Starting phenix.real_space_refine on Tue Jul 7 01:59:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qby_18324/07_2026/8qby_18324.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qby_18324/07_2026/8qby_18324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qby_18324/07_2026/8qby_18324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qby_18324/07_2026/8qby_18324.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qby_18324/07_2026/8qby_18324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qby_18324/07_2026/8qby_18324.map" } resolution = 2.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Ca 4 9.91 5 Fe 28 7.16 5 Zn 1 6.06 5 P 36 5.49 5 S 312 5.16 5 Na 1 4.78 5 C 26922 2.51 5 N 6789 2.21 5 O 8449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42542 Number of models: 1 Model: "" Number of chains: 50 Chain: "K" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Link IDs: {'TRANS': 100} Chain: "G" Number of atoms: 5073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5073 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 36, 'TRANS': 629} Chain: "t" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1641 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 203} Chain: "I" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1294 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 147} Chain: "E" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1814 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 218} Chain: "N" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3549 Classifications: {'peptide': 479} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 466} Chain: "H" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2730 Classifications: {'peptide': 342} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 325} Chain: "F" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3234 Classifications: {'peptide': 421} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 402} Chain: "D" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3268 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 387} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1025 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "A" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 968 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1498 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "R" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 470 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "Q" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 848 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 8, 'TRANS': 94} Chain: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1565 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain: "B" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1161 Classifications: {'peptide': 148} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 137} Chain: "L" Number of atoms: 5198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5198 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 25, 'TRANS': 633} Chain breaks: 1 Chain: "M" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3913 Classifications: {'peptide': 503} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 482} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "I" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 104 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'3PH': 1, 'SF4': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 217 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'3PE': 3, '3PH': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "H" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 245 Unusual residues: {'3PE': 2, '3PH': 3, 'CDL': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 101 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "q" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "J" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 119 Unusual residues: {'3PH': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'SF4': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 242 Unusual residues: {'3PE': 1, '3PH': 4} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 55 Chain: "M" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 305 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'3PE': 3, '3PH': 4, 'CDL': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 140 Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "G" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 220 Classifications: {'water': 220} Link IDs: {None: 219} Chain: "t" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "I" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "D" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 151 Classifications: {'water': 151} Link IDs: {None: 150} Chain: "q" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "Q" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "C" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "L" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "M" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1652 SG CYS G 119 83.457 75.823 213.192 1.00 26.06 S ATOM 1591 SG CYS G 110 80.240 70.028 212.538 1.00 19.34 S ATOM 1612 SG CYS G 113 77.680 75.235 215.471 1.00 25.73 S ATOM 1987 SG CYS G 161 88.278 81.895 221.735 1.00 28.38 S ATOM 1967 SG CYS G 158 84.429 77.892 225.564 1.00 26.39 S ATOM 2011 SG CYS G 164 84.289 84.292 225.865 1.00 31.82 S ATOM 2345 SG CYS G 208 82.422 81.313 220.255 1.00 22.93 S ATOM 1155 SG CYS G 51 100.511 80.345 217.691 1.00 33.91 S ATOM 1253 SG CYS G 66 99.856 83.046 219.857 1.00 30.26 S ATOM 1043 SG CYS G 37 95.527 81.806 221.406 1.00 23.65 S ATOM 1130 SG CYS G 48 95.285 78.477 219.168 1.00 27.68 S ATOM 8051 SG CYS I 74 68.658 69.364 194.327 1.00 23.99 S ATOM 8280 SG CYS I 103 64.669 64.660 192.338 1.00 20.69 S ATOM 8306 SG CYS I 106 71.185 63.642 193.084 1.00 31.59 S ATOM 8327 SG CYS I 109 67.669 63.993 198.061 1.00 28.09 S ATOM 8356 SG CYS I 113 68.749 64.040 206.495 1.00 29.70 S ATOM 7982 SG CYS I 64 64.675 69.057 207.819 1.00 23.48 S ATOM 8024 SG CYS I 70 67.894 68.904 202.282 1.00 22.28 S ATOM 8001 SG CYS I 67 71.476 69.361 207.349 1.00 29.68 S ATOM 9553 SG CYS E 96 97.725 62.051 249.723 1.00 33.11 S ATOM 9584 SG CYS E 101 99.429 59.547 251.726 1.00 42.40 S ATOM 9863 SG CYS E 137 102.027 64.718 248.421 1.00 41.15 S ATOM 9886 SG CYS E 141 104.294 62.779 249.787 1.00 43.85 S ATOM 19521 SG CYS F 349 98.650 74.473 227.499 1.00 19.30 S ATOM 19541 SG CYS F 352 97.867 70.290 231.289 1.00 29.63 S ATOM 19863 SG CYS F 392 102.473 74.413 233.017 1.00 21.26 S ATOM 19502 SG CYS F 346 96.543 76.543 233.394 1.00 29.70 S ATOM 26978 SG CYS R 18 68.636 61.183 222.148 1.00 24.34 S ATOM 27182 SG CYS R 44 68.926 64.656 220.864 1.00 16.75 S ATOM 27204 SG CYS R 47 66.057 62.487 220.322 1.00 26.07 S ATOM 29958 SG CYS B 54 69.114 61.222 179.417 1.00 20.23 S ATOM 30461 SG CYS B 119 65.928 66.579 181.002 1.00 22.63 S ATOM 30691 SG CYS B 149 67.095 62.825 185.269 1.00 29.97 S ATOM 29964 SG CYS B 55 62.856 60.940 180.444 1.00 28.95 S Time building chain proxies: 8.78, per 1000 atoms: 0.21 Number of scatterers: 42542 At special positions: 0 Unit cell: (143.04, 153.47, 280.865, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 Ca 4 19.99 S 312 16.00 P 36 15.00 Na 1 11.00 O 8449 8.00 N 6789 7.00 C 26922 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 96 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 101 