT: I 31 GLN cc_start: 0.8225 (pm20) cc_final: 0.7961 (pm20) REVERT: I 52 MET cc_start: 0.9373 (tpp) cc_final: 0.9058 (tpp) REVERT: J 52 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8573 (p0) REVERT: J 55 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8987 (tmm) REVERT: J 70 MET cc_start: 0.8666 (tpp) cc_final: 0.8235 (mmt) REVERT: J 77 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8574 (pm20) REVERT: J 94 MET cc_start: 0.8904 (ttp) cc_final: 0.8154 (tmm) REVERT: K 68 MET cc_start: 0.4421 (ppp) cc_final: 0.3424 (ppp) REVERT: K 157 VAL cc_start: 0.3034 (OUTLIER) cc_final: 0.2732 (t) REVERT: K 482 HIS cc_start: 0.4554 (t-170) cc_final: 0.3991 (m170) REVERT: K 526 LEU cc_start: -0.0648 (OUTLIER) cc_final: -0.0853 (pp) REVERT: L 149 TYR cc_start: 0.7007 (t80) cc_final: 0.6289 (t80) REVERT: L 375 GLU cc_start: 0.7709 (tp30) cc_final: 0.7098 (tp30) REVERT: L 466 ASP cc_start: 0.7412 (t0) cc_final: 0.6674 (p0) outliers start: 97 outliers final: 66 residues processed: 320 average time/residue: 0.2142 time to fit residues: 119.3504 Evaluate side-chains 304 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 225 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 371 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 613 HIS Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain G residue 761 ASP Chi-restraints excluded: chain G residue 854 LEU Chi-restraints excluded: chain G residue 885 LEU Chi-restraints excluded: chain G residue 905 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 119 ILE Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 526 LEU Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 216 THR Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain L residue 545 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 214 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 411 optimal weight: 0.9980 chunk 308 optimal weight: 0.5980 chunk 239 optimal weight: 10.0000 chunk 426 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 367 optimal weight: 9.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.118344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072059 restraints weight = 123310.338| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.05 r_work: 0.3046 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 44422 Z= 0.143 Angle : 0.598 12.947 61035 Z= 0.299 Chirality : 0.040 0.232 7092 Planarity : 0.003 0.052 7223 Dihedral : 12.752 127.741 7968 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 1.78 % Allowed : 14.63 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.12), residues: 5082 helix: 0.71 (0.12), residues: 1976 sheet: -0.46 (0.22), residues: 556 loop : -1.10 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 96 TYR 0.016 0.001 TYR L 217 PHE 0.016 0.001 PHE F 182 TRP 0.013 0.001 TRP L 506 HIS 0.007 0.001 HIS G 613 Details of bonding type rmsd covalent geometry : bond 0.00325 (44358) covalent geometry : angle 0.58516 (60983) hydrogen bonds : bond 0.03441 ( 1813) hydrogen bonds : angle 4.13135 ( 4986) metal coordination : bond 0.00829 ( 64) metal coordination : angle 4.21676 ( 52) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 238 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8139 (m-30) cc_final: 0.7821 (t0) REVERT: A 153 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7926 (p0) REVERT: A 551 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8237 (pttp) REVERT: A 615 MET cc_start: 0.9172 (ttm) cc_final: 0.8933 (ttm) REVERT: A 899 MET cc_start: 0.8340 (ttm) cc_final: 0.8015 (ttm) REVERT: A 911 ASN cc_start: 0.8159 (t0) cc_final: 0.7842 (m-40) REVERT: B 65 GLN cc_start: 0.8964 (mm110) cc_final: 0.8472 (tm-30) REVERT: B 174 MET cc_start: 0.9041 (tpt) cc_final: 0.8507 (tpp) REVERT: C 34 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8056 (tm-30) REVERT: C 38 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: D 22 TYR cc_start: 0.5050 (t80) cc_final: 0.4604 (t80) REVERT: D 67 MET cc_start: 0.8970 (ttm) cc_final: 0.8524 (mtp) REVERT: D 70 MET cc_start: 0.8683 (tmm) cc_final: 0.8122 (tmm) REVERT: D 77 GLU cc_start: 0.8614 (pp20) cc_final: 0.8392 (pp20) REVERT: D 158 GLN cc_start: 0.6475 (OUTLIER) cc_final: 0.5848 (tm-30) REVERT: F 378 MET cc_start: 0.7112 (tmm) cc_final: 0.6806 (tmm) REVERT: F 474 MET cc_start: 0.7212 (mtt) cc_final: 0.6937 (mtm) REVERT: F 526 LEU cc_start: 0.5463 (OUTLIER) cc_final: 0.5030 (tp) REVERT: F 545 ILE cc_start: 0.7806 (mm) cc_final: 0.7293 (pt) REVERT: G 83 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8327 (mm-30) REVERT: G 371 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8475 (mm) REVERT: G 380 MET cc_start: 0.8627 (mmm) cc_final: 0.8372 (tpt) REVERT: G 855 MET cc_start: 0.8392 (mmt) cc_final: 0.8149 (mmt) REVERT: G 900 LEU cc_start: 0.9050 (tp) cc_final: 0.8807 (tt) REVERT: I 31 GLN cc_start: 0.8329 (pm20) cc_final: 0.8084 (pm20) REVERT: I 52 MET cc_start: 0.9312 (tpp) cc_final: 0.9004 (tpp) REVERT: I 70 LYS cc_start: 0.9193 (mmmt) cc_final: 0.8804 (mttt) REVERT: J 52 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8426 (p0) REVERT: J 55 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8973 (tmm) REVERT: J 70 MET cc_start: 0.8655 (tpp) cc_final: 0.8232 (mmt) REVERT: J 77 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8583 (pm20) REVERT: K 68 MET cc_start: 0.4514 (ppp) cc_final: 0.3525 (ppp) REVERT: K 157 VAL cc_start: 0.3086 (OUTLIER) cc_final: 0.2802 (t) REVERT: K 482 HIS cc_start: 0.4524 (t-170) cc_final: 0.3977 (m170) REVERT: L 149 TYR cc_start: 0.6884 (t80) cc_final: 0.5975 (t80) REVERT: L 156 GLU cc_start: 0.6431 (mt-10) cc_final: 0.5638 (mt-10) REVERT: L 197 GLU cc_start: 0.7920 (mp0) cc_final: 0.7657 (pm20) REVERT: L 274 MET cc_start: 0.7876 (tmm) cc_final: 0.7611 (tmm) REVERT: L 375 GLU cc_start: 0.7734 (tp30) cc_final: 0.7157 (tp30) REVERT: L 466 ASP cc_start: 0.7393 (t0) cc_final: 0.6644 (p0) outliers start: 78 outliers final: 61 residues processed: 303 average time/residue: 0.2102 time to fit residues: 111.1538 Evaluate side-chains 303 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 232 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 371 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 613 HIS Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain G residue 885 LEU Chi-restraints excluded: chain G residue 905 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 119 ILE Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 545 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 430 optimal weight: 50.0000 chunk 428 optimal weight: 30.0000 chunk 491 optimal weight: 0.9990 chunk 420 optimal weight: 1.9990 chunk 480 optimal weight: 8.9990 chunk 322 optimal weight: 0.0050 chunk 346 optimal weight: 0.8980 chunk 402 optimal weight: 5.9990 chunk 211 optimal weight: 0.0570 chunk 309 optimal weight: 0.2980 chunk 351 optimal weight: 4.9990 overall best weight: 0.4514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 HIS G 177 ASN G 468 GLN G 752 HIS ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 GLN L 230 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.120068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.074291 restraints weight = 123896.226| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.10 r_work: 0.3104 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 44422 Z= 0.102 Angle : 0.574 12.212 61035 Z= 0.285 Chirality : 0.039 0.221 7092 Planarity : 0.003 0.047 7223 Dihedral : 12.569 126.077 7967 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 1.44 % Allowed : 14.86 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.29 (0.12), residues: 5082 helix: 0.91 (0.12), residues: 1964 sheet: -0.31 (0.23), residues: 536 loop : -1.03 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 96 TYR 0.016 0.001 TYR L 217 PHE 0.012 0.001 PHE G 741 TRP 0.015 0.001 TRP F 506 HIS 0.005 0.001 HIS G 613 Details of bonding type rmsd covalent geometry : bond 0.00218 (44358) covalent geometry : angle 0.56371 (60983) hydrogen bonds : bond 0.03074 ( 1813) hydrogen bonds : angle 3.96425 ( 4986) metal coordination : bond 0.00788 ( 64) metal coordination : angle 3.68774 ( 52) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 269 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8109 (m-30) cc_final: 0.7806 (t0) REVERT: A 525 ASP cc_start: 0.9057 (m-30) cc_final: 0.8830 (m-30) REVERT: A 551 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8184 (pttp) REVERT: A 555 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7951 (ptp-110) REVERT: A 615 MET cc_start: 0.9172 (ttm) cc_final: 0.8961 (ttm) REVERT: A 756 MET cc_start: 0.9049 (ttp) cc_final: 0.8795 (ttp) REVERT: A 814 SER cc_start: 0.9434 (m) cc_final: 0.9044 (t) REVERT: A 911 ASN cc_start: 0.7951 (t0) cc_final: 0.7735 (m-40) REVERT: B 65 GLN cc_start: 0.8986 (mm110) cc_final: 0.8468 (tm-30) REVERT: B 174 MET cc_start: 0.9056 (tpt) cc_final: 0.8575 (tpp) REVERT: C 34 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8142 (tm-30) REVERT: C 38 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7939 (m-30) REVERT: C 52 MET cc_start: 0.9206 (tpp) cc_final: 0.8469 (tpt) REVERT: D 22 TYR cc_start: 0.5037 (t80) cc_final: 0.4571 (t80) REVERT: D 70 MET cc_start: 0.8649 (tmm) cc_final: 0.8100 (tmm) REVERT: D 77 GLU cc_start: 0.8582 (pp20) cc_final: 0.8346 (pp20) REVERT: D 94 MET cc_start: 0.8788 (ttp) cc_final: 0.8417 (tmm) REVERT: D 158 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.6008 (tm-30) REVERT: F 378 MET cc_start: 0.7115 (tmm) cc_final: 0.6806 (tmm) REVERT: F 474 MET cc_start: 0.7152 (mtt) cc_final: 0.6789 (mpp) REVERT: F 526 LEU cc_start: 0.5360 (OUTLIER) cc_final: 0.4868 (tp) REVERT: F 545 ILE cc_start: 0.7791 (mm) cc_final: 0.7224 (pt) REVERT: H 57 ARG cc_start: 0.8105 (mmt-90) cc_final: 0.7866 (mpt-90) REVERT: G 83 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8108 (mm-30) REVERT: G 371 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8436 (mm) REVERT: G 380 MET cc_start: 0.8437 (mmm) cc_final: 0.8231 (tpt) REVERT: G 855 MET cc_start: 0.8359 (mmt) cc_final: 0.8137 (mmt) REVERT: G 900 LEU cc_start: 0.9034 (tp) cc_final: 0.8747 (tt) REVERT: I 31 GLN cc_start: 0.8330 (pm20) cc_final: 0.8066 (pm20) REVERT: I 52 MET cc_start: 0.9243 (tpp) cc_final: 0.8925 (tpp) REVERT: I 70 LYS cc_start: 0.9209 (mmmt) cc_final: 0.8800 (mttt) REVERT: J 22 TYR cc_start: 0.3984 (t80) cc_final: 0.3708 (t80) REVERT: J 52 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8395 (p0) REVERT: J 55 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8990 (tmm) REVERT: J 70 MET cc_start: 0.8608 (tpp) cc_final: 0.8174 (mmt) REVERT: J 87 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8156 (ppp) REVERT: K 68 MET cc_start: 0.4603 (ppp) cc_final: 0.3530 (ppp) REVERT: K 157 VAL cc_start: 0.2892 (OUTLIER) cc_final: 0.2617 (t) REVERT: K 257 ASN cc_start: 0.7405 (m-40) cc_final: 0.7022 (t0) REVERT: K 274 MET cc_start: 0.6133 (pmm) cc_final: 0.5838 (pmm) REVERT: K 482 HIS cc_start: 0.4496 (t-170) cc_final: 0.3935 (m170) REVERT: L 149 TYR cc_start: 0.6866 (t80) cc_final: 0.5991 (t80) REVERT: L 156 GLU cc_start: 0.5821 (mt-10) cc_final: 0.4980 (mt-10) REVERT: L 375 GLU cc_start: 0.7698 (tp30) cc_final: 0.7147 (tp30) REVERT: L 466 ASP cc_start: 0.7241 (t0) cc_final: 0.6606 (p0) outliers start: 63 outliers final: 43 residues processed: 321 average time/residue: 0.2009 time to fit residues: 111.5482 Evaluate side-chains 292 residues out of total 4460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 239 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 371 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 613 HIS Chi-restraints excluded: chain G residue 673 LEU Chi-restraints excluded: chain G residue 758 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 228 THR Chi-restraints excluded: chain L residue 372 VAL Chi-restraints excluded: chain L residue 545 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 518 random chunks: chunk 234 optimal weight: 10.0000 chunk 514 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 446 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 322 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 472 optimal weight: 3.9990 chunk 405 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN G 468 GLN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** 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 = 0.4167 r_free = 0.4167 target = 0.118170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.071859 restraints weight = 123928.023| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.03 r_work: 0.3045 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 44422 Z= 0.168 Angle : 0.606 13.261 61035 Z= 0.303 Chirality : 0.040 0.230 7092 Planarity : 0.004 0.046 7223 Dihedral : 12.538 125.574 7966 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.46 % Allowed : 15.15 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.31 (0.12), residues: 5082 helix: 0.89 (0.12), residues: 1998 sheet: -0.37 (0.22), residues: 568 loop : -1.05 (0.13), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 332 TYR 0.014 0.001 TYR F 217 PHE 0.017 0.001 PHE G 340 TRP 0.012 0.001 TRP G 916 HIS 0.008 0.001 HIS G 309 Details of bonding type rmsd covalent geometry : bond 0.00385 (44358) covalent geometry : angle 0.59470 (60983) hydrogen bonds : bond 0.03472 ( 1813) hydrogen bonds : angle 4.05803 ( 4986) metal coordination : bond 0.00821 ( 64) metal coordination : angle 4.08139 ( 52) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14411.86 seconds wall clock time: 246 minutes 11.70 seconds (14771.70 seconds total)