Starting phenix.real_space_refine on Wed Apr 8 19:38:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cu1_45925/04_2026/9cu1_45925.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cu1_45925/04_2026/9cu1_45925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cu1_45925/04_2026/9cu1_45925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cu1_45925/04_2026/9cu1_45925.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cu1_45925/04_2026/9cu1_45925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cu1_45925/04_2026/9cu1_45925.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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: 8 Type Number sf(0) Gaussians Mo 4 10.26 5 Fe 76 7.16 5 P 8 5.49 5 Mg 4 5.21 5 S 385 5.16 5 C 26777 2.51 5 N 7174 2.21 5 O 9079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 226 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43507 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3790 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3871 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} bond proxies already assigned to first conformer: 3874 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "E" Number of atoms: 2077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2077 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 8, 'TRANS': 265} Chain: "F" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2145 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "G" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "H" Number of atoms: 3790 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3871 Chain: "I" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "J" Number of atoms: 3793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} bond proxies already assigned to first conformer: 3874 Chain: "K" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "L" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2060 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 8, 'TRANS': 263} Chain: "M" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2121 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 8, 'TRANS': 271} Chain: "N" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'CLF': 1, 'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'CLF': 1, 'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "D" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "E" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "F" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "H" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "I" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 108 Classifications: {'water': 108} Link IDs: {None: 107} Chain: "J" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "K" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "M" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "N" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 56.865 106.130 157.289 1.00 64.74 S ATOM 4549 SG CYS B 95 77.205 95.128 151.915 1.00 66.94 S ATOM 1167 SG CYS A 154 75.658 97.913 147.043 1.00 59.68 S ATOM 462 SG CYS A 62 71.036 98.223 151.667 1.00 60.91 S ATOM 649 SG CYS A 88 72.839 92.039 147.925 1.00 79.60 S ATOM 649 SG CYS A 88 72.839 92.039 147.925 1.00 79.60 S ATOM 5002 SG CYS B 153 77.899 93.632 146.654 1.00 65.79 S ATOM 4369 SG CYS B 70 77.003 88.478 151.450 1.00 65.61 S ATOM 4549 SG CYS B 95 77.205 95.128 151.915 1.00 66.94 S ATOM 10056 SG CYS C 275 46.150 30.273 172.086 1.00154.19 S ATOM 12516 SG CYS D 95 53.521 40.105 192.195 1.00 98.61 S ATOM 9134 SG CYS C 154 48.831 37.596 193.783 1.00109.82 S ATOM 8429 SG CYS C 62 49.874 37.701 187.526 1.00108.28 S ATOM 8616 SG CYS C 88 47.590 42.761 188.986 1.00124.78 S ATOM 12969 SG CYS D 153 50.011 41.918 196.084 1.00123.11 S ATOM 12336 SG CYS D 70 53.147 47.278 192.299 1.00 92.75 S ATOM 12516 SG CYS D 95 53.521 40.105 192.195 1.00 98.61 S ATOM 18693 SG CYS F 98 88.794 132.761 133.030 1.00 82.95 S ATOM 18964 SG CYS F 133 94.038 131.688 137.248 1.00107.43 S ATOM 16615 SG CYS E 98 88.767 131.470 139.682 1.00 92.44 S ATOM 16886 SG CYS E 133 90.296 137.027 136.852 1.00118.44 S ATOM 20463 SG CYS G 42 89.323 117.914 140.293 1.00 81.81 S ATOM 20498 SG CYS G 47 88.648 121.022 139.102 1.00 92.41 S ATOM 20514 SG CYS G 50 83.458 118.847 137.784 1.00 71.92 S ATOM 20925 SG CYS G 102 84.334 115.846 139.602 1.00 76.81 S ATOM 23160 SG CYS H 275 71.009 124.984 92.589 1.00 59.35 S ATOM 25620 SG CYS I 95 47.294 126.025 94.504 1.00 49.45 S ATOM 22238 SG CYS H 154 49.100 124.300 99.523 1.00 60.78 S ATOM 21533 SG CYS H 62 54.026 124.421 95.238 1.00 59.25 S ATOM 21720 SG CYS H 88 48.221 119.650 95.082 1.00 76.93 S ATOM 21720 SG CYS H 88 48.221 119.650 95.082 1.00 76.93 S ATOM 26073 SG CYS I 153 44.834 122.600 97.877 1.00 64.55 S ATOM 25440 SG CYS I 70 43.621 121.629 91.014 1.00 65.66 S ATOM 25620 SG CYS I 95 47.294 126.025 94.504 1.00 49.45 S ATOM 31127 SG CYS J 275 41.228 81.756 34.668 1.00 74.94 S ATOM 33587 SG CYS K 95 43.503 104.055 26.511 1.00 66.04 S ATOM 30205 SG CYS J 154 47.397 100.499 22.603 1.00 57.36 S ATOM 29500 SG CYS J 62 45.274 97.286 27.853 1.00 64.49 S ATOM 29687 SG CYS J 88 50.565 101.828 27.863 1.00 74.96 S ATOM 29687 SG CYS J 88 50.565 101.828 27.863 1.00 74.96 S ATOM 34040 SG CYS K 153 49.436 105.015 23.211 1.00 68.56 S ATOM 33407 SG CYS K 70 48.683 107.787 29.876 1.00 63.01 S ATOM 39751 SG CYS M 98 54.558 144.322 133.653 1.00 89.49 S ATOM 40022 SG CYS M 133 50.663 148.312 130.202 1.00102.67 S ATOM 37686 SG CYS L 98 55.320 147.031 127.508 1.00 91.71 S ATOM 37957 SG CYS L 133 56.560 149.498 133.588 1.00106.56 S ATOM 41495 SG CYS N 42 47.449 139.280 118.938 1.00 85.64 S ATOM 41530 SG CYS N 47 49.315 140.632 121.495 1.00 79.27 S ATOM 41546 SG CYS N 50 52.303 135.701 120.674 1.00 68.06 S ATOM 41957 SG CYS N 102 50.047 135.287 117.718 1.00 74.67 S Time building chain proxies: 12.70, per 1000 atoms: 0.29 Number of scatterers: 43507 At special positions: 0 Unit cell: (135.3, 201.3, 225.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Mo 4 41.97 Fe 76 26.01 S 385 16.00 P 8 15.00 Mg 4 11.99 O 9079 8.00 N 7174 7.00 C 26777 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=34, symmetry=0 Number of additional bonds: simple=34, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES G 201 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 42 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 50 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 47 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 102 " pdb=" FES N 201 " pdb="FE2 FES N 201 " - pdb=" SG CYS N 102 " pdb="FE2 FES N 201 " - pdb=" SG CYS N 50 " pdb="FE1 FES N 201 " - pdb=" SG CYS N 42 " pdb="FE1 FES N 201 " - pdb=" SG CYS N 47 " pdb=" SF4 F 301 " pdb="FE4 SF4 F 301 " - pdb=" SG CYS E 133 " pdb="FE3 SF4 F 301 " - pdb=" SG CYS E 98 " pdb="FE2 SF4 F 301 " - pdb=" SG CYS F 133 " pdb="FE1 SF4 F 301 " - pdb=" SG CYS F 98 " pdb=" SF4 L 303 " pdb="FE3 SF4 L 303 " - pdb=" SG CYS L 98 " pdb="FE2 SF4 L 303 " - pdb=" SG CYS M 133 " pdb="FE4 SF4 L 303 " - pdb=" SG CYS L 133 " pdb="FE1 SF4 L 303 " - pdb=" SG CYS M 98 " Number of angles added : 36 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9778 Finding SS restraints... Secondary structure from input PDB file: 265 helices and 30 sheets defined 54.7% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.064A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.829A pdb=" N LYS A 44 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.530A pdb=" N SER A 92 " --> pdb=" O CYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.812A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.668A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.236A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 210 removed outlier: 4.502A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.500A pdb=" N MET A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 290 removed outlier: 5.928A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 283 " --> pdb=" O MET A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 314 removed outlier: 4.269A pdb=" N LYS A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 347 removed outlier: 3.526A pdb=" N GLN A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 383 through 393 removed outlier: 4.439A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 433 removed outlier: 4.493A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.700A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 removed outlier: 4.191A pdb=" N LEU A 475 " --> pdb=" O TRP A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 31 Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 80 removed outlier: 4.033A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.132A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 removed outlier: 3.666A pdb=" N PHE B 165 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 209 Processing helix chain 'B' and resid 233 through 246 removed outlier: 3.768A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 3.542A pdb=" N THR B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 4.075A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.532A pdb=" N LYS B 458 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.680A pdb=" N ARG B 481 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.504A pdb=" N ASN B 518 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 30 removed outlier: 4.319A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.590A pdb=" N LYS C 44 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 85 through 92 removed outlier: 4.538A pdb=" N GLY C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 92 " --> pdb=" O CYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 162 through 175 removed outlier: 4.011A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.107A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 4.278A pdb=" N ARG C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 211' Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 280 through 290 Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'C' and resid 317 through 343 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 344 through 346 No H-bonds generated for 'chain 'C' and resid 344 through 346' Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 370 Processing helix chain 'C' and resid 383 through 394 removed outlier: 3.808A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 433 removed outlier: 4.647A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 4.188A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 475 removed outlier: 4.060A pdb=" N LEU C 475 " --> pdb=" O TRP C 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 31 Processing helix chain 'D' and resid 36 through 48 removed outlier: 3.535A pdb=" N THR D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 71 through 80 removed outlier: 3.612A pdb=" N ALA D 75 " --> pdb=" O GLN D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.175A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.562A pdb=" N VAL D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 158 removed outlier: 3.537A pdb=" N GLU D 156 " --> pdb=" O THR D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 209 Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.853A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 283 Processing helix chain 'D' and resid 284 through 287 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.001A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 387 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.782A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 445 through 447 No H-bonds generated for 'chain 'D' and resid 445 through 447' Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.668A pdb=" N ARG D 481 " --> pdb=" O HIS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'E' and resid 15 through 30 removed outlier: 3.658A pdb=" N GLU E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 51 Processing helix chain 'E' and resid 57 through 65 removed outlier: 3.629A pdb=" N MET E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 72 through 77 removed outlier: 3.681A pdb=" N VAL E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 114 removed outlier: 3.537A pdb=" N ILE E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 155 through 172 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 216 through 225 removed outlier: 3.502A pdb=" N ARG E 220 " --> pdb=" O ASN E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 235 through 250 Processing helix chain 'E' and resid 261 through 273 Processing helix chain 'F' and resid 15 through 30 removed outlier: 3.716A pdb=" N MET F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 51 Processing helix chain 'F' and resid 57 through 66 Processing helix chain 'F' and resid 100 through 114 removed outlier: 3.605A pdb=" N ASN F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 Processing helix chain 'F' and resid 155 through 172 Processing helix chain 'F' and resid 192 through 205 Processing helix chain 'F' and resid 216 through 223 removed outlier: 3.631A pdb=" N ARG F 220 " --> pdb=" O ASN F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 235 through 250 Processing helix chain 'F' and resid 261 through 272 removed outlier: 3.741A pdb=" N PHE F 272 " --> pdb=" O LEU F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 3.779A pdb=" N ILE F 282 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL F 283 " --> pdb=" O GLU F 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 279 through 283' Processing helix chain 'G' and resid 26 through 34 Processing helix chain 'G' and resid 68 through 79 Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'H' and resid 5 through 17 removed outlier: 3.613A pdb=" N VAL H 9 " --> pdb=" O SER H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 30 removed outlier: 4.066A pdb=" N LYS H 30 " --> pdb=" O LYS H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 45 removed outlier: 3.536A pdb=" N LYS H 44 " --> pdb=" O GLN H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 86 through 92 removed outlier: 3.695A pdb=" N SER H 92 " --> pdb=" O CYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 125 Processing helix chain 'H' and resid 127 through 142 Processing helix chain 'H' and resid 153 through 160 removed outlier: 4.233A pdb=" N GLY H 157 " --> pdb=" O GLU H 153 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU H 158 " --> pdb=" O CYS H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 175 removed outlier: 3.725A pdb=" N VAL H 166 " --> pdb=" O ASP H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 206 removed outlier: 3.538A pdb=" N HIS H 196 " --> pdb=" O SER H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 212 removed outlier: 3.805A pdb=" N ASP H 211 " --> pdb=" O GLY H 208 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLU H 212 " --> pdb=" O LYS H 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 208 through 212' Processing helix chain 'H' and resid 230 through 232 No H-bonds generated for 'chain 'H' and resid 230 through 232' Processing helix chain 'H' and resid 233 through 245 removed outlier: 3.682A pdb=" N LEU H 241 " --> pdb=" O SER H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 265 Processing helix chain 'H' and resid 266 through 268 No H-bonds generated for 'chain 'H' and resid 266 through 268' Processing helix chain 'H' and resid 275 through 291 removed outlier: 3.584A pdb=" N MET H 279 " --> pdb=" O CYS H 275 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR H 281 " --> pdb=" O ARG H 277 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE H 282 " --> pdb=" O SER H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 314 Processing helix chain 'H' and resid 317 through 347 removed outlier: 3.536A pdb=" N GLN H 321 " --> pdb=" O ASP H 317 " (cutoff:3.500A) Proline residue: H 333 - end of helix Proline residue: H 344 - end of helix Processing helix chain 'H' and resid 358 through 370 removed outlier: 3.644A pdb=" N HIS H 362 " --> pdb=" O LEU H 358 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY H 365 " --> pdb=" O ARG H 361 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA H 366 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU H 370 " --> pdb=" O ALA H 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 391 Processing helix chain 'H' and resid 405 through 417 Processing helix chain 'H' and resid 427 through 434 removed outlier: 3.688A pdb=" N MET H 434 " --> pdb=" O ILE H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 447 Processing helix chain 'H' and resid 451 through 468 removed outlier: 3.726A pdb=" N ALA H 457 " --> pdb=" O PHE H 453 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE H 458 " --> pdb=" O ASP H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 469 through 474 removed outlier: 3.587A pdb=" N TRP H 472 " --> pdb=" O ASN H 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 15 Processing helix chain 'I' and resid 17 through 32 removed outlier: 3.779A pdb=" N GLU I 32 " --> pdb=" O ARG I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 48 removed outlier: 3.514A pdb=" N THR I 48 " --> pdb=" O PHE I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 58 Processing helix chain 'I' and resid 70 through 80 removed outlier: 4.062A pdb=" N GLY I 74 " --> pdb=" O CYS I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 108 removed outlier: 4.272A pdb=" N VAL I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 126 Processing helix chain 'I' and resid 127 through 143 Processing helix chain 'I' and resid 152 through 158 Processing helix chain 'I' and resid 161 through 172 removed outlier: 3.629A pdb=" N PHE I 165 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 210 Processing helix chain 'I' and resid 233 through 247 removed outlier: 3.715A pdb=" N PHE I 237 " --> pdb=" O TYR I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 263 removed outlier: 4.122A pdb=" N THR I 263 " --> pdb=" O VAL I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 283 Processing helix chain 'I' and resid 284 through 287 Processing helix chain 'I' and resid 294 through 297 removed outlier: 3.512A pdb=" N HIS I 297 " --> pdb=" O GLN I 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 294 through 297' Processing helix chain 'I' and resid 298 through 308 Processing helix chain 'I' and resid 322 through 337 Processing helix chain 'I' and resid 341 through 358 removed outlier: 3.538A pdb=" N THR I 345 " --> pdb=" O PRO I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 363 Processing helix chain 'I' and resid 372 through 386 Processing helix chain 'I' and resid 399 through 412 Processing helix chain 'I' and resid 426 through 437 Processing helix chain 'I' and resid 445 through 447 No H-bonds generated for 'chain 'I' and resid 445 through 447' Processing helix chain 'I' and resid 448 through 459 Processing helix chain 'I' and resid 460 through 463 removed outlier: 3.538A pdb=" N GLU I 463 " --> pdb=" O LYS I 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 460 through 463' Processing helix chain 'I' and resid 478 through 482 removed outlier: 3.560A pdb=" N ARG I 481 " --> pdb=" O HIS I 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 485 through 509 Processing helix chain 'I' and resid 515 through 519 Processing helix chain 'J' and resid 5 through 17 Processing helix chain 'J' and resid 21 through 29 Processing helix chain 'J' and resid 62 through 69 Processing helix chain 'J' and resid 86 through 92 removed outlier: 3.608A pdb=" N SER J 92 " --> pdb=" O CYS J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 125 Processing helix chain 'J' and resid 127 through 142 Processing helix chain 'J' and resid 153 through 159 removed outlier: 3.533A pdb=" N GLY J 157 " --> pdb=" O GLU J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 175 removed outlier: 3.843A pdb=" N VAL J 166 " --> pdb=" O ASP J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 206 removed outlier: 4.177A pdb=" N GLY J 194 " --> pdb=" O SER J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 246 Processing helix chain 'J' and resid 258 through 265 Processing helix chain 'J' and resid 266 through 268 No H-bonds generated for 'chain 'J' and resid 266 through 268' Processing helix chain 'J' and resid 275 through 291 removed outlier: 5.696A pdb=" N TYR J 281 " --> pdb=" O ARG J 277 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE J 282 " --> pdb=" O SER J 278 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER J 283 " --> pdb=" O MET J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 314 Processing helix chain 'J' and resid 317 through 347 Proline residue: J 333 - end of helix Proline residue: J 344 - end of helix Processing helix chain 'J' and resid 357 through 369 removed outlier: 4.557A pdb=" N ARG J 361 " --> pdb=" O GLY J 357 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLY J 365 " --> pdb=" O ARG J 361 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA J 366 " --> pdb=" O HIS J 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 394 removed outlier: 3.642A pdb=" N TYR J 387 " --> pdb=" O HIS J 383 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS J 392 " --> pdb=" O ASP J 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 417 Processing helix chain 'J' and resid 424 through 434 removed outlier: 3.813A pdb=" N PHE J 429 " --> pdb=" O ILE J 425 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE J 430 " --> pdb=" O LYS J 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 468 removed outlier: 3.768A pdb=" N ALA J 457 " --> pdb=" O PHE J 453 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE J 458 " --> pdb=" O ASP J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 469 through 474 Processing helix chain 'K' and resid 10 through 15 Processing helix chain 'K' and resid 17 through 31 Processing helix chain 'K' and resid 36 through 48 Processing helix chain 'K' and resid 49 through 58 Processing helix chain 'K' and resid 70 through 80 removed outlier: 4.041A pdb=" N GLY K 74 " --> pdb=" O CYS K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 108 removed outlier: 4.379A pdb=" N VAL K 96 " --> pdb=" O SER K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 126 Processing helix chain 'K' and resid 127 through 143 Processing helix chain 'K' and resid 152 through 159 Processing helix chain 'K' and resid 161 through 172 Processing helix chain 'K' and resid 192 through 209 Processing helix chain 'K' and resid 233 through 247 removed outlier: 3.828A pdb=" N PHE K 237 " --> pdb=" O TYR K 233 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET K 247 " --> pdb=" O MET K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 283 Processing helix chain 'K' and resid 284 through 287 Processing helix chain 'K' and resid 294 through 297 removed outlier: 3.595A pdb=" N HIS K 297 " --> pdb=" O GLN K 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 294 through 297' Processing helix chain 'K' and resid 298 through 308 Processing helix chain 'K' and resid 322 through 337 Processing helix chain 'K' and resid 341 through 363 removed outlier: 3.526A pdb=" N THR K 345 " --> pdb=" O PRO K 341 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N THR K 360 " --> pdb=" O THR K 356 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N TRP K 361 " --> pdb=" O ASP K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 386 Processing helix chain 'K' and resid 399 through 412 removed outlier: 3.502A pdb=" N ALA K 412 " --> pdb=" O ALA K 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 413 through 417 removed outlier: 3.906A pdb=" N LYS K 417 " --> pdb=" O PRO K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 426 through 437 Processing helix chain 'K' and resid 445 through 447 No H-bonds generated for 'chain 'K' and resid 445 through 447' Processing helix chain 'K' and resid 448 through 459 Processing helix chain 'K' and resid 460 through 463 Processing helix chain 'K' and resid 485 through 509 Processing helix chain 'K' and resid 515 through 519 Processing helix chain 'L' and resid 15 through 30 removed outlier: 3.556A pdb=" N MET L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 51 removed outlier: 3.652A pdb=" N LEU L 50 " --> pdb=" O THR L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 65 Processing helix chain 'L' and resid 67 through 71 Processing helix chain 'L' and resid 72 through 77 removed outlier: 3.729A pdb=" N VAL L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 100 through 114 removed outlier: 3.579A pdb=" N ILE L 104 " --> pdb=" O GLY L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 142 Processing helix chain 'L' and resid 155 through 172 Processing helix chain 'L' and resid 193 through 204 Processing helix chain 'L' and resid 216 through 224 removed outlier: 3.746A pdb=" N ARG L 224 " --> pdb=" O ARG L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 232 Processing helix chain 'L' and resid 235 through 250 Processing helix chain 'L' and resid 261 through 271 Processing helix chain 'M' and resid 15 through 30 Processing helix chain 'M' and resid 46 through 51 removed outlier: 3.521A pdb=" N LEU M 50 " --> pdb=" O THR M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 65 removed outlier: 3.569A pdb=" N MET M 61 " --> pdb=" O THR M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 77 removed outlier: 3.672A pdb=" N VAL M 76 " --> pdb=" O GLU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 114 removed outlier: 3.501A pdb=" N ILE M 104 " --> pdb=" O GLY M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 136 Processing helix chain 'M' and resid 137 through 142 Processing helix chain 'M' and resid 155 through 172 Processing helix chain 'M' and resid 193 through 205 Processing helix chain 'M' and resid 216 through 224 removed outlier: 3.786A pdb=" N ARG M 224 " --> pdb=" O ARG M 220 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 232 Processing helix chain 'M' and resid 235 through 251 removed outlier: 3.626A pdb=" N ASP M 239 " --> pdb=" O ALA M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 261 through 271 Processing helix chain 'N' and resid 26 through 34 Processing helix chain 'N' and resid 68 through 78 Processing helix chain 'N' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.150A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 378 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 7.016A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 7.165A pdb=" N ILE A 225 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN A 252 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLY A 227 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER A 254 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN A 271 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.620A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.606A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE B 367 " --> pdb=" O PRO B 390 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS B 392 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.792A pdb=" N LEU C 399 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LYS C 349 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL C 375 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL C 351 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N THR C 377 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU C 353 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TYR C 379 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.856A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE C 79 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLN C 151 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE C 81 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 6.502A pdb=" N VAL C 223 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA C 251 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.393A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.693A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 85 through 88 removed outlier: 6.495A pdb=" N MET E 35 " --> pdb=" O PHE E 124 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP E 126 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL E 37 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU E 128 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY E 10 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN E 5 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N TYR E 149 " --> pdb=" O GLN E 5 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA E 7 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL E 151 " --> pdb=" O ALA E 7 