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 141 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 137 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 48 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 37 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 51 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 66 " pdb=" SF4 B 402 " pdb="FE1 SF4 B 402 " - pdb=" SG CYS B 54 " pdb="FE2 SF4 B 402 " - pdb=" SG CYS B 119 " pdb="FE3 SF4 B 402 " - pdb=" SG CYS B 149 " pdb="FE4 SF4 B 402 " - pdb=" SG CYS B 55 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 352 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 346 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 392 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 349 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 106 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 113 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 110 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 119 " pdb=" SF4 G 802 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 164 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 208 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 158 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 161 " pdb=" SF4 I 201 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 74 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 103 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 106 " pdb=" SF4 I 202 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 113 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 64 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 67 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 301 " pdb="ZN ZN R 301 " - pdb=" NE2 HIS R 28 " pdb="ZN ZN R 301 " - pdb=" SG CYS R 44 " pdb="ZN ZN R 301 " - pdb=" SG CYS R 47 " pdb="ZN ZN R 301 " - pdb=" SG CYS R 18 " Number of angles added : 3 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9392 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 35 sheets defined 61.5% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'K' and resid 3 through 25 removed outlier: 3.793A pdb=" N TYR K 7 " --> pdb=" O GLY K 3 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE K 23 " --> pdb=" O ILE K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 55 removed outlier: 3.747A pdb=" N ILE K 32 " --> pdb=" O ASN K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 89 Processing helix chain 'K' and resid 92 through 96 Processing helix chain 'G' and resid 21 through 29 Processing helix chain 'G' and resid 69 through 73 Processing helix chain 'G' and resid 76 through 80 Processing helix chain 'G' and resid 88 through 104 Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 155 through 158 Processing helix chain 'G' and resid 162 through 171 Processing helix chain 'G' and resid 182 through 186 Processing helix chain 'G' and resid 192 through 194 No H-bonds generated for 'chain 'G' and resid 192 through 194' Processing helix chain 'G' and resid 202 through 208 removed outlier: 4.181A pdb=" N ASP G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 227 Processing helix chain 'G' and resid 269 through 275 Processing helix chain 'G' and resid 276 through 279 Processing helix chain 'G' and resid 299 through 312 Processing helix chain 'G' and resid 325 through 339 Processing helix chain 'G' and resid 356 through 361 Processing helix chain 'G' and resid 367 through 372 removed outlier: 4.488A pdb=" N ASP G 371 " --> pdb=" O GLU G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 386 Processing helix chain 'G' and resid 386 through 399 Processing helix chain 'G' and resid 422 through 432 removed outlier: 3.501A pdb=" N LEU G 426 " --> pdb=" O ASP G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 440 Processing helix chain 'G' and resid 456 through 472 Processing helix chain 'G' and resid 483 through 490 Processing helix chain 'G' and resid 496 through 503 removed outlier: 3.585A pdb=" N ALA G 500 " --> pdb=" O GLY G 496 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 538 Processing helix chain 'G' and resid 576 through 588 removed outlier: 3.510A pdb=" N GLU G 587 " --> pdb=" O ALA G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 596 through 608 Processing helix chain 'G' and resid 609 through 613 Processing helix chain 'G' and resid 646 through 651 Processing helix chain 'G' and resid 652 through 667 Processing helix chain 't' and resid 3 through 16 Processing helix chain 't' and resid 17 through 20 removed outlier: 3.647A pdb=" N GLU t 20 " --> pdb=" O ARG t 17 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 17 through 20' Processing helix chain 't' and resid 23 through 31 Processing helix chain 't' and resid 34 through 39 removed outlier: 3.588A pdb=" N VAL t 39 " --> pdb=" O GLU t 36 " (cutoff:3.500A) Processing helix chain 't' and resid 40 through 47 removed outlier: 5.122A pdb=" N ASP t 45 " --> pdb=" O SER t 42 " (cutoff:3.500A) Processing helix chain 't' and resid 63 through 75 Processing helix chain 't' and resid 90 through 98 removed outlier: 3.519A pdb=" N ARG t 98 " --> pdb=" O ALA t 94 " (cutoff:3.500A) Processing helix chain 't' and resid 109 through 123 Processing helix chain 't' and resid 134 through 138 Processing helix chain 't' and resid 139 through 143 removed outlier: 3.507A pdb=" N GLN t 142 " --> pdb=" O CYS t 139 " (cutoff:3.500A) Processing helix chain 't' and resid 158 through 164 removed outlier: 3.832A pdb=" N GLN t 164 " --> pdb=" O ALA t 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 13 Processing helix chain 'I' and resid 14 through 29 Processing helix chain 'I' and resid 68 through 74 Processing helix chain 'I' and resid 107 through 113 Processing helix chain 'I' and resid 130 through 133 Processing helix chain 'I' and resid 137 through 160 removed outlier: 5.884A pdb=" N ALA I 150 " --> pdb=" O GLU I 146 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU I 151 " --> pdb=" O ARG I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 163 No H-bonds generated for 'chain 'I' and resid 161 through 163' Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.719A pdb=" N THR E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 37 Processing helix chain 'E' and resid 38 through 51 Processing helix chain 'E' and resid 54 through 66 Processing helix chain 'E' and resid 68 through 79 Processing helix chain 'E' and resid 98 through 103 Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 158 through 171 Processing helix chain 'E' and resid 195 through 199 removed outlier: 3.561A pdb=" N LEU E 198 " --> pdb=" O LEU E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 215 Processing helix chain 'E' and resid 230 through 235 Processing helix chain 'N' and resid 2 through 9 Processing helix chain 'N' and resid 9 through 29 Processing helix chain 'N' and resid 30 through 33 Processing helix chain 'N' and resid 34 through 55 Processing helix chain 'N' and resid 71 through 99 removed outlier: 4.969A pdb=" N ASP N 94 " --> pdb=" O ALA N 90 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N TYR N 95 " --> pdb=" O MET N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 122 removed outlier: 3.635A pdb=" N SER N 122 " --> pdb=" O MET N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 145 Processing helix chain 'N' and resid 150 through 183 Processing helix chain 'N' and resid 186 through 194 removed outlier: 