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR E 9 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE E 148 " --> pdb=" O GLY E 182 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE E 184 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE E 150 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN E 186 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N CYS E 152 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 12.801A pdb=" N MET E 208 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 10.348A pdb=" N GLY E 181 " --> pdb=" O MET E 208 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N HIS E 210 " --> pdb=" O GLY E 181 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU E 183 " --> pdb=" O HIS E 210 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N VAL E 212 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N CYS E 185 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 78 through 80 removed outlier: 6.345A pdb=" N MET F 35 " --> pdb=" O PHE F 124 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASP F 126 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL F 37 " --> pdb=" O ASP F 126 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN F 5 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N TYR F 149 " --> pdb=" O GLN F 5 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA F 7 " --> pdb=" O TYR F 149 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL F 151 " --> pdb=" O ALA F 7 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR F 9 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE F 148 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY F 182 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE F 150 " --> pdb=" O GLY F 182 " (cutoff:3.500A) removed outlier: 12.975A pdb=" N MET F 208 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N GLY F 181 " --> pdb=" O MET F 208 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N HIS F 210 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU F 183 " --> pdb=" O HIS F 210 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL F 212 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS F 185 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 15 through 18 Processing sheet with id=AB7, first strand: chain 'H' and resid 32 through 34 removed outlier: 9.929A pdb=" N LEU H 399 " --> pdb=" O GLU H 373 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL H 375 " --> pdb=" O LEU H 399 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N TYR H 401 " --> pdb=" O VAL H 375 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR H 377 " --> pdb=" O TYR H 401 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL H 351 " --> pdb=" O VAL H 374 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY H 376 " --> pdb=" O VAL H 351 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE H 421 " --> pdb=" O ARG H 439 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 178 through 181 removed outlier: 6.876A pdb=" N ILE H 148 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL H 181 " --> pdb=" O ILE H 148 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL H 150 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE H 114 " --> pdb=" O HIS H 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 248 through 254 removed outlier: 7.455A pdb=" N VAL H 223 " --> pdb=" O ALA H 251 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N TRP H 253 " --> pdb=" O VAL H 223 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE H 225 " --> pdb=" O TRP H 253 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 270 " --> pdb=" O ASP H 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 114 through 115 removed outlier: 8.563A pdb=" N VAL I 114 " --> pdb=" O THR I 85 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 251 through 253 removed outlier: 6.605A pdb=" N ILE I 224 " --> pdb=" O SER I 252 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASN I 225 " --> pdb=" O VAL I 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'I' and resid 420 through 423 removed outlier: 8.546A pdb=" N THR I 420 " --> pdb=" O GLU I 389 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL I 391 " --> pdb=" O THR I 420 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N TYR I 422 " --> pdb=" O VAL I 391 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE I 393 " --> pdb=" O TYR I 422 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE I 367 " --> pdb=" O VAL I 391 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE I 393 " --> pdb=" O PHE I 367 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU I 369 " --> pdb=" O ILE I 393 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N CYS I 395 " --> pdb=" O LEU I 369 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG I 366 " --> pdb=" O PHE I 441 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE I 443 " --> pdb=" O ARG I 366 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA I 368 " --> pdb=" O ILE I 443 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 32 through 34 removed outlier: 3.667A pdb=" N LEU J 399 " --> pdb=" O VAL J 375 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL J 351 " --> pdb=" O VAL J 374 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY J 376 " --> pdb=" O VAL J 351 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE J 421 " --> pdb=" O ARG J 439 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 178 through 181 removed outlier: 4.332A pdb=" N PHE J 114 " --> pdb=" O HIS J 80 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 248 through 254 removed outlier: 6.443A pdb=" N VAL J 223 " --> pdb=" O CYS J 249 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA J 251 " --> pdb=" O VAL J 223 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 114 through 115 removed outlier: 8.636A pdb=" N VAL K 114 " --> pdb=" O THR K 85 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 251 through 253 removed outlier: 6.345A pdb=" N ILE K 224 " --> pdb=" O SER K 252 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASN K 225 " --> pdb=" O VAL K 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'K' and resid 420 through 423 removed outlier: 8.647A pdb=" N THR K 420 " --> pdb=" O GLU K 389 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL K 391 " --> pdb=" O THR K 420 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR K 422 " --> pdb=" O VAL K 391 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE K 393 " --> pdb=" O TYR K 422 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU K 369 " --> pdb=" O VAL K 391 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE K 393 " --> pdb=" O LEU K 369 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG K 366 " --> pdb=" O PHE K 441 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE K 443 " --> pdb=" O ARG K 366 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA K 368 " --> pdb=" O ILE K 443 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 78 through 79 removed outlier: 6.444A pdb=" N GLN L 5 " --> pdb=" O GLU L 147 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N TYR L 149 " --> pdb=" O GLN L 5 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA L 7 " --> pdb=" O TYR L 149 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL L 151 " --> pdb=" O ALA L 7 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR L 9 " --> pdb=" O VAL L 151 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE L 148 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY L 182 " --> pdb=" O ILE L 148 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE L 150 " --> pdb=" O GLY L 182 " (cutoff:3.500A) removed outlier: 12.886A pdb=" N MET L 208 " --> pdb=" O ARG L 179 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N GLY L 181 " --> pdb=" O MET L 208 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N HIS L 210 " --> pdb=" O GLY L 181 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU L 183 " --> pdb=" O HIS L 210 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL L 212 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS L 185 " --> pdb=" O VAL L 212 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 78 through 80 removed outlier: 6.505A pdb=" N GLN M 5 " --> pdb=" O GLU M 147 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N TYR M 149 " --> pdb=" O GLN M 5 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ALA M 7 " --> pdb=" O TYR M 149 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL M 151 " --> pdb=" O ALA M 7 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR M 9 " --> pdb=" O VAL M 151 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE M 148 " --> pdb=" O LEU M 180 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY M 182 " --> pdb=" O ILE M 148 " (cutoff:3.500A) removed outlier: 12.541A pdb=" N MET M 208 " --> pdb=" O ARG M 179 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N GLY M 181 " --> pdb=" O MET M 208 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N HIS M 210 " --> pdb=" O GLY M 181 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU M 183 " --> pdb=" O HIS M 210 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL M 212 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS M 185 " --> pdb=" O VAL M 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 15 through 18 1983 hydrogen bonds defined for protein. 5748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.23 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.84: 43173 1.84 - 2.48: 239 2.48 - 3.12: 41 3.12 - 3.75: 16 3.75 - 4.39: 8 Bond restraints: 43477 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 4.393 -2.193 2.00e-02 2.50e+03 1.20e+04 bond pdb="FE2 CLF A 503 " pdb="FE8 CLF A 503 " ideal model delta sigma weight residual 2.200 4.388 -2.188 2.00e-02 2.50e+03 1.20e+04 bond pdb="FE2 CLF H 503 " pdb="FE8 CLF H 503 " ideal model delta sigma weight residual 2.200 4.382 -2.182 2.00e-02 2.50e+03 1.19e+04 bond pdb="FE2 CLF K 602 " pdb="FE8 CLF K 602 " ideal model delta sigma weight residual 2.200 4.372 -2.172 2.00e-02 2.50e+03 1.18e+04 bond pdb="FE5 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.931 -1.731 2.00e-02 2.50e+03 7.49e+03 ... (remaining 43472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.81: 58658 6.81 - 13.62: 10 13.62 - 20.43: 4 20.43 - 27.25: 0 27.25 - 34.06: 8 Bond angle restraints: 58680 Sorted by residual: angle pdb=" S1 CLF A 503 " pdb="FE2 CLF A 503 " pdb="FE4 CLF A 503 " ideal model delta sigma weight residual 90.00 55.94 34.06 3.00e+00 1.11e-01 1.29e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.96 34.04 3.00e+00 1.11e-01 1.29e+02 angle pdb=" S1 CLF K 602 " pdb="FE2 CLF K 602 " pdb="FE4 CLF K 602 " ideal model delta sigma weight residual 90.00 56.08 33.92 3.00e+00 1.11e-01 1.28e+02 angle pdb=" S1 CLF H 503 " pdb="FE2 CLF H 503 " pdb="FE4 CLF H 503 " ideal model delta sigma weight residual 90.00 56.11 33.89 3.00e+00 1.11e-01 1.28e+02 angle pdb=" S1 CLF A 503 " pdb="FE2 CLF A 503 " pdb="FE1 CLF A 503 " ideal model delta sigma weight residual 90.00 60.55 29.45 3.00e+00 1.11e-01 9.63e+01 ... (remaining 58675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 22455 18.00 - 36.00: 2985 36.00 - 54.00: 920 54.00 - 72.00: 207 72.00 - 90.00: 81 Dihedral angle restraints: 26648 sinusoidal: 11337 harmonic: 15311 Sorted by residual: dihedral pdb=" CA GLU E 117 " pdb=" C GLU E 117 " pdb=" N ASP E 118 " pdb=" CA ASP E 118 " ideal model delta harmonic sigma weight residual 180.00 149.23 30.77 0 5.00e+00 4.00e-02 3.79e+01 dihedral pdb=" CA GLN F 207 " pdb=" C GLN F 207 " pdb=" N MET F 208 " pdb=" CA MET F 208 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" C5' ADP F 302 " pdb=" O5' ADP F 302 " pdb=" PA ADP F 302 " pdb=" O2A ADP F 302 " ideal model delta sinusoidal sigma weight residual -60.00 14.67 -74.67 1 2.00e+01 2.50e-03 1.77e+01 ... (remaining 26645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 5415 0.062 - 0.125: 814 0.125 - 0.187: 53 0.187 - 0.250: 10 0.250 - 0.312: 3 Chirality restraints: 6295 Sorted by residual: chirality pdb=" CA ILE J 430 " pdb=" N ILE J 430 " pdb=" C ILE J 430 " pdb=" CB ILE J 430 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA LYS N 28 " pdb=" N LYS N 28 " pdb=" C LYS N 28 " pdb=" CB LYS N 28 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ILE H 355 " pdb=" N ILE H 355 " pdb=" C ILE H 355 " pdb=" CB ILE H 355 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 6292 not shown) Planarity restraints: 7554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY H 357 " -0.028 2.00e-02 2.50e+03 5.62e-02 3.16e+01 pdb=" C GLY H 357 " 0.097 2.00e-02 2.50e+03 pdb=" O GLY H 357 " -0.036 2.00e-02 2.50e+03 pdb=" N LEU H 358 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP K 256 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" C ASP K 256 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP K 256 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO K 257 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP K 256 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO K 257 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO K 257 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 257 " -0.033 5.00e-02 4.00e+02 ... (remaining 7551 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 540 2.57 - 3.16: 34375 3.16 - 3.74: 71469 3.74 - 4.32: 103513 4.32 - 4.90: 170598 Nonbonded interactions: 380495 Sorted by model distance: nonbonded pdb=" O2B ADP F 302 " pdb="MG MG F 303 " model vdw 1.992 2.170 nonbonded pdb=" OD2 ASP I 357 " pdb="FE FE I 601 " model vdw 2.000 2.260 nonbonded pdb=" OG SER M 17 " pdb="MG MG M 302 " model vdw 2.008 2.170 nonbonded pdb=" OG SER L 17 " pdb="MG MG L 302 " model vdw 2.013 2.170 nonbonded pdb=" O3A ADP L 301 " pdb="MG MG L 302 " model vdw 2.030 2.170 ... (remaining 380490 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' and (resid 4 through 248 or resid 250 through 502)) selection = (chain 'C' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 248 or resid 250 through 502)) selection = (chain 'H' and (resid 4 through 248 or resid 250 through 502)) selection = (chain 'J' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 248 or resid 250 through 502)) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 2 through 601) selection = chain 'I' selection = (chain 'K' and resid 2 through 601) } ncs_group { reference = (chain 'E' and (resid 3 through 82 or resid 84 through 274)) selection = (chain 'F' and resid 3 through 274) selection = (chain 'L' and (resid 3 through 82 or resid 84 through 274)) selection = (chain 'M' and (resid 3 through 82 or resid 84 through 274)) } ncs_group { reference = (chain 'G' and (resid 2 through 26 or resid 29 through 201)) selection = (chain 'N' and (resid 2 through 26 or resid 29 through 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 12.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 50.180 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.120 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:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 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 : 0.039 2.193 43527 Z= 1.951 Angle : 0.794 34.057 58716 Z= 0.399 Chirality : 0.045 0.312 6295 Planarity : 0.004 0.060 7554 Dihedral : 18.357 90.001 16870 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.11 % Allowed : 29.24 % Favored : 68.65 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.20 (0.11), residues: 5323 helix: 1.15 (0.11), residues: 2453 sheet: -0.06 (0.20), residues: 608 loop : -0.91 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 246 TYR 0.029 0.001 TYR M 160 PHE 0.019 0.001 PHE J 429 TRP 0.021 0.001 TRP C 444 HIS 0.009 0.001 HIS H 383 Details of bonding type rmsd covalent geometry : bond 0.03832 (43477) covalent geometry : angle 0.75750 (58680) hydrogen bonds : bond 0.15320 ( 1983) hydrogen bonds : angle 6.62396 ( 5748) metal coordination : bond 0.01049 ( 16) metal coordination : angle 9.70252 ( 36) Misc. bond : bond 0.19004 ( 34) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1500 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1405 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLU cc_start: 0.7238 (tt0) cc_final: 0.7019 (mt-10) REVERT: A 318 GLU cc_start: 0.6552 (pm20) cc_final: 0.5785 (pt0) REVERT: A 373 GLU cc_start: 0.6206 (pt0) cc_final: 0.5636 (tp30) REVERT: B 24 LEU cc_start: 0.7165 (mt) cc_final: 0.6837 (mt) REVERT: B 32 GLU cc_start: 0.4561 (mt-10) cc_final: 0.4208 (mt-10) REVERT: B 207 TYR cc_start: 0.7143 (t80) cc_final: 0.6891 (t80) REVERT: B 288 LEU cc_start: 0.6636 (mt) cc_final: 0.6406 (tp) REVERT: B 409 ILE cc_start: 0.8274 (mt) cc_final: 0.8063 (tt) REVERT: C 35 ASN cc_start: 0.5727 (t0) cc_final: 0.4439 (OUTLIER) REVERT: C 36 ASP cc_start: 0.2541 (t0) cc_final: 0.2028 (p0) REVERT: C 50 LYS cc_start: 0.7052 (mmmt) cc_final: 0.6547 (mmtt) REVERT: C 91 TYR cc_start: 0.7049 (m-80) cc_final: 0.6799 (m-80) REVERT: C 125 PHE cc_start: 0.7217 (m-80) cc_final: 0.7010 (m-10) REVERT: C 134 LEU cc_start: 0.5861 (tt) cc_final: 0.5500 (tt) REVERT: C 209 LYS cc_start: 0.5349 (mptt) cc_final: 0.4787 (ttmt) REVERT: C 265 THR cc_start: 0.7145 (m) cc_final: 0.6747 (t) REVERT: C 282 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.5919 (mt) REVERT: C 352 MET cc_start: 0.5574 (mtm) cc_final: 0.5307 (mtm) REVERT: C 367 TYR cc_start: 0.7139 (m-80) cc_final: 0.6854 (m-80) REVERT: C 372 MET cc_start: 0.5131 (ttm) cc_final: 0.3974 (tmm) REVERT: C 390 THR cc_start: 0.6059 (m) cc_final: 0.4800 (t) REVERT: C 391 MET cc_start: 0.3362 (mmt) cc_final: 0.2422 (mmt) REVERT: C 394 MET cc_start: 0.5761 (tpp) cc_final: 0.4598 (ptt) REVERT: D 12 TYR cc_start: 0.5115 (t80) cc_final: 0.4428 (t80) REVERT: D 50 LYS cc_start: 0.7277 (mtpp) cc_final: 0.6990 (mptt) REVERT: D 118 MET cc_start: 0.5581 (mtm) cc_final: 0.5221 (mtp) REVERT: D 270 ARG cc_start: 0.6711 (mtt90) cc_final: 0.6328 (mpp80) REVERT: D 312 GLU cc_start: 0.6625 (pm20) cc_final: 0.6400 (pm20) REVERT: D 386 LEU cc_start: 0.6107 (mt) cc_final: 0.5830 (mt) REVERT: D 523 ARG cc_start: 0.5094 (mmt180) cc_final: 0.3776 (mtt-85) REVERT: E 117 GLU cc_start: 0.4936 (pm20) cc_final: 0.4730 (pt0) REVERT: E 239 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.6258 (p0) REVERT: E 260 ILE cc_start: 0.7039 (mt) cc_final: 0.6678 (pp) REVERT: E 275 MET cc_start: 0.5082 (ptt) cc_final: 0.4878 (ptm) REVERT: F 44 ASP cc_start: 0.6705 (p0) cc_final: 0.6073 (m-30) REVERT: F 210 HIS cc_start: 0.5915 (t70) cc_final: 0.5202 (t-170) REVERT: F 239 ASP cc_start: 0.6948 (m-30) cc_final: 0.6668 (m-30) REVERT: G 20 VAL cc_start: 0.5150 (t) cc_final: 0.4809 (t) REVERT: H 47 ILE cc_start: 0.6777 (mt) cc_final: 0.6450 (mt) REVERT: H 168 LYS cc_start: 0.7571 (mtpp) cc_final: 0.7055 (mttm) REVERT: H 321 GLN cc_start: 0.6327 (mt0) cc_final: 0.5942 (mp10) REVERT: H 380 GLU cc_start: 0.5078 (OUTLIER) cc_final: 0.4812 (pt0) REVERT: H 397 SER cc_start: 0.6649 (m) cc_final: 0.6321 (p) REVERT: I 104 ASN cc_start: 0.6635 (m110) cc_final: 0.6409 (m110) REVERT: I 309 TRP cc_start: 0.7207 (m-10) cc_final: 0.6907 (m-10) REVERT: J 7 GLU cc_start: 0.7207 (mp0) cc_final: 0.6970 (pm20) REVERT: J 380 GLU cc_start: 0.7028 (tt0) cc_final: 0.6799 (mt-10) REVERT: K 12 TYR cc_start: 0.7556 (t80) cc_final: 0.6960 (t80) REVERT: K 288 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.5655 (tt) REVERT: K 289 ASN cc_start: 0.6965 (t0) cc_final: 0.6765 (t0) REVERT: K 415 TYR cc_start: 0.5816 (m-80) cc_final: 0.5507 (m-80) REVERT: L 224 ARG cc_start: 0.6376 (mtt180) cc_final: 0.6017 (mmp-170) REVERT: L 253 LEU cc_start: 0.5933 (tt) cc_final: 0.5181 (mm) REVERT: M 3 MET cc_start: 0.6231 (tpt) cc_final: 0.5872 (mpp) REVERT: M 105 THR cc_start: 0.6127 (m) cc_final: 0.5746 (p) REVERT: M 127 VAL cc_start: 0.3106 (OUTLIER) cc_final: 0.2242 (m) REVERT: N 66 LEU cc_start: 0.4917 (tp) cc_final: 0.4717 (tp) outliers start: 95 outliers final: 14 residues processed: 1471 average time/residue: 0.7076 time to fit residues: 1288.6531 Evaluate side-chains 761 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 743 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain H residue 380 GLU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 362 HIS Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 210 HIS Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 127 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 265 optimal weight: 9.9990 chunk 523 optimal weight: 0.5980 chunk 497 optimal weight: 0.4980 chunk 414 optimal weight: 0.9980 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 0.0470 chunk 366 optimal weight: 7.9990 chunk 223 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 98 ASN A 230 ASN A 280 ASN A 362 HIS A 384 ASN A 469 ASN B 363 HIS ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN C 469 ASN D 199 ASN ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 GLN F 51 HIS F 237 GLN H 98 ASN H 113 ASN H 145 ASN ** H 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 GLN I 106 HIS I 128 GLN ** I 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 225 ASN I 363 HIS I 513 GLN J 49 ASN J 113 ASN J 199 ASN J 271 ASN J 469 ASN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN K 168 ASN K 185 HIS K 297 HIS K 338 GLN K 418 ASN K 513 GLN ** L 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 216 ASN L 219 GLN M 5 GLN M 186 ASN ** M 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.128954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.099373 restraints weight = 109107.457| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.46 r_work: 0.3248 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.797 43527 Z= 0.269 Angle : 0.854 57.062 58716 Z= 0.374 Chirality : 0.046 0.301 6295 Planarity : 0.005 0.086 7554 Dihedral : 5.554 72.640 6565 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.19 % Allowed : 32.15 % Favored : 62.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.11), residues: 5323 helix: 1.16 (0.11), residues: 2472 sheet: -0.04 (0.21), residues: 599 loop : -0.83 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 6 TYR 0.020 0.002 TYR K 88 PHE 0.032 0.002 PHE N 40 TRP 0.018 0.002 TRP J 444 HIS 0.012 0.002 HIS M 210 Details of bonding type rmsd covalent geometry : bond 0.00542 (43477) covalent geometry : angle 0.77607 (58680) hydrogen bonds : bond 0.04348 ( 1983) hydrogen bonds : angle 5.49301 ( 5748) metal coordination : bond 0.02014 ( 16) metal coordination : angle 14.39533 ( 36) Misc. bond : bond 0.19689 ( 34) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 813 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.6473 (tptp) cc_final: 0.5463 (ttmm) REVERT: A 279 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6834 (tpp) REVERT: A 307 GLU cc_start: 0.7369 (tt0) cc_final: 0.7112 (mt-10) REVERT: A 373 GLU cc_start: 0.6113 (pt0) cc_final: 0.5667 (tp30) REVERT: A 415 ARG cc_start: 0.7716 (ttm110) cc_final: 0.7469 (ttm110) REVERT: B 142 TYR cc_start: 0.4814 (m-80) cc_final: 0.4485 (m-10) REVERT: B 143 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.6421 (mppt) REVERT: B 207 TYR cc_start: 0.7430 (t80) cc_final: 0.7086 (t80) REVERT: B 277 THR cc_start: 0.7433 (OUTLIER) cc_final: 0.6989 (m) REVERT: B 288 LEU cc_start: 0.6785 (mt) cc_final: 0.6526 (tp) REVERT: B 385 GLU cc_start: 0.5337 (mt-10) cc_final: 0.5064 (mt-10) REVERT: B 409 ILE cc_start: 0.8362 (mt) cc_final: 0.8065 (tt) REVERT: B 435 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7521 (t80) REVERT: C 28 ARG cc_start: 0.5747 (mmm160) cc_final: 0.5379 (mmm160) REVERT: C 36 ASP cc_start: 0.2557 (t0) cc_final: 0.2234 (p0) REVERT: C 50 LYS cc_start: 0.6930 (mmmt) cc_final: 0.6517 (mmtt) REVERT: C 125 PHE cc_start: 0.7285 (m-80) cc_final: 0.7055 (m-10) REVERT: C 152 SER cc_start: 0.6885 (m) cc_final: 0.6682 (t) REVERT: C 191 GLN cc_start: 0.6450 (mp10) cc_final: 0.6109 (mp-120) REVERT: C 205 TRP cc_start: 0.6697 (m100) cc_final: 0.6334 (m100) REVERT: C 209 LYS cc_start: 0.5372 (OUTLIER) cc_final: 0.4655 (ttmt) REVERT: C 265 THR cc_start: 0.7123 (m) cc_final: 0.6856 (t) REVERT: C 282 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.5868 (mm) REVERT: C 367 TYR cc_start: 0.6890 (m-80) cc_final: 0.6508 (m-80) REVERT: C 368 GLU cc_start: 0.3095 (OUTLIER) cc_final: 0.2791 (mp0) REVERT: C 430 ILE cc_start: 0.6789 (tt) cc_final: 0.6500 (pp) REVERT: D 50 LYS cc_start: 0.7437 (mtpp) cc_final: 0.7145 (mptt) REVERT: D 118 MET cc_start: 0.5521 (mtm) cc_final: 0.5284 (mtm) REVERT: D 133 ASP cc_start: 0.6542 (OUTLIER) cc_final: 0.5926 (t0) REVERT: D 213 MET cc_start: 0.5102 (mmm) cc_final: 0.4704 (mmm) REVERT: D 523 ARG cc_start: 0.5818 (mmt180) cc_final: 0.5317 (mmt180) REVERT: E 275 MET cc_start: 0.4840 (ptt) cc_final: 0.4604 (ptm) REVERT: F 22 ASN cc_start: 0.7217 (m-40) cc_final: 0.6856 (m-40) REVERT: F 44 ASP cc_start: 0.6571 (p0) cc_final: 0.6308 (m-30) REVERT: H 10 GLU cc_start: 0.7083 (mm-30) cc_final: 0.5935 (mt-10) REVERT: H 47 ILE cc_start: 0.6998 (mt) cc_final: 0.6572 (mt) REVERT: H 407 TYR cc_start: 0.6918 (t80) cc_final: 0.6699 (t80) REVERT: I 142 TYR cc_start: 0.6730 (m-80) cc_final: 0.6347 (m-80) REVERT: I 213 MET cc_start: 0.6309 (mmp) cc_final: 0.6096 (tpt) REVERT: I 372 ASP cc_start: 0.7218 (m-30) cc_final: 0.7001 (m-30) REVERT: J 209 LYS cc_start: 0.7940 (ttmt) cc_final: 0.7736 (tppp) REVERT: J 467 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6460 (tt) REVERT: J 469 ASN cc_start: 0.7939 (OUTLIER) cc_final: 0.7579 (m-40) REVERT: K 12 TYR cc_start: 0.8083 (t80) cc_final: 0.7625 (t80) REVERT: K 21 LYS cc_start: 0.7253 (ttmm) cc_final: 0.6664 (mmmt) REVERT: K 288 LEU cc_start: 0.7095 (mp) cc_final: 0.5959 (tt) REVERT: K 289 ASN cc_start: 0.7297 (t0) cc_final: 0.7087 (t0) REVERT: L 59 MET cc_start: 0.7169 (tpp) cc_final: 0.6844 (ttm) REVERT: L 253 LEU cc_start: 0.6008 (tt) cc_final: 0.5251 (mm) REVERT: M 59 MET cc_start: 0.7019 (mmp) cc_final: 0.6376 (mmt) REVERT: M 71 LEU cc_start: 0.4736 (OUTLIER) cc_final: 0.4427 (tp) REVERT: M 150 ILE cc_start: 0.7278 (mp) cc_final: 0.7027 (mt) REVERT: M 200 LEU cc_start: 0.6125 (tt) cc_final: 0.5820 (tt) REVERT: M 207 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: M 239 ASP cc_start: 0.7074 (t0) cc_final: 0.6632 (p0) REVERT: M 269 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7708 (mp) REVERT: N 53 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.6942 (tptm) outliers start: 235 outliers final: 53 residues processed: 968 average time/residue: 0.6380 time to fit residues: 785.9676 Evaluate side-chains 704 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 637 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 152 CYS Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 484 THR Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 253 TRP Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 362 HIS Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 467 LEU Chi-restraints excluded: chain J residue 469 ASN Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 276 THR Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 53 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 147 optimal weight: 0.9980 chunk 188 optimal weight: 7.9990 chunk 439 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 476 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 529 optimal weight: 0.0980 chunk 475 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 252 GLN A 468 ASN B 71 GLN B 363 HIS B 396 HIS B 429 HIS ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** C 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 145 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN D 106 HIS ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN D 396 HIS H 98 ASN H 196 HIS ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 ASN I 130 ASN I 392 HIS J 49 ASN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN K 513 GLN L 143 ASN M 186 ASN N 14 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101697 restraints weight = 82769.147| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.02 r_work: 0.3306 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.856 43527 Z= 0.291 Angle : 0.959 53.526 58716 Z= 0.435 Chirality : 0.051 0.354 6295 Planarity : 0.006 0.133 7554 Dihedral : 5.577 67.399 6546 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 6.51 % Allowed : 30.94 % Favored : 62.55 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.11), residues: 5323 helix: 0.59 (0.10), residues: 2496 sheet: -0.28 (0.21), residues: 584 loop : -1.10 (0.12), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 187 TYR 0.136 0.002 TYR C 401 PHE 0.043 0.003 PHE I 44 TRP 0.038 0.002 TRP H 253 HIS 0.012 0.002 HIS I 457 Details of bonding