3.627A pdb=" N SER N 192 " --> pdb=" O GLU N 188 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR N 193 " --> pdb=" O GLY N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 199 removed outlier: 4.157A pdb=" N LEU N 199 " --> pdb=" O ALA N 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 218 removed outlier: 4.151A pdb=" N LYS N 217 " --> pdb=" O GLY N 213 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL N 218 " --> pdb=" O LEU N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 234 removed outlier: 4.419A pdb=" N ASP N 229 " --> pdb=" O MET N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 235 through 261 Proline residue: N 246 - end of helix Processing helix chain 'N' and resid 265 through 289 removed outlier: 3.941A pdb=" N GLN N 271 " --> pdb=" O GLY N 267 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE N 272 " --> pdb=" O ASP N 268 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE N 289 " --> pdb=" O SER N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 315 removed outlier: 3.554A pdb=" N TYR N 300 " --> pdb=" O ARG N 296 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY N 312 " --> pdb=" O PHE N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 317 through 344 removed outlier: 3.550A pdb=" N SER N 344 " --> pdb=" O ALA N 340 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 359 Processing helix chain 'N' and resid 360 through 364 Processing helix chain 'N' and resid 365 through 381 Processing helix chain 'N' and resid 385 through 401 removed outlier: 3.606A pdb=" N PHE N 389 " --> pdb=" O THR N 385 " (cutoff:3.500A) Processing helix chain 'N' and resid 403 through 431 removed outlier: 3.712A pdb=" N PHE N 419 " --> pdb=" O VAL N 415 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR N 420 " --> pdb=" O ILE N 416 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR N 421 " --> pdb=" O GLY N 417 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE N 424 " --> pdb=" O TYR N 420 " (cutoff:3.500A) Processing helix chain 'N' and resid 442 through 462 Proline residue: N 452 - end of helix removed outlier: 3.847A pdb=" N LEU N 457 " --> pdb=" O ALA N 453 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA N 460 " --> pdb=" O MET N 456 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE N 461 " --> pdb=" O LEU N 457 " (cutoff:3.500A) Processing helix chain 'N' and resid 465 through 479 removed outlier: 3.553A pdb=" N LEU N 477 " --> pdb=" O ALA N 473 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 6 removed outlier: 3.607A pdb=" N ALA H 6 " --> pdb=" O ALA H 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 2 through 6' Processing helix chain 'H' and resid 7 through 45 removed outlier: 3.850A pdb=" N PHE H 32 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR H 35 " --> pdb=" O ILE H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 58 Processing helix chain 'H' and resid 59 through 70 Processing helix chain 'H' and resid 80 through 98 Proline residue: H 88 - end of helix removed outlier: 3.654A pdb=" N ALA H 95 " --> pdb=" O SER H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 102 Processing helix chain 'H' and resid 115 through 139 removed outlier: 3.632A pdb=" N VAL H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR H 129 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY H 130 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL H 131 " --> pdb=" O GLU H 127 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN H 139 " --> pdb=" O GLY H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 159 removed outlier: 4.087A pdb=" N VAL H 159 " --> pdb=" O ILE H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 173 removed outlier: 3.693A pdb=" N ILE H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY H 167 " --> pdb=" O LEU H 163 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE H 168 " --> pdb=" O ILE H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 Processing helix chain 'H' and resid 188 through 193 Processing helix chain 'H' and resid 198 through 213 removed outlier: 3.644A pdb=" N VAL H 203 " --> pdb=" O LEU H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 233 Processing helix chain 'H' and resid 236 through 263 removed outlier: 3.502A pdb=" N PHE H 243 " --> pdb=" O PRO H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 298 removed outlier: 3.787A pdb=" N MET H 280 " --> pdb=" O GLY H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 313 Processing helix chain 'H' and resid 313 through 331 Processing helix chain 'F' and resid 3 through 7 Processing helix chain 'F' and resid 19 through 26 Processing helix chain 'F' and resid 31 through 37 Processing helix chain 'F' and resid 39 through 51 removed outlier: 3.713A pdb=" N GLY F 51 " --> pdb=" O MET F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 67 Processing helix chain 'F' and resid 92 through 101 removed outlier: 4.071A pdb=" N GLU F 96 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE F 97 " --> pdb=" O LYS F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 116 removed outlier: 3.952A pdb=" N LEU F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 146 Processing helix chain 'F' and resid 152 through 156 Processing helix chain 'F' and resid 170 through 174 Processing helix chain 'F' and resid 175 through 184 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 212 through 217 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 225 through 232 removed outlier: 3.951A pdb=" N PHE F 232 " --> pdb=" O TRP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 272 removed outlier: 3.684A pdb=" N GLY F 272 " --> pdb=" O GLU F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 279 No H-bonds generated for 'chain 'F' and resid 277 through 279' Processing helix chain 'F' and resid 297 through 301 removed outlier: 3.979A pdb=" N ASN F 301 " --> pdb=" O GLN F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 312 Processing helix chain 'F' and resid 329 through 345 Processing helix chain 'F' and resid 349 through 369 removed outlier: 4.684A pdb=" N GLY F 357 " --> pdb=" O ARG F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 387 removed outlier: 4.301A pdb=" N ASP F 377 " --> pdb=" O VAL F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 409 Proline residue: F 401 - end of helix Processing helix chain 'F' and resid 409 through 421 Processing helix chain 'D' and resid 16 through 21 removed outlier: 3.621A pdb=" N GLU D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 71 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 85 removed outlier: 3.501A pdb=" N LEU D 80 " --> pdb=" O TYR D 76 " (cutoff:3.500A) Proline residue: D 81 - end of helix removed outlier: 3.848A pdb=" N ASP D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG D 85 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 107 removed outlier: 3.895A pdb=" N GLN D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA D 97 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 141 Processing helix chain 'D' and resid 144 through 166 removed outlier: 4.436A pdb=" N LEU D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 153 " --> pdb=" O TRP D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 210 removed outlier: 3.571A pdb=" N ARG D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Proline residue: D 199 - end of helix Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 237 through 242 Processing helix chain 'D' and resid 248 through 253 Processing helix chain 'D' and resid 257 through 261 Processing helix chain 'D' and resid 272 through 301 Processing helix chain 'D' and resid 316 through 321 Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 375 through 383 removed outlier: 3.942A pdb=" N ALA D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER D 383 " --> pdb=" O ALA D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 Processing helix chain 'D' and resid 394 through 404 removed outlier: 4.493A pdb=" N ALA D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP D 404 " --> pdb=" O ILE D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 412 Processing helix chain 'q' and resid 2 through 9 Processing helix chain 'q' and resid 15 through 26 Processing helix chain 'q' and resid 56 through 60 Processing helix chain 'q' and resid 61 through 69 removed outlier: 4.354A pdb=" N GLY q 66 " --> pdb=" O PRO q 62 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP q 67 " --> pdb=" O GLU q 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 8 through 33 removed outlier: 4.015A pdb=" N ALA A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.514A pdb=" N ILE A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 86 removed outlier: 4.002A pdb=" N TRP A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 91 through 116 removed outlier: 3.637A pdb=" N MET A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 23 removed outlier: 3.572A pdb=" N VAL J 21 " --> pdb=" O GLY J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 47 Processing helix chain 'J' and resid 49 through 74 removed outlier: 3.727A pdb=" N GLY J 62 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 110 removed outlier: 3.848A pdb=" N GLY J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 140 removed outlier: 3.611A pdb=" N VAL J 138 " --> pdb=" O GLY J 134 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR J 140 " --> pdb=" O GLY J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 166 Processing helix chain 'J' and resid 176 through 183 Processing helix chain 'J' and resid 184 through 188 Processing helix chain 'Q' and resid 17 through 21 removed outlier: 4.029A pdb=" N ARG Q 21 " --> pdb=" O ALA Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 50 Processing helix chain 'Q' and resid 57 through 68 Processing helix chain 'Q' and resid 87 through 94 Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 43 through 54 Processing helix chain 'C' and resid 113 through 126 removed outlier: 4.398A pdb=" N TYR C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 44 Processing helix chain 'B' and resid 54 through 64 removed outlier: 3.973A pdb=" N GLU B 58 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 63 " --> pdb=" O MET B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 96 through 106 Processing helix chain 'B' and resid 117 through 123 Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 152 through 171 Processing helix chain 'L' and resid 2 through 49 Proline residue: L 9 - end of helix removed outlier: 6.710A pdb=" N ARG L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU L 25 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N LYS L 26 " --> pdb=" O ALA L 22 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA L 27 " --> pdb=" O ILE L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 102 removed outlier: 4.025A pdb=" N GLY L 100 " --> pdb=" O MET L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 134 Processing helix chain 'L' and resid 137 through 157 Processing helix chain 'L' and resid 162 through 195 removed outlier: 3.877A pdb=" N GLY L 182 " --> pdb=" O VAL L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 205 removed outlier: 3.558A pdb=" N GLN L 205 " --> pdb=" O GLU L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 211 removed outlier: 3.675A pdb=" N GLN L 211 " --> pdb=" O PRO L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 239 removed outlier: 3.750A pdb=" N GLY L 234 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 251 removed outlier: 4.075A pdb=" N ASP L 250 " --> pdb=" O THR L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 254 No H-bonds generated for 'chain 'L' and resid 252 through 254' Processing helix chain 'L' and resid 255 through 265 Processing helix chain 'L' and resid 268 through 278 removed outlier: 4.348A pdb=" N VAL L 272 " --> pdb=" O VAL L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 283 Processing helix chain 'L' and resid 285 through 310 removed outlier: 3.562A pdb=" N LEU L 308 " --> pdb=" O ALA L 304 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL L 309 " --> pdb=" O THR L 305 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN L 310 " --> pdb=" O VAL L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 334 Processing helix chain 'L' and resid 336 through 365 removed outlier: 3.718A pdb=" N PHE L 349 " --> pdb=" O LEU L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 370 through 374 Processing helix chain 'L' and resid 381 through 397 Processing helix chain 'L' and resid 407 through 424 removed outlier: 3.689A pdb=" N LEU L 411 " --> pdb=" O PHE L 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 424 through 451 Processing helix chain 'L' and resid 457 through 464 removed outlier: 3.648A pdb=" N HIS L 461 " --> pdb=" O ASP L 457 " (cutoff:3.500A) Processing helix chain 'L' and resid 468 through 480 Proline residue: L 474 - end of helix Processing helix chain 'L' and resid 484 through 494 removed outlier: 5.176A pdb=" N GLY L 491 " --> pdb=" O MET L 487 " (cutoff:3.500A) Proline residue: L 492 - end of helix Processing helix chain 'L' and resid 496 through 504 Processing helix chain 'L' and resid 566 through 573 Processing helix chain 'L' and resid 575 through 598 Proline residue: L 582 - end of helix Processing helix chain 'L' and resid 602 through 611 removed outlier: 3.715A pdb=" N ALA L 608 " --> pdb=" O PRO L 604 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA L 609 " --> pdb=" O ARG L 605 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 620 removed outlier: 3.610A pdb=" N LEU L 618 " --> pdb=" O LEU L 614 " (cutoff:3.500A) Processing helix chain 'L' and resid 623 through 632 Processing helix chain 'L' and resid 632 through 646 Processing helix chain 'L' and resid 651 through 661 Processing helix chain 'L' and resid 662 through 675 Processing helix chain 'L' and resid 678 through 701 Processing helix chain 'M' and resid 3 through 23 Proline residue: M 12 - end of helix Processing helix chain 'M' and resid 27 through 56 removed outlier: 3.632A pdb=" N PHE M 51 " --> pdb=" O VAL M 47 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL M 52 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 103 Proline residue: M 97 - end of helix removed outlier: 3.522A pdb=" N THR M 103 " --> pdb=" O THR M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 130 removed outlier: 3.932A pdb=" N PHE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 143 removed outlier: 3.527A pdb=" N GLY M 143 " --> pdb=" O PHE M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 155 removed outlier: 3.504A pdb=" N MET M 147 " --> pdb=" O GLY M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 189 removed outlier: 3.984A pdb=" N LEU M 176 " --> pdb=" O LEU M 172 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET M 177 " --> pdb=" O