type rmsd covalent geometry : bond 0.00598 (43477) covalent geometry : angle 0.88468 (58680) hydrogen bonds : bond 0.04713 ( 1983) hydrogen bonds : angle 5.49419 ( 5748) metal coordination : bond 0.01931 ( 16) metal coordination : angle 15.01063 ( 36) Misc. bond : bond 0.17680 ( 34) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 295 poor density : 687 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7654 (tp30) REVERT: A 158 LEU cc_start: 0.8180 (mt) cc_final: 0.7908 (mt) REVERT: A 209 LYS cc_start: 0.6830 (tptp) cc_final: 0.6181 (ttmm) REVERT: A 336 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6762 (mm-30) REVERT: B 88 TYR cc_start: 0.8145 (t80) cc_final: 0.7893 (t80) REVERT: B 207 TYR cc_start: 0.8482 (t80) cc_final: 0.7932 (t80) REVERT: B 211 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.6960 (mmmt) REVERT: B 288 LEU cc_start: 0.7461 (mt) cc_final: 0.7103 (tp) REVERT: B 358 SER cc_start: 0.7174 (m) cc_final: 0.6959 (m) REVERT: B 409 ILE cc_start: 0.8262 (mt) cc_final: 0.8062 (tt) REVERT: B 452 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.6462 (tp40) REVERT: C 35 ASN cc_start: 0.5154 (t0) cc_final: 0.4868 (t0) REVERT: C 50 LYS cc_start: 0.7021 (mmmt) cc_final: 0.6486 (mmtt) REVERT: C 99 TYR cc_start: 0.5979 (m-10) cc_final: 0.5707 (m-10) REVERT: C 125 PHE cc_start: 0.7297 (m-80) cc_final: 0.6987 (m-10) REVERT: C 173 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6783 (mp0) REVERT: C 191 GLN cc_start: 0.7146 (mp10) cc_final: 0.6940 (mp-120) REVERT: C 209 LYS cc_start: 0.5601 (OUTLIER) cc_final: 0.4931 (ttmt) REVERT: C 252 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7801 (mp10) REVERT: C 367 TYR cc_start: 0.6822 (m-80) cc_final: 0.6454 (m-80) REVERT: C 391 MET cc_start: 0.3429 (OUTLIER) cc_final: 0.2628 (mtm) REVERT: C 430 ILE cc_start: 0.8009 (tt) cc_final: 0.7584 (mt) REVERT: D 16 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7999 (mm) REVERT: D 50 LYS cc_start: 0.7730 (mtpp) cc_final: 0.7398 (mptt) REVERT: D 118 MET cc_start: 0.6455 (mtm) cc_final: 0.5848 (mtp) REVERT: D 222 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7146 (mtmm) REVERT: D 231 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.6055 (tp30) REVERT: D 330 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6989 (mpp) REVERT: E 61 MET cc_start: 0.6583 (mtp) cc_final: 0.6366 (mtp) REVERT: E 208 MET cc_start: 0.5646 (OUTLIER) cc_final: 0.5377 (tpp) REVERT: E 262 MET cc_start: 0.6613 (mpp) cc_final: 0.6032 (ttt) REVERT: E 270 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7041 (mmm) REVERT: F 217 VAL cc_start: 0.4827 (OUTLIER) cc_final: 0.4476 (t) REVERT: F 239 ASP cc_start: 0.7265 (m-30) cc_final: 0.6679 (p0) REVERT: F 274 ILE cc_start: 0.5572 (OUTLIER) cc_final: 0.5236 (pp) REVERT: G 103 GLN cc_start: 0.8575 (mt0) cc_final: 0.8371 (mt0) REVERT: H 10 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7620 (mm-30) REVERT: H 30 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7387 (pttt) REVERT: H 47 ILE cc_start: 0.7819 (mt) cc_final: 0.7524 (mt) REVERT: H 315 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7209 (mtpt) REVERT: H 379 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: I 178 GLU cc_start: 0.7463 (tp30) cc_final: 0.7148 (mp0) REVERT: I 218 VAL cc_start: 0.7196 (OUTLIER) cc_final: 0.6783 (t) REVERT: I 279 GLU cc_start: 0.8110 (tp30) cc_final: 0.7821 (tp30) REVERT: I 312 GLU cc_start: 0.7848 (tt0) cc_final: 0.7524 (tm-30) REVERT: I 330 MET cc_start: 0.7078 (mtt) cc_final: 0.6854 (mtm) REVERT: I 338 GLN cc_start: 0.8008 (tp40) cc_final: 0.7442 (mp10) REVERT: I 496 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8807 (p) REVERT: J 223 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8214 (m) REVERT: J 347 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6674 (tt0) REVERT: J 467 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7241 (tt) REVERT: J 476 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6641 (mm-40) REVERT: K 7 LYS cc_start: 0.7228 (ttmt) cc_final: 0.7027 (tppp) REVERT: L 5 GLN cc_start: 0.4418 (OUTLIER) cc_final: 0.3497 (mt0) REVERT: L 27 LEU cc_start: 0.5015 (mt) cc_final: 0.4716 (tp) REVERT: L 33 LYS cc_start: 0.5877 (OUTLIER) cc_final: 0.5424 (tppt) REVERT: L 53 LYS cc_start: 0.6736 (pmtt) cc_final: 0.6465 (tttm) REVERT: L 59 MET cc_start: 0.7950 (tpp) cc_final: 0.7624 (ttm) REVERT: L 72 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.5456 (pm20) REVERT: L 122 PHE cc_start: 0.7897 (m-80) cc_final: 0.7491 (m-80) REVERT: L 132 VAL cc_start: 0.8583 (t) cc_final: 0.8241 (p) REVERT: L 147 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7235 (pt0) REVERT: M 59 MET cc_start: 0.7192 (mmp) cc_final: 0.6585 (mmt) REVERT: M 207 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7418 (pm20) REVERT: M 239 ASP cc_start: 0.7292 (t0) cc_final: 0.6941 (p0) REVERT: N 32 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.8009 (pt0) REVERT: N 83 LYS cc_start: 0.8373 (mmmm) cc_final: 0.8120 (tppt) REVERT: N 87 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7028 (tm-30) outliers start: 295 outliers final: 74 residues processed: 907 average time/residue: 0.7141 time to fit residues: 808.6653 Evaluate side-chains 638 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 538 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 469 ASN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 152 CYS Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 315 LYS Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain I residue 153 CYS Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 245 SER Chi-restraints excluded: chain I residue 420 THR Chi-restraints excluded: chain I residue 484 THR Chi-restraints excluded: chain I residue 496 THR Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 347 GLU Chi-restraints excluded: chain J residue 351 VAL Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 467 LEU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 276 THR Chi-restraints excluded: chain K residue 345 THR Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 33 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 210 HIS Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain N residue 32 GLN Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 388 optimal weight: 5.9990 chunk 42 optimal weight: 0.0770 chunk 117 optimal weight: 6.9990 chunk 468 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 387 optimal weight: 0.9980 chunk 485 optimal weight: 7.9990 chunk 291 optimal weight: 1.9990 chunk 361 optimal weight: 0.9990 chunk 356 optimal weight: 0.4980 chunk 124 optimal weight: 0.9980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN C 98 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN D 106 HIS ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN ** I 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 ASN J 49 ASN J 199 ASN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN K 130 ASN ** L 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 ASN ** M 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 HIS N 34 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.129895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.100547 restraints weight = 94063.997| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.05 r_work: 0.3275 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.7056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.666 43527 Z= 0.203 Angle : 0.821 50.457 58716 Z= 0.350 Chirality : 0.045 0.284 6295 Planarity : 0.005 0.062 7554 Dihedral : 5.045 57.535 6542 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.22 % Allowed : 33.20 % Favored : 62.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.11), residues: 5323 helix: 1.06 (0.10), residues: 2465 sheet: -0.27 (0.20), residues: 621 loop : -1.04 (0.12), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 284 TYR 0.030 0.001 TYR C 401 PHE 0.024 0.002 PHE D 165 TRP 0.024 0.001 TRP D 296 HIS 0.031 0.001 HIS L 210 Details of bonding type rmsd covalent geometry : bond 0.00423 (43477) covalent geometry : angle 0.74039 (58680) hydrogen bonds : bond 0.03661 ( 1983) hydrogen bonds : angle 5.16899 ( 5748) metal coordination : bond 0.01100 ( 16) metal coordination : angle 14.31593 ( 36) Misc. bond : bond 0.14073 ( 34) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 551 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6389 (pm20) REVERT: A 158 LEU cc_start: 0.8340 (mt) cc_final: 0.8090 (mt) REVERT: A 178 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7849 (mt) REVERT: A 209 LYS cc_start: 0.6909 (tptp) cc_final: 0.6484 (ttmm) REVERT: A 372 MET cc_start: 0.7837 (mtt) cc_final: 0.7459 (mtp) REVERT: B 88 TYR cc_start: 0.8393 (t80) cc_final: 0.8065 (t80) REVERT: B 143 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7058 (mppt) REVERT: B 200 MET cc_start: 0.8696 (mmm) cc_final: 0.8419 (tpt) REVERT: B 207 TYR cc_start: 0.8639 (t80) cc_final: 0.7939 (t80) REVERT: B 211 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7070 (mmmt) REVERT: B 277 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8347 (m) REVERT: B 281 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7344 (tpt) REVERT: B 288 LEU cc_start: 0.7924 (mt) cc_final: 0.7408 (tp) REVERT: C 50 LYS cc_start: 0.7235 (mmmt) cc_final: 0.6723 (mmtt) REVERT: C 125 PHE cc_start: 0.7373 (m-80) cc_final: 0.7024 (m-10) REVERT: C 152 SER cc_start: 0.7811 (m) cc_final: 0.7604 (t) REVERT: C 209 LYS cc_start: 0.5888 (OUTLIER) cc_final: 0.4964 (ttmp) REVERT: C 225 ILE cc_start: 0.7266 (mm) cc_final: 0.6714 (mm) REVERT: C 368 GLU cc_start: 0.3600 (OUTLIER) cc_final: 0.3153 (mp0) REVERT: C 394 MET cc_start: 0.5975 (tpp) cc_final: 0.5768 (tpp) REVERT: C 430 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7780 (mt) REVERT: D 50 LYS cc_start: 0.7888 (mtpp) cc_final: 0.7602 (mptt) REVERT: D 118 MET cc_start: 0.6995 (mtm) cc_final: 0.6326 (mtm) REVERT: D 222 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7165 (mtmm) REVERT: D 231 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6206 (tp30) REVERT: D 292 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6826 (mp) REVERT: E 138 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.6771 (tpt) REVERT: E 208 MET cc_start: 0.5770 (OUTLIER) cc_final: 0.5276 (tpp) REVERT: E 262 MET cc_start: 0.6640 (mpp) cc_final: 0.6158 (ttt) REVERT: F 68 VAL cc_start: 0.8020 (p) cc_final: 0.7715 (t) REVERT: F 241 TYR cc_start: 0.5794 (m-80) cc_final: 0.5535 (m-80) REVERT: F 270 MET cc_start: 0.6817 (ppp) cc_final: 0.6524 (ppp) REVERT: G 118 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8755 (pm20) REVERT: I 218 VAL cc_start: 0.7372 (OUTLIER) cc_final: 0.6982 (t) REVERT: I 338 GLN cc_start: 0.8181 (tp40) cc_final: 0.7667 (mp10) REVERT: I 399 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8253 (p0) REVERT: J 197 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8218 (mm) REVERT: J 248 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6860 (ptm-80) REVERT: J 374 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.8031 (t) REVERT: J 469 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7789 (m-40) REVERT: K 4 GLN cc_start: 0.6409 (mt0) cc_final: 0.6181 (mm-40) REVERT: L 35 MET cc_start: 0.5742 (OUTLIER) cc_final: 0.4607 (tpt) REVERT: L 59 MET cc_start: 0.8182 (tpp) cc_final: 0.7958 (ttm) REVERT: L 124 PHE cc_start: 0.7483 (m-80) cc_final: 0.7275 (m-80) REVERT: L 147 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7314 (pt0) REVERT: L 267 GLU cc_start: 0.6774 (pp20) cc_final: 0.6520 (pp20) REVERT: M 59 MET cc_start: 0.7522 (mmp) cc_final: 0.6885 (mmt) REVERT: M 142 GLU cc_start: 0.6473 (mm-30) cc_final: 0.5615 (mt-10) REVERT: M 207 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: M 270 MET cc_start: 0.7151 (mtp) cc_final: 0.6736 (mmm) REVERT: N 44 ASP cc_start: 0.7707 (p0) cc_final: 0.7478 (p0) REVERT: N 87 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7475 (tm-30) outliers start: 191 outliers final: 60 residues processed: 690 average time/residue: 0.6939 time to fit residues: 599.4031 Evaluate side-chains 552 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 469 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 220 SER Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 399 ASN Chi-restraints excluded: chain I residue 484 THR Chi-restraints excluded: chain I residue 503 GLU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 248 ARG Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 469 ASN Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 289 ASN Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain K residue 484 THR Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 425 optimal weight: 0.0870 chunk 282 optimal weight: 0.0020 chunk 118 optimal weight: 0.9990 chunk 374 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 444 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 272 optimal weight: 0.7980 chunk 475 optimal weight: 6.9990 chunk 337 optimal weight: 0.0370 chunk 428 optimal weight: 2.9990 overall best weight: 0.