GLY M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 199 removed outlier: 3.794A pdb=" N THR M 198 " --> pdb=" O PRO M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 233 Processing helix chain 'M' and resid 241 through 249 removed outlier: 3.857A pdb=" N VAL M 247 " --> pdb=" O PRO M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 260 Processing helix chain 'M' and resid 262 through 272 removed outlier: 3.913A pdb=" N GLY M 266 " --> pdb=" O LEU M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 272 through 277 Processing helix chain 'M' and resid 277 through 305 Proline residue: M 286 - end of helix Processing helix chain 'M' and resid 308 through 331 removed outlier: 3.720A pdb=" N VAL M 318 " --> pdb=" O ALA M 314 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR M 323 " --> pdb=" O ALA M 319 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL M 324 " --> pdb=" O HIS M 320 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 365 removed outlier: 3.644A pdb=" N PHE M 348 " --> pdb=" O LEU M 344 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE M 360 " --> pdb=" O CYS M 356 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG M 363 " --> pdb=" O VAL M 359 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 372 Processing helix chain 'M' and resid 374 through 378 Processing helix chain 'M' and resid 379 through 394 Processing helix chain 'M' and resid 399 through 414 removed outlier: 4.255A pdb=" N VAL M 403 " --> pdb=" O THR M 399 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY M 404 " --> pdb=" O SER M 400 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU M 405 " --> pdb=" O GLY M 401 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 425 Processing helix chain 'M' and resid 425 through 443 removed outlier: 3.525A pdb=" N ALA M 431 " --> pdb=" O VAL M 427 " (cutoff:3.500A) Processing helix chain 'M' and resid 458 through 478 removed outlier: 3.515A pdb=" N PHE M 465 " --> pdb=" O GLU M 461 " (cutoff:3.500A) Proline residue: M 467 - end of helix Processing helix chain 'M' and resid 479 through 500 removed outlier: 4.556A pdb=" N VAL M 485 " --> pdb=" O LEU M 481 " (cutoff:3.500A) Proline residue: M 488 - end of helix Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 16 removed outlier: 3.985A pdb=" N SER G 82 " --> pdb=" O LYS G 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 151 through 153 Processing sheet with id=AA3, first strand: chain 'G' and resid 177 through 180 Processing sheet with id=AA4, first strand: chain 'G' and resid 228 through 233 removed outlier: 7.908A pdb=" N SER G 242 " --> pdb=" O PRO G 257 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG G 244 " --> pdb=" O ILE G 255 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE G 255 " --> pdb=" O ARG G 244 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASP G 246 " --> pdb=" O MET G 253 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU G 251 " --> pdb=" O LYS G 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 294 through 297 removed outlier: 6.535A pdb=" N ALA G 317 " --> pdb=" O TYR G 509 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU G 511 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU G 319 " --> pdb=" O LEU G 511 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 417 through 420 removed outlier: 6.965A pdb=" N VAL G 403 " --> pdb=" O ALA G 417 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL G 419 " --> pdb=" O VAL G 403 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU G 405 " --> pdb=" O VAL G 419 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET G 374 " --> pdb=" O ILE G 444 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE G 446 " --> pdb=" O MET G 374 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN G 376 " --> pdb=" O ILE G 446 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLY G 448 " --> pdb=" O GLN G 376 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE G 378 " --> pdb=" O GLY G 448 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER G 443 " --> pdb=" O GLY G 474 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU G 476 " --> pdb=" O SER G 443 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL G 445 " --> pdb=" O LEU G 476 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU G 478 " --> pdb=" O VAL G 445 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL G 447 " --> pdb=" O LEU G 478 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 552 through 555 Processing sheet with id=AA8, first strand: chain 't' and resid 53 through 56 removed outlier: 6.853A pdb=" N ARG t 59 " --> pdb=" O LEU t 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 't' and resid 128 through 132 removed outlier: 6.580A pdb=" N VAL t 103 " --> pdb=" O ALA t 129 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL t 131 " --> pdb=" O VAL t 103 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ALA t 105 " --> pdb=" O VAL t 131 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL t 82 " --> pdb=" O VAL t 104 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL t 106 " --> pdb=" O VAL t 82 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP t 84 " --> pdb=" O VAL t 106 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU t 81 " --> pdb=" O ALA t 147 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU t 149 " --> pdb=" O LEU t 81 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU t 83 " --> pdb=" O LEU t 149 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLU t 151 " --> pdb=" O LEU t 83 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL t 85 " --> pdb=" O GLU t 151 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ALA t 153 " --> pdb=" O VAL t 85 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR t 145 " --> pdb=" O ARG t 166 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLY t 168 " --> pdb=" O TYR t 145 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA t 147 " --> pdb=" O GLY t 168 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG t 170 " --> pdb=" O ALA t 147 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU t 149 " --> pdb=" O ARG t 170 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL t 172 " --> pdb=" O LEU t 149 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLU t 151 " --> pdb=" O VAL t 172 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU t 174 " --> pdb=" O GLU t 151 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA t 153 " --> pdb=" O LEU t 174 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG t 176 " --> pdb=" O ALA t 153 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY t 169 " --> pdb=" O LYS t 188 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY t 181 " --> pdb=" O ASN t 200 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN t 200 " --> pdb=" O GLY t 181 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL t 183 " --> pdb=" O ALA t 198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 52 through 54 Processing sheet with id=AB2, first strand: chain 'I' and resid 79 through 85 removed outlier: 6.505A pdb=" N THR I 80 " --> pdb=" O TYR I 96 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR I 96 " --> pdb=" O THR I 80 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASP I 82 " --> pdb=" O THR I 94 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG I 92 " --> pdb=" O GLU I 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 