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN D 71 GLN D 167 ASN ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN F 237 GLN G 13 HIS G 73 ASN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN I 129 GLN J 49 ASN J 252 GLN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 ASN ** M 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.130410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.099835 restraints weight = 111298.062| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.45 r_work: 0.3266 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.7356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.699 43527 Z= 0.186 Angle : 0.789 49.708 58716 Z= 0.330 Chirality : 0.044 0.287 6295 Planarity : 0.004 0.054 7554 Dihedral : 4.780 58.071 6542 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.89 % Allowed : 33.73 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.11), residues: 5323 helix: 1.19 (0.11), residues: 2474 sheet: -0.19 (0.21), residues: 598 loop : -0.96 (0.12), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 389 TYR 0.025 0.001 TYR E 160 PHE 0.024 0.001 PHE C 429 TRP 0.020 0.001 TRP D 296 HIS 0.024 0.001 HIS L 210 Details of bonding type rmsd covalent geometry : bond 0.00376 (43477) covalent geometry : angle 0.70888 (58680) hydrogen bonds : bond 0.03362 ( 1983) hydrogen bonds : angle 5.02202 ( 5748) metal coordination : bond 0.00819 ( 16) metal coordination : angle 13.96571 ( 36) Misc. bond : bond 0.14189 ( 34) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 491 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6633 (tp) REVERT: A 158 LEU cc_start: 0.8408 (mt) cc_final: 0.8109 (mt) REVERT: A 209 LYS cc_start: 0.6934 (tptp) cc_final: 0.6561 (ttmm) REVERT: A 372 MET cc_start: 0.7916 (mtt) cc_final: 0.7577 (mtp) REVERT: B 88 TYR cc_start: 0.8516 (t80) cc_final: 0.8171 (t80) REVERT: B 143 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.7045 (mppt) REVERT: B 200 MET cc_start: 0.8708 (mmm) cc_final: 0.8436 (tpt) REVERT: B 207 TYR cc_start: 0.8601 (t80) cc_final: 0.7966 (t80) REVERT: B 211 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7050 (mmmt) REVERT: B 263 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8344 (p) REVERT: B 288 LEU cc_start: 0.8059 (mt) cc_final: 0.7521 (tp) REVERT: B 358 SER cc_start: 0.7231 (m) cc_final: 0.6983 (m) REVERT: C 28 ARG cc_start: 0.5959 (mmm160) cc_final: 0.5541 (mmm160) REVERT: C 50 LYS cc_start: 0.7295 (mmmt) cc_final: 0.6806 (mmtt) REVERT: C 57 MET cc_start: 0.7689 (ttm) cc_final: 0.7396 (OUTLIER) REVERT: C 125 PHE cc_start: 0.7347 (m-80) cc_final: 0.7020 (m-10) REVERT: C 152 SER cc_start: 0.7753 (m) cc_final: 0.7553 (t) REVERT: C 209 LYS cc_start: 0.5982 (OUTLIER) cc_final: 0.4979 (ttmp) REVERT: C 225 ILE cc_start: 0.7293 (mm) cc_final: 0.6720 (mm) REVERT: C 240 ILE cc_start: 0.4848 (OUTLIER) cc_final: 0.4613 (mp) REVERT: C 248 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.5471 (ttp-170) REVERT: C 252 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7512 (mp10) REVERT: C 358 LEU cc_start: 0.7692 (tp) cc_final: 0.7134 (mp) REVERT: C 368 GLU cc_start: 0.3920 (OUTLIER) cc_final: 0.3495 (mp0) REVERT: C 430 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7478 (mt) REVERT: D 50 LYS cc_start: 0.7912 (mtpp) cc_final: 0.7610 (mptt) REVERT: D 118 MET cc_start: 0.7121 (mtm) cc_final: 0.6785 (mtm) REVERT: D 167 ASN cc_start: 0.5812 (m-40) cc_final: 0.5537 (m110) REVERT: D 222 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7237 (mtmm) REVERT: D 231 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6305 (tp30) REVERT: D 292 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6867 (mp) REVERT: D 297 HIS cc_start: 0.5807 (OUTLIER) cc_final: 0.5549 (m-70) REVERT: E 61 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.5861 (mpp) REVERT: E 138 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.6895 (tpt) REVERT: E 208 MET cc_start: 0.5764 (OUTLIER) cc_final: 0.5280 (tpp) REVERT: E 262 MET cc_start: 0.6729 (mpp) cc_final: 0.6298 (ttt) REVERT: F 68 VAL cc_start: 0.7897 (p) cc_final: 0.7618 (t) REVERT: F 217 VAL cc_start: 0.4922 (OUTLIER) cc_final: 0.4550 (t) REVERT: F 270 MET cc_start: 0.6897 (ppp) cc_final: 0.6607 (ppp) REVERT: F 274 ILE cc_start: 0.5698 (OUTLIER) cc_final: 0.5329 (pp) REVERT: G 118 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8749 (pm20) REVERT: I 218 VAL cc_start: 0.7535 (OUTLIER) cc_final: 0.7116 (t) REVERT: I 338 GLN cc_start: 0.8235 (tp40) cc_final: 0.7747 (mp10) REVERT: J 197 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8250 (mm) REVERT: J 223 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8449 (m) REVERT: J 248 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6792 (ptm-80) REVERT: J 463 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7320 (mpp) REVERT: J 469 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7714 (m-40) REVERT: K 4 GLN cc_start: 0.6475 (mt0) cc_final: 0.6135 (mm110) REVERT: L 4 ARG cc_start: 0.6408 (OUTLIER) cc_final: 0.6080 (ttm170) REVERT: L 30 MET cc_start: 0.6363 (mpt) cc_final: 0.6106 (mpp) REVERT: L 35 MET cc_start: 0.5899 (OUTLIER) cc_final: 0.4719 (tpt) REVERT: L 147 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7269 (pt0) REVERT: L 224 ARG cc_start: 0.7338 (mtt180) cc_final: 0.7118 (mtp180) REVERT: L 231 TYR cc_start: 0.5087 (t80) cc_final: 0.4811 (t80) REVERT: L 267 GLU cc_start: 0.6707 (pp20) cc_final: 0.6186 (pp20) REVERT: M 57 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7267 (t) REVERT: M 59 MET cc_start: 0.7495 (mmp) cc_final: 0.6871 (mmt) REVERT: M 207 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7681 (pm20) REVERT: M 270 MET cc_start: 0.7191 (mtp) cc_final: 0.6871 (mmm) REVERT: N 44 ASP cc_start: 0.7912 (p0) cc_final: 0.7652 (p0) REVERT: N 86 GLU cc_start: 0.7397 (tt0) cc_final: 0.7117 (tt0) REVERT: N 87 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7609 (tm-30) outliers start: 176 outliers final: 59 residues processed: 623 average time/residue: 0.6865 time to fit residues: 535.6872 Evaluate side-chains 541 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 453 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 248 ARG Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 HIS Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 152 CYS Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 105 ARG Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 247 MET Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 484 THR Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 248 ARG Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 401 TYR Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain J residue 466 THR Chi-restraints excluded: chain J residue 469 ASN Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain L residue 4 ARG Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 169 ILE Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 175 optimal weight: 1.9990 chunk 404 optimal weight: 0.9980 chunk 365 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 508 optimal weight: 2.9990 chunk 341 optimal weight: 0.9980 chunk 344 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 403 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN C 49 ASN C 98 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 HIS H 98 ASN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.128411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.099332 restraints weight = 76224.289| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.90 r_work: 0.3255 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.8070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.676 43527 Z= 0.199 Angle : 0.802 47.650 58716 Z= 0.340 Chirality : 0.044 0.267 6295 Planarity : 0.004 0.056 7554 Dihedral : 4.671 55.465 6540 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.78 % Allowed : 33.47 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.11), residues: 5323 helix: 1.20 (0.11), residues: 2499 sheet: -0.15 (0.21), residues: 600 loop : -0.90 (0.12), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 242 TYR 0.024 0.001 TYR C 401 PHE 0.028 0.001 PHE F 109 TRP 0.031 0.001 TRP D 296 HIS 0.020 0.001 HIS L 210 Details of bonding type rmsd covalent geometry : bond 0.00423 (43477) covalent geometry : angle 0.72332 (58680) hydrogen bonds : bond 0.03558 ( 1983) hydrogen bonds : angle 4.96597 ( 5748) metal coordination : bond 0.01090 ( 16) metal coordination : angle 13.99194 ( 36) Misc. bond : bond 0.14030 ( 34) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 481 time to evaluate : 1.898 Fit side-chains revert: symmetry clash REVERT: A 158 LEU cc_start: 0.8459 (mt) cc_final: 0.8127 (mt) REVERT: A 209 LYS cc_start: 0.7248 (tptp) cc_final: 0.6946 (ttmm) REVERT: A 302 PRO cc_start: 0.6845 (Cg_exo) cc_final: 0.6627 (Cg_endo) REVERT: A 372 MET cc_start: 0.8090 (mtt) cc_final: 0.7797 (mtp) REVERT: A 417 LYS cc_start: 0.8401 (mptt) cc_final: 0.8086 (mmmt) REVERT: B 8 ILE cc_start: 0.7790 (mt) cc_final: 0.7557 (mt) REVERT: B 143 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7391 (mppt) REVERT: B 200 MET cc_start: 0.8801 (mmm) cc_final: 0.8532 (tpt) REVERT: B 207 TYR cc_start: 0.8646 (t80) cc_final: 0.7909 (t80) REVERT: B 263 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8354 (p) REVERT: C 28 ARG cc_start: 0.5986 (mmm160) cc_final: 0.5746 (mmm160) REVERT: C 50 LYS cc_start: 0.7318 (mmmt) cc_final: 0.6937 (mmtt) REVERT: C 125 PHE cc_start: 0.7495 (m-80) cc_final: 0.7098 (m-10) REVERT: C 152 SER cc_start: 0.7923 (m) cc_final: 0.7716 (t) REVERT: C 209 LYS cc_start: 0.6352 (OUTLIER) cc_final: 0.5235 (ttmp) REVERT: C 225 ILE cc_start: 0.7500 (mm) cc_final: 0.7036 (mt) REVERT: C 240 ILE cc_start: 0.5185 (OUTLIER) cc_final: 0.4967 (mp) REVERT: C 248 ARG cc_start: 0.5955 (OUTLIER) cc_final: 0.5461 (ttt180) REVERT: C 265 THR cc_start: 0.7535 (m) cc_final: 0.7121 (p) REVERT: C 368 GLU cc_start: 0.4141 (OUTLIER) cc_final: 0.3716 (mp0) REVERT: C 430 ILE cc_start: 0.8151 (tt) cc_final: 0.7577 (mt) REVERT: D 50 LYS cc_start: 0.7923 (mtpp) cc_final: 0.7604 (mptt) REVERT: D 118 MET cc_start: 0.7277 (mtm) cc_final: 0.6923 (mtm) REVERT: D 222 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7191 (mppt) REVERT: D 231 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6365 (tp30) REVERT: D 279 GLU cc_start: 0.7602 (mp0) cc_final: 0.6866 (mm-30) REVERT: D 292 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7172 (mp) REVERT: D 297 HIS cc_start: 0.5752 (OUTLIER) cc_final: 0.5483 (m-70) REVERT: E 138 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.6879 (tpt) REVERT: E 208 MET cc_start: 0.5864 (OUTLIER) cc_final: 0.5392 (tpp) REVERT: E 262 MET cc_start: 0.6653 (mpp) cc_final: 0.6292 (ttt) REVERT: E 275 MET cc_start: 0.1176 (pp-130) cc_final: -0.0272 (mtm) REVERT: F 35 MET cc_start: 0.7798 (ttp) cc_final: 0.7569 (ttm) REVERT: F 68 VAL cc_start: 0.7939 (p) cc_final: 0.7669 (t) REVERT: F 217 VAL cc_start: 0.4922 (OUTLIER) cc_final: 0.4216 (t) REVERT: F 267 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5508 (mm-30) REVERT: F 270 MET cc_start: 0.6974 (ppp) cc_final: 0.6593 (ppp) REVERT: F 274 ILE cc_start: 0.5828 (OUTLIER) cc_final: 0.5408 (pp) REVERT: H 25 ARG cc_start: 0.7178 (mtp85) cc_final: 0.6958 (mtp-110) REVERT: H 129 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7997 (tppt) REVERT: I 218 VAL cc_start: 0.7687 (OUTLIER) cc_final: 0.7235 (t) REVERT: I 338 GLN cc_start: 0.8394 (tp40) cc_final: 0.7901 (mp10) REVERT: I 491 MET cc_start: 0.8744 (mtt) cc_final: 0.8459 (mtt) REVERT: I 516 ASP cc_start: 0.8854 (p0) cc_final: 0.8590 (p0) REVERT: J 248 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6831 (ptm-80) REVERT: J 284 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7927 (mtt180) REVERT: J 347 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6760 (tt0) REVERT: J 355 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7731 (mt) REVERT: J 463 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7616 (mpp) REVERT: J 469 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7937 (m-40) REVERT: K 39 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.6961 (ttmm) REVERT: K 146 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7530 (tmm) REVERT: K 404 LYS cc_start: 0.7886 (tttm) cc_final: 0.7486 (mtpp) REVERT: L 107 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8266 (mp) REVERT: L 147 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7241 (pt0) REVERT: L 179 ARG cc_start: 0.7011 (mmp-170) cc_final: 0.6539 (mmm160) REVERT: L 231 TYR cc_start: 0.5076 (t80) cc_final: 0.4829 (t80) REVERT: L 246 ARG cc_start: 0.6743 (mmm160) cc_final: 0.6247 (tpp80) REVERT: L 267 GLU cc_start: 0.6883 (pp20) cc_final: 0.6396 (pp20) REVERT: L 271 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7042 (pm20) REVERT: M 81 TYR cc_start: 0.6340 (t80) cc_final: 0.6101 (t80) REVERT: M 207 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: N 10 LEU cc_start: 0.8090 (mt) cc_final: 0.7837 (mp) REVERT: N 44 ASP cc_start: 0.8309 (p0) cc_final: 0.8098 (p0) outliers start: 171 outliers final: 65 residues processed: 610 average time/residue: 0.7517 time to fit residues: 567.3843 Evaluate side-chains 532 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 439 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 248 ARG Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain D residue 297 HIS Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 152 CYS Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 105 ARG Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 484 THR Chi-restraints excluded: chain I residue 503 GLU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 248 ARG Chi-restraints excluded: chain J residue 284 ARG Chi-restraints excluded: chain J residue 347 GLU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain J residue 469 ASN Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 169 ILE Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 164 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 307 optimal weight: 0.9980 chunk 461 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 362 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 HIS C 98 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 GLN ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN G 13 HIS G 73 ASN H 41 GLN H 252 GLN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 ASN ** I 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 ASN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 237 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.127150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.097050 restraints weight = 94991.026| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.07 r_work: 0.3219 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.8730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.664 43527 Z= 0.201 Angle : 0.800 47.501 58716 Z= 0.340 Chirality : 0.045 0.270 6295 Planarity : 0.004 0.062 7554 Dihedral : 4.672 55.518 6539 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.56 % Allowed : 33.60 % Favored : 62.