130 through 135 removed outlier: 7.041A pdb=" N PHE E 153 " --> pdb=" O GLY E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 61 through 63 Processing sheet with id=AB5, first strand: chain 'N' and resid 350 through 351 Processing sheet with id=AB6, first strand: chain 'F' and resid 161 through 166 removed outlier: 6.467A pdb=" N ALA F 121 " --> pdb=" O TYR F 163 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N HIS F 165 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE F 123 " --> pdb=" O HIS F 165 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU F 80 " --> pdb=" O ALA F 120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 253 through 258 removed outlier: 8.183A pdb=" N MET F 321 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY F 244 " --> pdb=" O MET F 321 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL F 323 " --> pdb=" O GLY F 244 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR F 246 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ASP F 325 " --> pdb=" O THR F 246 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 261 through 262 removed outlier: 3.941A pdb=" N ILE F 261 " --> pdb=" O MET F 304 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 27 through 31 removed outlier: 4.414A pdb=" N PHE D 27 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP D 49 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N VAL D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 174 through 175 Processing sheet with id=AC2, first strand: chain 'D' and resid 265 through 268 Processing sheet with id=AC3, first strand: chain 'D' and resid 343 through 351 Processing sheet with id=AC4, first strand: chain 'q' and resid 27 through 31 removed outlier: 6.671A pdb=" N TYR q 38 " --> pdb=" O VAL q 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 8 through 11 removed outlier: 6.319A pdb=" N GLN R 9 " --> pdb=" O VAL R 52 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 15 through 18 Processing sheet with id=AC7, first strand: chain 'Q' and resid 52 through 55 Processing sheet with id=AC8, first strand: chain 'Q' and resid 34 through 35 Processing sheet with id=AC9, first strand: chain 'C' and resid 25 through 31 removed outlier: 6.775A pdb=" N ASN C 38 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR C 28 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR C 36 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL C 30 " --> pdb=" O GLU C 34 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU C 35 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LYS C 95 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL C 37 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N GLN C 97 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA C 39 " --> pdb=" O GLN C 97 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU C 84 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU C 62 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.433A pdb=" N VAL C 104 " --> pdb=" O SER C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 159 through 164 Processing sheet with id=AD3, first strand: chain 'B' and resid 47 through 48 removed outlier: 5.898A pdb=" N TRP B 47 " --> pdb=" O ARG B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.445A pdb=" N MET B 86 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N MET B 116 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL B 88 " --> pdb=" O MET B 116 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 55 through 65 removed outlier: 6.862A pdb=" N TRP L 72 " --> pdb=" O VAL L 59 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASP L 61 " --> pdb=" O ALA L 70 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA L 70 " --> pdb=" O ASP L 61 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL L 63 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE L 68 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 213 through 216 removed outlier: 3.793A pdb=" N ARG L 219 " --> pdb=" O PHE L 216 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 64 through 70 removed outlier: 4.237A pdb=" N VAL M 66 " --> pdb=" O MET M 79 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET M 79 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP M 68 " --> pdb=" O TYR M 77 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR M 77 " --> pdb=" O ASP M 68 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 206 through 208 removed outlier: 3.891A pdb=" N PHE M 206 " --> pdb=" O VAL M 213 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET M 211 " --> pdb=" O LEU M 208 " (cutoff:3.500A) 2277 hydrogen bonds defined for protein. 6465 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: 10.18 Time building geometry restraints manager: 5.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 17242 1.40 - 1.63: 24580 1.63 - 1.85: 543 1.85 - 2.08: 0 2.08 - 2.30: 80 Bond restraints: 42445 Sorted by residual: bond pdb=" C13 U10 B 401 " pdb=" C14 U10 B 401 " ideal model delta sigma weight residual 1.335 1.533 -0.198 2.00e-02 2.50e+03 9.85e+01 bond pdb=" C8 U10 B 401 " pdb=" C9 U10 B 401 " ideal model delta sigma weight residual 1.335 1.528 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" C18 U10 B 401 " pdb=" C19 U10 B 401 " ideal model delta sigma weight residual 1.336 1.524 -0.188 2.00e-02 2.50e+03 8.84e+01 bond pdb=" C4 FMN F 501 " pdb=" C4A FMN F 501 " ideal model delta sigma weight residual 1.485 1.377 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" OB5 CDL M 606 " pdb=" PB2 CDL M 606 " ideal model delta sigma weight residual 1.657 1.576 0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 42440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 56945 2.87 - 5.74: 421 5.74 - 8.61: 26 8.61 - 11.48: 3 11.48 - 14.35: 3 Bond angle restraints: 57398 Sorted by residual: angle pdb=" C17 U10 B 401 " pdb=" C18 U10 B 401 " pdb=" C19 U10 B 401 " ideal model delta sigma weight residual 127.47 113.12 14.35 3.00e+00 1.11e-01 2.29e+01 angle pdb=" C7 U10 B 401 " pdb=" C8 U10 B 401 " pdb=" C9 U10 B 401 " ideal model delta sigma weight residual 128.16 115.25 12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" C12 U10 B 401 " pdb=" C13 U10 B 401 " pdb=" C14 U10 B 401 " ideal model delta sigma weight residual 128.24 116.68 11.56 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C10 U10 B 401 " pdb=" C9 U10 B 401 " pdb=" C8 U10 B 401 " ideal model delta sigma weight residual 124.87 114.77 10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C18 U10 B 401 " pdb=" C19 U10 B 401 " pdb=" C20 U10 B 401 " ideal model delta sigma weight residual 124.21 114.46 9.75 3.00e+00 1.11e-01 1.06e+01 ... (remaining 57393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 24361 35.84 - 71.68: 767 71.68 - 107.52: 67 107.52 - 143.36: 10 143.36 - 179.20: 3 Dihedral angle restraints: 25208 sinusoidal: 10524 harmonic: 14684 Sorted by residual: dihedral pdb=" CB5 CDL H 402 " pdb=" CB4 CDL H 402 " pdb=" OB6 CDL H 402 " pdb=" CB6 CDL H 402 " ideal model delta sinusoidal sigma weight residual 144.75 -36.05 -179.20 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 P5S I 204 " pdb=" C34 P5S I 204 " pdb=" C35 P5S I 204 " pdb=" C36 P5S I 204 " ideal model delta sinusoidal sigma weight residual 294.83 123.92 170.91 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CB P5S I 204 " pdb=" OG P5S I 204 " pdb=" P12 P5S I 204 " pdb=" O16 P5S I 204 " ideal model delta sinusoidal sigma