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.11), residues: 5323 helix: 1.22 (0.11), residues: 2482 sheet: -0.22 (0.21), residues: 610 loop : -0.87 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 246 TYR 0.027 0.001 TYR B 88 PHE 0.029 0.001 PHE D 165 TRP 0.033 0.001 TRP C 294 HIS 0.019 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00424 (43477) covalent geometry : angle 0.72503 (58680) hydrogen bonds : bond 0.03571 ( 1983) hydrogen bonds : angle 4.95614 ( 5748) metal coordination : bond 0.01132 ( 16) metal coordination : angle 13.70200 ( 36) Misc. bond : bond 0.13932 ( 34) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 471 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.7268 (tptp) cc_final: 0.6992 (ttmm) REVERT: A 284 ARG cc_start: 0.8640 (mtt-85) cc_final: 0.8249 (mtt180) REVERT: A 286 MET cc_start: 0.8438 (tpp) cc_final: 0.8209 (mtt) REVERT: A 372 MET cc_start: 0.8329 (mtt) cc_final: 0.8060 (mtp) REVERT: B 8 ILE cc_start: 0.7948 (mt) cc_final: 0.7742 (mt) REVERT: B 88 TYR cc_start: 0.8997 (t80) cc_final: 0.8764 (t80) REVERT: B 200 MET cc_start: 0.8914 (mmm) cc_final: 0.8707 (tpt) REVERT: B 263 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8503 (p) REVERT: C 50 LYS cc_start: 0.7344 (mmmt) cc_final: 0.6789 (mmtt) REVERT: C 125 PHE cc_start: 0.7470 (m-80) cc_final: 0.7063 (m-10) REVERT: C 152 SER cc_start: 0.8062 (m) cc_final: 0.7818 (t) REVERT: C 209 LYS cc_start: 0.6430 (OUTLIER) cc_final: 0.5314 (ttmp) REVERT: C 248 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.5564 (ttt180) REVERT: C 265 THR cc_start: 0.7525 (m) cc_final: 0.7108 (p) REVERT: C 350 ARG cc_start: 0.5959 (OUTLIER) cc_final: 0.5288 (mtp-110) REVERT: C 368 GLU cc_start: 0.4347 (OUTLIER) cc_final: 0.4029 (mp0) REVERT: C 430 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7778 (mt) REVERT: D 50 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7587 (mppt) REVERT: D 104 ASN cc_start: 0.7887 (m110) cc_final: 0.7676 (m-40) REVERT: D 118 MET cc_start: 0.7357 (mtm) cc_final: 0.6788 (mtm) REVERT: D 222 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7139 (mppt) REVERT: D 231 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6469 (tp30) REVERT: D 347 GLU cc_start: 0.7862 (tp30) cc_final: 0.7640 (mm-30) REVERT: D 491 MET cc_start: 0.8730 (mtp) cc_final: 0.8528 (mtm) REVERT: E 138 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.6968 (tpt) REVERT: E 208 MET cc_start: 0.5998 (OUTLIER) cc_final: 0.5559 (tpp) REVERT: E 262 MET cc_start: 0.6647 (mpp) cc_final: 0.6342 (ttt) REVERT: E 275 MET cc_start: 0.1544 (pp-130) cc_final: -0.0046 (mtm) REVERT: F 35 MET cc_start: 0.8083 (ttp) cc_final: 0.7695 (ttm) REVERT: F 68 VAL cc_start: 0.7881 (p) cc_final: 0.7511 (t) REVERT: F 156 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7324 (tpt) REVERT: F 210 HIS cc_start: 0.7546 (t-170) cc_final: 0.7221 (t70) REVERT: F 217 VAL cc_start: 0.5419 (OUTLIER) cc_final: 0.5093 (t) REVERT: F 239 ASP cc_start: 0.6813 (m-30) cc_final: 0.6238 (p0) REVERT: F 267 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.5504 (mm-30) REVERT: F 270 MET cc_start: 0.6998 (ppp) cc_final: 0.6602 (ppp) REVERT: F 274 ILE cc_start: 0.6068 (OUTLIER) cc_final: 0.5599 (pp) REVERT: H 15 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7394 (mp0) REVERT: H 25 ARG cc_start: 0.7305 (mtp85) cc_final: 0.7056 (mtp-110) REVERT: H 129 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8080 (tppt) REVERT: I 218 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7351 (t) REVERT: I 338 GLN cc_start: 0.8608 (tp40) cc_final: 0.8360 (tp40) REVERT: I 491 MET cc_start: 0.8835 (mtt) cc_final: 0.8586 (mtt) REVERT: J 284 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7967 (mtt90) REVERT: J 347 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6928 (tt0) REVERT: J 355 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7619 (mt) REVERT: J 463 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7914 (mpp) REVERT: K 39 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7177 (ttmm) REVERT: K 146 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7680 (tmm) REVERT: K 404 LYS cc_start: 0.7987 (tttm) cc_final: 0.7612 (mtpp) REVERT: L 35 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.5350 (tpt) REVERT: L 50 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7425 (tt) REVERT: L 147 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7371 (pt0) REVERT: L 188 ARG cc_start: 0.6397 (OUTLIER) cc_final: 0.5661 (mtp-110) REVERT: L 231 TYR cc_start: 0.5126 (t80) cc_final: 0.4864 (t80) REVERT: L 246 ARG cc_start: 0.7250 (mmm160) cc_final: 0.6581 (tpp80) REVERT: L 267 GLU cc_start: 0.6678 (pp20) cc_final: 0.6234 (pp20) REVERT: L 271 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6694 (pm20) REVERT: M 142 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6604 (mt-10) REVERT: M 207 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: N 44 ASP cc_start: 0.8508 (p0) cc_final: 0.8301 (p0) outliers start: 161 outliers final: 71 residues processed: 589 average time/residue: 0.6723 time to fit residues: 488.0592 Evaluate side-chains 526 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 428 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 248 ARG Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 350 ARG Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 152 CYS Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 105 ARG Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 484 THR Chi-restraints excluded: chain I residue 503 GLU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 284 ARG Chi-restraints excluded: chain J residue 347 GLU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain L residue 35 MET Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 169 ILE Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 498 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 424 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 414 optimal weight: 1.9990 chunk 368 optimal weight: 1.9990 chunk 363 optimal weight: 5.9990 chunk 459 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 HIS ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 HIS H 41 GLN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 HIS ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.124745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.094212 restraints weight = 86637.434| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.07 r_work: 0.3189 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.9273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.709 43527 Z= 0.218 Angle : 0.819 46.657 58716 Z= 0.351 Chirality : 0.045 0.266 6295 Planarity : 0.005 0.066 7554 Dihedral : 4.748 55.584 6539 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.10 % Allowed : 33.91 % Favored : 62.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.11), residues: 5323 helix: 1.19 (0.10), residues: 2492 sheet: -0.22 (0.20), residues: 611 loop : -0.93 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 246 TYR 0.027 0.002 TYR E 160 PHE 0.036 0.002 PHE M 109 TRP 0.038 0.002 TRP C 294 HIS 0.053 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00468 (43477) covalent geometry : angle 0.74541 (58680) hydrogen bonds : bond 0.03824 ( 1983) hydrogen bonds : angle 4.99102 ( 5748) metal coordination : bond 0.01340 ( 16) metal coordination : angle 13.74660 ( 36) Misc. bond : bond 0.14938 ( 34) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 431 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: A 262 ILE cc_start: 0.8923 (mm) cc_final: 0.8714 (mp) REVERT: A 284 ARG cc_start: 0.8654 (mtt-85) cc_final: 0.8275 (mtt180) REVERT: A 286 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8282 (mtt) REVERT: A 372 MET cc_start: 0.8498 (mtt) cc_final: 0.8188 (mtp) REVERT: A 391 MET cc_start: 0.8513 (mmt) cc_final: 0.7658 (mmt) REVERT: A 417 LYS cc_start: 0.8633 (mptt) cc_final: 0.8197 (mmmt) REVERT: A 476 GLN cc_start: 0.7733 (tp40) cc_final: 0.7449 (tp40) REVERT: B 222 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7198 (mppt) REVERT: B 263 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8522 (p) REVERT: C 28 ARG cc_start: 0.6237 (mmm160) cc_final: 0.5817 (mmm160) REVERT: C 50 LYS cc_start: 0.7369 (mmmt) cc_final: 0.6814 (mmtt) REVERT: C 125 PHE cc_start: 0.7626 (m-80) cc_final: 0.7257 (m-10) REVERT: C 152 SER cc_start: 0.8277 (m) cc_final: 0.7989 (t) REVERT: C 209 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.5558 (ttmp) REVERT: C 240 ILE cc_start: 0.5605 (OUTLIER) cc_final: 0.5274 (mp) REVERT: C 248 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5695 (ttp-170) REVERT: C 265 THR cc_start: 0.7516 (m) cc_final: 0.7125 (p) REVERT: C 430 ILE cc_start: 0.8348 (tt) cc_final: 0.7896 (mt) REVERT: C 434 MET cc_start: 0.7560 (mtm) cc_final: 0.7126 (mtp) REVERT: D 118 MET cc_start: 0.7544 (mtm) cc_final: 0.6964 (mtm) REVERT: D 222 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7142 (mppt) REVERT: D 279 GLU cc_start: 0.7966 (mp0) cc_final: 0.7303 (mm-30) REVERT: D 466 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8047 (pt) REVERT: D 523 ARG cc_start: 0.8659 (mmt180) cc_final: 0.8283 (mmt90) REVERT: E 61 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6137 (mpp) REVERT: E 130 ASP cc_start: 0.5944 (m-30) cc_final: 0.5406 (m-30) REVERT: E 157 MET cc_start: 0.7355 (tpt) cc_final: 0.7076 (mmm) REVERT: E 208 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5757 (tpp) REVERT: E 275 MET cc_start: 0.1591 (pp-130) cc_final: 0.0225 (mtm) REVERT: F 35 MET cc_start: 0.8126 (ttp) cc_final: 0.7770 (ttm) REVERT: F 130 ASP cc_start: 0.7679 (p0) cc_final: 0.7357 (t0) REVERT: F 156 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7077 (tpt) REVERT: F 210 HIS cc_start: 0.7646 (t-170) cc_final: 0.7268 (t70) REVERT: F 217 VAL cc_start: 0.5511 (OUTLIER) cc_final: 0.5172 (t) REVERT: F 267 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.5423 (mm-30) REVERT: F 270 MET cc_start: 0.7083 (ppp) cc_final: 0.6680 (ppp) REVERT: H 25 ARG cc_start: 0.7549 (mtp85) cc_final: 0.6884 (ttp-170) REVERT: H 129 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8061 (tppt) REVERT: H 465 MET cc_start: 0.9362 (ttm) cc_final: 0.8990 (ttm) REVERT: I 218 VAL cc_start: 0.7740 (OUTLIER) cc_final: 0.7367 (t) REVERT: I 338 GLN cc_start: 0.8607 (tp40) cc_final: 0.8366 (tp40) REVERT: J 284 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7963 (mtt90) REVERT: J 347 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: J 355 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7828 (mt) REVERT: J 463 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.7991 (mpp) REVERT: J 467 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8621 (tt) REVERT: K 39 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7488 (ttmm) REVERT: K 118 MET cc_start: 0.8783 (mtp) cc_final: 0.8384 (mtp) REVERT: K 146 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7799 (tmm) REVERT: K 404 LYS cc_start: 0.8107 (tttm) cc_final: 0.7730 (mtpp) REVERT: L 50 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7445 (tt) REVERT: L 147 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7855 (mt-10) REVERT: L 159 MET cc_start: 0.7794 (mmm) cc_final: 0.7414 (mmm) REVERT: L 179 ARG cc_start: 0.7480 (mmp-170) cc_final: 0.6787 (mmm160) REVERT: L 188 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.5841 (mtp-110) REVERT: L 231 TYR cc_start: 0.5212 (t80) cc_final: 0.4888 (t80) REVERT: L 246 ARG cc_start: 0.7435 (mmm160) cc_final: 0.6622 (tpp80) REVERT: L 267 GLU cc_start: 0.6902 (pp20) cc_final: 0.6420 (pp20) REVERT: L 271 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6665 (pm20) REVERT: M 207 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: N 44 ASP cc_start: 0.8741 (p0) cc_final: 0.8528 (p0) outliers start: 140 outliers final: 61 residues processed: 535 average time/residue: 0.6572 time to fit residues: 432.9578 Evaluate side-chains 482 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 395 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 248 ARG Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 152 CYS Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 467 LEU Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 484 THR Chi-restraints excluded: chain I residue 503 GLU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 284 ARG Chi-restraints excluded: chain J residue 347 GLU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain J residue 467 LEU Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 169 ILE Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 525 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 461 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 336 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 410 optimal weight: 7.9990 chunk 237 optimal weight: 0.5980 chunk 86 optimal weight: 8.9990 chunk 517 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 HIS C 98 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 HIS H 41 GLN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 199 ASN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.125953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095526 restraints weight = 89437.236| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.05 r_work: 0.3213 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.9591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.618 43527 Z= 0.192 Angle : 0.795 46.768 58716 Z= 0.337 Chirality : 0.044 0.292 6295 Planarity : 0.004 0.067 7554 Dihedral : 4.627 57.457 6537 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.27 % Allowed : 34.54 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.11), residues: 5323 helix: 1.26 (0.11), residues: 2484 sheet: -0.30 (0.21), residues: 606 loop : -0.90 (0.13), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 246 TYR 0.023 0.001 TYR E 160 PHE 0.027 0.001 PHE D 165 TRP 0.039 0.001 TRP C 294 HIS 0.014 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00403 (43477) covalent geometry : angle 0.71956 (58680) hydrogen bonds : bond 0.03500 ( 1983) hydrogen bonds : angle 4.94992 ( 5748) metal coordination : bond 0.01004 ( 16) metal coordination : angle 13.68108 ( 36) Misc. bond : bond 0.13333 ( 34) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 431 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8629 (mtt-85) cc_final: 0.8365 (mtt180) REVERT: A 286 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8231 (mtt) REVERT: A 312 ILE cc_start: 0.7956 (tt) cc_final: 0.7743 (mt) REVERT: A 372 MET cc_start: 0.8476 (mtt) cc_final: 0.8139 (mtp) REVERT: A 417 LYS cc_start: 0.8701 (mptt) cc_final: 0.8240 (mmmt) REVERT: B 21 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8139 (mtmt) REVERT: B 222 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7188 (mptp) REVERT: C 28 ARG cc_start: 0.6218 (mmm160) cc_final: 0.5793 (mmm160) REVERT: C 50 LYS cc_start: 0.7231 (mmmt) cc_final: 0.6762 (mmtt) REVERT: C 78 MET cc_start: 0.7303 (mmm) cc_final: 0.6921 (mpt) REVERT: C 125 PHE cc_start: 0.7703 (m-80) cc_final: 0.7367 (m-10) REVERT: C 152 SER cc_start: 0.8378 (m) cc_final: 0.8011 (t) REVERT: C 209 LYS cc_start: 0.6797 (OUTLIER) cc_final: 0.5616 (ttmp) REVERT: C 240 ILE cc_start: 0.5198 (OUTLIER) cc_final: 0.4778 (mp) REVERT: C 245 MET cc_start: 0.6600 (tmm) cc_final: 0.6126 (tmm) REVERT: C 248 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.5607 (ttp-170) REVERT: C 265 THR cc_start: 0.7525 (m) cc_final: 0.7162 (p) REVERT: C 367 TYR cc_start: 0.6929 (m-80) cc_final: 0.6331 (m-80) REVERT: C 391 MET cc_start: 0.4481 (tpp) cc_final: 0.3671 (mtm) REVERT: C 430 ILE cc_start: 0.8295 (tt) cc_final: 0.7923 (mt) REVERT: C 434 MET cc_start: 0.7624 (mtm) cc_final: 0.7222 (mtp) REVERT: D 118 MET cc_start: 0.7529 (mtm) cc_final: 0.7087 (mtm) REVERT: D 222 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7307 (mppt) REVERT: D 279 GLU cc_start: 0.7924 (mp0) cc_final: 0.7342 (mp0) REVERT: D 466 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8028 (pt) REVERT: D 523 ARG cc_start: 0.8603 (mmt180) cc_final: 0.8302 (mmt90) REVERT: E 52 SER cc_start: 0.7324 (p) cc_final: 0.6961 (t) REVERT: E 138 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8063 (ttt) REVERT: E 157 MET cc_start: 0.7341 (tpt) cc_final: 0.7089 (mmm) REVERT: E 208 MET cc_start: 0.6121 (OUTLIER) cc_final: 0.5678 (tpp) REVERT: E 246 ARG cc_start: 0.6813 (mmm160) cc_final: 0.6065 (mpt-90) REVERT: E 275 MET cc_start: 0.1591 (pp-130) cc_final: 0.0309 (mtm) REVERT: F 22 ASN cc_start: 0.7873 (m-40) cc_final: 0.7518 (m-40) REVERT: F 35 MET cc_start: 0.8135 (ttp) cc_final: 0.7707 (ttm) REVERT: F 210 HIS cc_start: 0.7662 (t-170) cc_final: 0.7173 (t-90) REVERT: F 239 ASP cc_start: 0.6867 (m-30) cc_final: 0.6247 (p0) REVERT: F 267 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.5304 (mm-30) REVERT: F 270 MET cc_start: 0.7032 (ppp) cc_final: 0.6618 (ppp) REVERT: G 71 GLU cc_start: 0.8855 (tt0) cc_final: 0.8154 (tt0) REVERT: G 86 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7809 (tt0) REVERT: H 15 GLU cc_start: 0.7623 (tt0) cc_final: 0.7422 (tt0) REVERT: H 22 GLU cc_start: 0.6803 (tm-30) cc_final: 0.6510 (tp30) REVERT: H 25 ARG cc_start: 0.7723 (mtp85) cc_final: 0.7044 (ttp-170) REVERT: H 129 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8146 (tppt) REVERT: H 162 ASP cc_start: 0.6865 (p0) cc_final: 0.6587 (p0) REVERT: H 465 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.8974 (ttm) REVERT: I 23 MET cc_start: 0.8586 (ttp) cc_final: 0.8321 (ttp) REVERT: I 146 MET cc_start: 0.9233 (ttp) cc_final: 0.8987 (ttp) REVERT: I 218 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7519 (t) REVERT: I 338 GLN cc_start: 0.8526 (tp40) cc_final: 0.8304 (tp40) REVERT: J 245 MET cc_start: 0.8244 (tmm) cc_final: 0.7952 (ppp) REVERT: J 284 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7953 (mtt90) REVERT: J 347 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7131 (tt0) REVERT: J 355 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7542 (mt) REVERT: J 463 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8008 (mpp) REVERT: K 118 MET cc_start: 0.8680 (mtp) cc_final: 0.8319 (mtp) REVERT: K 146 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7798 (tmm) REVERT: K 404 LYS cc_start: 0.8115 (tttm) cc_final: 0.7718 (mtpp) REVERT: L 147 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7875 (mt-10) REVERT: L 159 MET cc_start: 0.7835 (mmm) cc_final: 0.7432 (mmm) REVERT: L 188 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.5961 (mtp-110) REVERT: L 231 TYR cc_start: 0.5288 (t80) cc_final: 0.4990 (t80) REVERT: L 246 ARG cc_start: 0.7232 (mmm160) cc_final: 0.6439 (tpp80) REVERT: L 267 GLU cc_start: 0.6960 (pp20) cc_final: 0.6533 (pp20) REVERT: L 271 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6593 (pm20) REVERT: M 59 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.5384 (mpt) REVERT: M 207 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: M 270 MET cc_start: 0.7439 (tpt) cc_final: 0.7070 (mmm) REVERT: N 44 ASP cc_start: 0.8828 (p0) cc_final: 0.8607 (p0) outliers start: 102 outliers final: 52 residues processed: 508 average time/residue: 0.5183 time to fit residues: 327.0245 Evaluate side-chains 470 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 396 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 248 ARG Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 152 CYS Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 465 MET Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 484 THR Chi-restraints excluded: chain I residue 503 GLU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 284 ARG Chi-restraints excluded: chain J residue 347 GLU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain M residue 59 MET Chi-restraints excluded: chain M residue 121 ASP Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 169 ILE Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 314 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 426 optimal weight: 0.7980 chunk 354 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 448 optimal weight: 0.9990 chunk 310 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 HIS C 98 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 41 GLN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 ASN ** I 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 ASN ** M 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.094660 restraints weight = 85997.805| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.97 r_work: 0.3201 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.9787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.618 43527 Z= 0.198 Angle : 0.801 46.987 58716 Z= 0.340 Chirality : 0.044 0.290 6295 Planarity : 0.004 0.085 7554 Dihedral : 4.624 58.659 6537 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.11 % Allowed : 34.79 % Favored : 63.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.11), residues: 5323 helix: 1.24 (0.11), residues: 2509 sheet: -0.26 (0.21), residues: 604 loop : -0.89 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 246 TYR 0.021 0.001 TYR H 407 PHE 0.038 0.001 PHE M 109 TRP 0.039 0.001 TRP C 294 HIS 0.039 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00421 (43477) covalent geometry : angle 0.72540 (58680) hydrogen bonds : bond 0.03587 ( 1983) hydrogen bonds : angle 4.94120 ( 5748) metal coordination : bond 0.01086 ( 16) metal coordination : angle 13.73643 ( 36) Misc. bond : bond 0.13377 ( 34) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10646 Ramachandran restraints generated. 5323 Oldfield, 0 Emsley, 5323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 410 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8652 (mtt-85) cc_final: 0.8393 (mtt180) REVERT: A 286 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8288 (mtt) REVERT: A 326 GLU cc_start: 0.7156 (pp20) cc_final: 0.6622 (pt0) REVERT: A 372 MET cc_start: 0.8531 (mtt) cc_final: 0.8193 (mtp) REVERT: A 391 MET cc_start: 0.8445 (mmt) cc_final: 0.7495 (mmt) REVERT: A 417 LYS cc_start: 0.8756 (mptt) cc_final: 0.8285 (mmmt) REVERT: B 21 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8176 (mtmt) REVERT: B 131 MET cc_start: 0.8977 (tpp) cc_final: 0.8637 (ttp) REVERT: B 222 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7203 (mptp) REVERT: B 281 MET cc_start: 0.8248 (mmt) cc_final: 0.7875 (tpt) REVERT: B 488 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7484 (tp30) REVERT: C 28 ARG cc_start: 0.6111 (mmm160) cc_final: 0.5674 (mmm160) REVERT: C 50 LYS cc_start: 0.7239 (mmmt) cc_final: 0.6763 (mmtt) REVERT: C 78 MET cc_start: 0.7185 (mmm) cc_final: 0.6937 (mmm) REVERT: C 125 PHE cc_start: 0.7717 (m-80) cc_final: 0.7472 (m-10) REVERT: C 152 SER cc_start: 0.8423 (m) cc_final: 0.8051 (t) REVERT: C 209 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.5628 (ttmp) REVERT: C 240 ILE cc_start: 0.5160 (OUTLIER) cc_final: 0.4893 (mp) REVERT: C 245 MET cc_start: 0.6982 (tmm) cc_final: 0.6501 (tmm) REVERT: C 248 ARG cc_start: 0.5983 (OUTLIER) cc_final: 0.5651 (ttp-170) REVERT: C 265 THR cc_start: 0.7495 (m) cc_final: 0.7149 (p) REVERT: C 367 TYR cc_start: 0.7039 (m-80) cc_final: 0.6568 (m-80) REVERT: C 391 MET cc_start: 0.4516 (tpp) cc_final: 0.3522 (mtm) REVERT: C 430 ILE cc_start: 0.8306 (tt) cc_final: 0.7966 (mt) REVERT: C 434 MET cc_start: 0.7771 (mtm) cc_final: 0.7369 (mtp) REVERT: D 118 MET cc_start: 0.7588 (mtm) cc_final: 0.7008 (mtm) REVERT: D 222 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7303 (mppt) REVERT: D 279 GLU cc_start: 0.7926 (mp0) cc_final: 0.7287 (mm-30) REVERT: D 466 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8050 (pt) REVERT: D 523 ARG cc_start: 0.8636 (mmt180) cc_final: 0.8341 (mmt90) REVERT: E 52 SER cc_start: 0.7483 (p) cc_final: 0.7155 (t) REVERT: E 157 MET cc_start: 0.7334 (tpt) cc_final: 0.6987 (mmm) REVERT: E 208 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5786 (tpp) REVERT: E 246 ARG cc_start: 0.6729 (mmm160) cc_final: 0.5997 (mpt-90) REVERT: E 275 MET cc_start: 0.1702 (pp-130) cc_final: 0.0670 (mtm) REVERT: F 22 ASN cc_start: 0.7921 (m-40) cc_final: 0.7659 (m-40) REVERT: F 35 MET cc_start: 0.8149 (ttp) cc_final: 0.7721 (ttm) REVERT: F 210 HIS cc_start: 0.7718 (t-170) cc_final: 0.7260 (t-90) REVERT: F 270 MET cc_start: 0.7015 (ppp) cc_final: 0.6676 (ppp) REVERT: G 86 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7805 (tt0) REVERT: H 25 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7169 (ttp-170) REVERT: H 129 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8209 (tppt) REVERT: H 162 ASP cc_start: 0.6887 (p0) cc_final: 0.6634 (p0) REVERT: H 391 MET cc_start: 0.8296 (mmt) cc_final: 0.7981 (mmt) REVERT: H 465 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.8995 (ttm) REVERT: I 218 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7600 (t) REVERT: I 280 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: I 338 GLN cc_start: 0.8572 (tp40) cc_final: 0.8360 (tp40) REVERT: J 245 MET cc_start: 0.8201 (tmm) cc_final: 0.7863 (ppp) REVERT: J 284 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7966 (mtt90) REVERT: J 347 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: J 463 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.7977 (mpp) REVERT: K 39 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7565 (ttmm) REVERT: K 118 MET cc_start: 0.8695 (mtp) cc_final: 0.8356 (mtp) REVERT: K 146 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7849 (tmm) REVERT: K 404 LYS cc_start: 0.8140 (tttm) cc_final: 0.7741 (mtpp) REVERT: L 107 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8271 (mp) REVERT: L 147 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7893 (mt-10) REVERT: L 175 SER cc_start: 0.8837 (t) cc_final: 0.8425 (p) REVERT: L 188 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.5932 (mtp-110) REVERT: L 231 TYR cc_start: 0.5318 (t80) cc_final: 0.5002 (t80) REVERT: L 246 ARG cc_start: 0.7336 (mmm160) cc_final: 0.6505 (tpp80) REVERT: L 267 GLU cc_start: 0.6840 (pp20) cc_final: 0.6389 (pp20) REVERT: L 271 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6479 (pm20) REVERT: M 207 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: M 208 MET cc_start: 0.7699 (tmm) cc_final: 0.7498 (tmm) REVERT: M 237 GLN cc_start: 0.7460 (tp40) cc_final: 0.7103 (tp40) REVERT: M 270 MET cc_start: 0.7611 (tpt) cc_final: 0.7326 (mmm) REVERT: N 44 ASP cc_start: 0.8878 (p0) cc_final: 0.8660 (p0) outliers start: 95 outliers final: 52 residues processed: 484 average time/residue: 0.4844 time to fit residues: 289.8168 Evaluate side-chains 468 residues out of total 4539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 394 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 248 ARG Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 152 CYS Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 427 GLU Chi-restraints excluded: chain H residue 465 MET Chi-restraints excluded: chain H residue 467 LEU Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 484 THR Chi-restraints excluded: chain I residue 503 GLU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 284 ARG Chi-restraints excluded: chain J residue 347 GLU Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain M residue 5 GLN Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 169 ILE Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 HIS Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 528 optimal weight: 6.9990 chunk 518 optimal weight: 4.9990 chunk 441 optimal weight: 0.2980 chunk 165 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 344 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 504 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 362 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 HIS C 98 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 41 GLN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.124840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094182 restraints weight = 93474.928| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.13 r_work: 0.3186 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 1.0148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.634 43527 Z= 0.195 Angle : 0.799 46.974 58716 Z= 0.338 Chirality : 0.045 0.300 6295 Planarity : 0.004 0.065 7554 Dihedral : 4.592 58.280 6535 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.18 % Allowed : 34.68 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.11), residues: 5323 helix: 1.27 (0.11), residues: 2482 sheet: -0.24 (0.20), residues: 607 loop : -0.87 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 246 TYR 0.022 0.001 TYR H 407 PHE 0.028 0.001 PHE F 109 TRP 0.040 0.001 TRP C 294 HIS 0.023 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00413 (43477) covalent geometry : angle 0.72432 (58680) hydrogen bonds : bond 0.03511 ( 1983) hydrogen bonds : angle 4.94107 ( 5748) metal coordination : bond 0.01064 ( 16) metal coordination : angle 13.65470 ( 36) Misc. bond : bond 0.13560 ( 34) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20025.66 seconds wall clock time: 339 minutes 57.21 seconds (20397.21 seconds total)