weight residual 295.68 145.87 149.81 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 25205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.272: 6216 4.272 - 8.544: 0 8.544 - 12.816: 0 12.816 - 17.088: 0 17.088 - 21.360: 16 Chirality restraints: 6232 Sorted by residual: chirality pdb="FE3 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.81 -21.36 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.77 -21.32 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE4 SF4 F 502 " pdb=" S1 SF4 F 502 " pdb=" S2 SF4 F 502 " pdb=" S3 SF4 F 502 " both_signs ideal model delta sigma weight residual False 10.55 -10.76 21.32 2.00e-01 2.50e+01 1.14e+04 ... (remaining 6229 not shown) Planarity restraints: 7186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 U10 B 401 " 0.060 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C11 U10 B 401 " 0.028 2.00e-02 2.50e+03 pdb=" C7 U10 B 401 " 0.326 2.00e-02 2.50e+03 pdb=" C8 U10 B 401 " -0.572 2.00e-02 2.50e+03 pdb=" C9 U10 B 401 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 U10 B 401 " -0.234 2.00e-02 2.50e+03 2.21e-01 6.09e+02 pdb=" C13 U10 B 401 " 0.219 2.00e-02 2.50e+03 pdb=" C14 U10 B 401 " 0.277 2.00e-02 2.50e+03 pdb=" C15 U10 B 401 " -0.009 2.00e-02 2.50e+03 pdb=" C16 U10 B 401 " -0.253 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 U10 B 401 " -0.178 2.00e-02 2.50e+03 2.07e-01 5.35e+02 pdb=" C18 U10 B 401 " 0.333 2.00e-02 2.50e+03 pdb=" C19 U10 B 401 " -0.235 2.00e-02 2.50e+03 pdb=" C20 U10 B 401 " 0.121 2.00e-02 2.50e+03 pdb=" C21 U10 B 401 " -0.042 2.00e-02 2.50e+03 ... (remaining 7183 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 393 2.53 - 3.12: 33216 3.12 - 3.72: 71786 3.72 - 4.31: 111255 4.31 - 4.90: 173331 Nonbonded interactions: 389981 Sorted by model distance: nonbonded pdb=" OG SER M 6 " pdb=" OE2 GLU M 67 " model vdw 1.938 3.040 nonbonded pdb=" OE2 GLU I 132 " pdb=" OG SER q 106 " model vdw 1.991 3.040 nonbonded pdb=" O GLU L 368 " pdb=" OH TYR L 374 " model vdw 2.015 3.040 nonbonded pdb="CA CA N 506 " pdb=" O HOH N 627 " model vdw 2.046 3.250 nonbonded pdb=" OG1 THR F 246 " pdb=" O MET F 321 " model vdw 2.063 3.040 ... (remaining 389976 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 23.140 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.030 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 52.870 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 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:7.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.198 42481 Z= 0.276 Angle : 0.694 17.018 57482 Z= 0.330 Chirality : 1.079 21.360 6232 Planarity : 0.007 0.304 7186 Dihedral : 16.870 179.201 15816 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.30 % Favored : 97.68 % Rotamer: Outliers : 0.34 % Allowed : 7.39 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.11), residues: 5089 helix: 0.61 (0.10), residues: 2726 sheet: 0.31 (0.25), residues: 420 loop : -0.30 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 142 TYR 0.025 0.002 TYR L 597 PHE 0.023 0.002 PHE K 23 TRP 0.017 0.002 TRP L 594 HIS 0.010 0.001 HIS R 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.27 (42445) covalent geometry : angle 0.64816 / 0.33 (57398) hydrogen bonds : bond 0.21429 / 14.12 ( 2277) hydrogen bonds : angle 7.39594 / 5.28 ( 6465) metal coordination : bond 0.03960 / 2.64 ( 36) metal coordination : angle 6.54634 / 4.09 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 483 time to evaluate : 1.773 Fit side-chains REVERT: G 312 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7788 (mmtm) REVERT: H 224 GLU cc_start: 0.7713 (mp0) cc_final: 0.7316 (mp0) outliers start: 14 outliers final: 9 residues processed: 492 average time/residue: 0.9519 time to fit residues: 557.0500 Evaluate side-chains 443 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 433 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 428 SER Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain t residue 92 SER Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 487 MET Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 450 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 494 optimal weight: 5.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 520 GLN N 136 GLN F 343 HIS q 122 GLN L 29 GLN L 505 HIS M 33 ASN M 499 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.101740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.078718 restraints weight = 39946.435| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.06 r_work: 0.2894 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.287 42481 Z= 0.307 Angle : 1.847 51.127 57482 Z= 1.058 Chirality : 0.322 6.654 6232 Planarity : 0.004 0.051 7186 Dihedral : 13.647 179.972 6757 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.28 % Allowed : 7.88 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.12), residues: 5089 helix: 1.43 (0.10), residues: 2774 sheet: 0.45 (0.26), residues: 399 loop : -0.11 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 605 TYR 0.021 0.002 TYR L 441 PHE 0.033 0.002 PHE L 350 TRP 0.021 0.001 TRP L 594 HIS 0.006 0.001 HIS N 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00869 / 0.31 (42445) covalent geometry : angle 1.62067 / 1.06 (57398) hydrogen bonds : bond 0.05278 / 3.52 ( 2277) hydrogen bonds : angle 5.08639 / 3.63 ( 6465) metal coordination : bond 0.03304 / 2.12 ( 36) metal coordination : angle 23.23328 / 16.31 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 476 time to evaluate : 1.497 Fit side-chains REVERT: G 311 MET cc_start: 0.8991 (mtp) cc_final: 0.8560 (mtp) REVERT: t 3 ASP cc_start: 0.7582 (t0) cc_final: 0.6395 (t70) REVERT: t 6 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7717 (mp10) REVERT: I 157 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: E 219 LYS cc_start: 0.8532 (ttpp) cc_final: 0.8301 (tttm) REVERT: N 146 MET cc_start: 0.8288 (ptm) cc_final: 0.7930 (ptt) REVERT: N 376 MET cc_start: 0.9251 (mmp) cc_final: 0.8864 (mmp) REVERT: H 224 GLU cc_start: 0.7827 (mp0) cc_final: 0.7326 (mp0) REVERT: D 7 LYS cc_start: 0.8592 (mtpm) cc_final: 0.8029 (mptt) REVERT: D 161 TYR cc_start: 0.9209 (OUTLIER) cc_final: 0.8478 (m-80) REVERT: Q 19 ARG cc_start: 0.7870 (mmm-85) cc_final: 0.7307 (mmp80) REVERT: Q 67 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7670 (mp0) REVERT: C 64 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8169 (p0) REVERT: B 34 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7804 (mp0) REVERT: L 700 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6828 (tpm170) REVERT: M 26 GLN cc_start: 0.6765 (mp-120) cc_final: 0.6387 (mt0) REVERT: M 112 GLU cc_start: 0.8592 (mp0) cc_final: 0.8328 (mp0) REVERT: M 368 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7472 (mp0) outliers start: 53 outliers final: 10 residues processed: 509 average time/residue: 0.9312 time to fit residues: 561.4032 Evaluate side-chains 450 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 434 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 6 GLN Chi-restraints excluded: chain I residue 157 GLN Chi-restraints excluded: chain N residue 136 GLN Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 402 LEU Chi-restraints excluded: chain L residue 405 LEU Chi-restraints excluded: chain L residue 700 ARG Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 200 ASP Chi-restraints excluded: chain M residue 368 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 325 optimal weight: 0.9990 chunk 275 optimal weight: 0.0970 chunk 21 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 450 optimal weight: 4.9990 chunk 59 optimal weight: 0.1980 chunk 426 optimal weight: 3.9990 chunk 375 optimal weight: 5.9990 chunk 444 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 329 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 520 GLN I 157 GLN N 100 ASN F 385 GLN q 122 GLN C 38 ASN M 499 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.079803 restraints weight = 38922.287| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.01 r_work: 0.2921 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.256 42481 Z= 0.291 Angle : 1.826 50.722 57482 Z= 1.048 Chirality : 0.324 6.459 6232 Planarity : 0.004 0.048 7186 Dihedral : 12.909 179.270 6744 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.28 % Allowed : 8.44 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.12), residues: 5089 helix: 1.75 (0.10), residues: 2784 sheet: 0.49 (0.26), residues: 398 loop : -0.02 (0.15), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 605 TYR 0.024 0.001 TYR L 441 PHE 0.031 0.001 PHE L 350 TRP 0.020 0.001 TRP L 594 HIS 0.007 0.001 HIS N 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.29 (42445) covalent geometry : angle 1.59927 / 1.05 (57398) hydrogen bonds : bond 0.04794 / 3.19 ( 2277) hydrogen bonds : angle 4.77058 / 3.39 ( 6465) metal coordination : bond 0.03595 / 2.31 ( 36) metal coordination : angle 23.10270 / 16.19 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 464 time to evaluate : 1.823 Fit side-chains revert: symmetry clash REVERT: G 311 MET cc_start: 0.9006 (mtp) cc_final: 0.8664 (mtp) REVERT: G 312 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7854 (mmtm) REVERT: G 374 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8498 (mtm) REVERT: G 454 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: G 621 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: E 219 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8333 (tttm) REVERT: N 146 MET cc_start: 0.8196 (ptm) cc_final: 0.7962 (ptt) REVERT: N 376 MET cc_start: 0.9167 (mmp) cc_final: 0.8884 (mmp) REVERT: N 438 THR cc_start: 0.8424 (p) cc_final: 0.8140 (t) REVERT: H 224 GLU cc_start: 0.7737 (mp0) cc_final: 0.7375 (mp0) REVERT: H 332 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8286 (mt-10) REVERT: D 7 LYS cc_start: 0.8587 (mtpm) cc_final: 0.8023 (mptt) REVERT: J 54 MET cc_start: 0.8648 (mpp) cc_final: 0.7498 (mpp) REVERT: Q 19 ARG cc_start: 0.7917 (mmm-85) cc_final: 0.7301 (mmp80) REVERT: Q 67 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7631 (mp0) REVERT: Q 73 GLU cc_start: 0.7861 (pt0) cc_final: 0.7657 (pt0) REVERT: B 34 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7815 (mp0) REVERT: L 282 TYR cc_start: 0.8189 (m-80) cc_final: 0.7964 (m-80) REVERT: L 700 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6916 (tpm170) REVERT: M 26 GLN cc_start: 0.6754 (mp-120) cc_final: 0.6381 (mt0) REVERT: M 112 GLU cc_start: 0.8580 (mp0) cc_final: 0.8334 (mp0) REVERT: M 368 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: M 452 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7577 (mptt) outliers start: 53 outliers final: 11 residues processed: 497 average time/residue: 0.8902 time to fit residues: 527.4195 Evaluate side-chains 463 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 444 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 374 MET Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain G residue 621 GLU Chi-restraints excluded: chain t residue 6 GLN Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 332 GLU Chi-restraints excluded: chain R residue 38 ASP Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 405 LEU Chi-restraints excluded: chain L residue 700 ARG Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 368 GLU Chi-restraints excluded: chain M residue 452 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 209 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 363 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 408 optimal weight: 4.9990 chunk 431 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 465 optimal weight: 7.9990 chunk 471 optimal weight: 1.9990 chunk 400 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 449 GLN G 520 GLN I 157 GLN N 271 GLN q 12 ASN q 83 HIS q 122 GLN Q 22 ASN M 320 HIS M 342 GLN M 499 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.076155 restraints weight = 38087.048| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 0.97 r_work: 0.2854 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.259 42481 Z= 0.333 Angle : 1.853 50.650 57482 Z= 1.061 Chirality : 0.329 6.621 6232 Planarity : 0.005 0.057 7186 Dihedral : 13.341 176.887 6742 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.84 % Allowed : 8.73 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.12), residues: 5089 helix: 1.53 (0.10), residues: 2786 sheet: 0.37 (0.26), residues: 403 loop : -0.10 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 85 TYR 0.026 0.002 TYR L 597 PHE 0.029 0.002 PHE L 350 TRP 0.021 0.002 TRP L 594 HIS 0.008 0.001 HIS R 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00911 / 0.33 (42445) covalent geometry : angle 1.63243 / 1.06 (57398) hydrogen bonds : bond 0.06087 / 4.04 ( 2277) hydrogen bonds : angle 4.98750 / 3.55 ( 6465) metal coordination : bond 0.05871 / 4.02 ( 36) metal coordination : angle 22.98395 / 16.04 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 448 time to evaluate : 1.614 Fit side-chains revert: symmetry clash REVERT: G 309 ARG cc_start: 0.8531 (mtm-85) cc_final: 0.8152 (mtm110) REVERT: G 312 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7979 (mmtm) REVERT: G 454 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7550 (mm-30) REVERT: G 621 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: I 41 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.7947 (mmtp) REVERT: E 219 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8416 (tttm) REVERT: N 146 MET cc_start: 0.8290 (ptm) cc_final: 0.8089 (ptt) REVERT: N 450 MET cc_start: 0.9181 (mmt) cc_final: 0.8825 (mmt) REVERT: H 332 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: D 161 TYR cc_start: 0.9313 (OUTLIER) cc_final: 0.8847 (m-80) REVERT: D 296 GLN cc_start: 0.7865 (tm130) cc_final: 0.7597 (tm-30) REVERT: J 146 MET cc_start: 0.8863 (mmp) cc_final: 0.8613 (mmp) REVERT: Q 19 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7460 (mmp80) REVERT: Q 73 GLU cc_start: 0.7982 (pt0) cc_final: 0.7744 (pt0) REVERT: B 34 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8003 (mt-10) REVERT: B 102 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.8530 (tppp) REVERT: B 166 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8547 (ttt-90) REVERT: L 198 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: L 282 TYR cc_start: 0.8508 (m-80) cc_final: 0.8277 (m-80) REVERT: L 700 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7044 (tpm170) REVERT: M 112 GLU cc_start: 0.8622 (mp0) cc_final: 0.8364 (mp0) REVERT: M 184 MET cc_start: 0.8978 (mtp) cc_final: 0.8753 (mtp) REVERT: M 368 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: M 452 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7321 (mptt) outliers start: 76 outliers final: 24 residues processed: 492 average time/residue: 0.9032 time to fit residues: 528.9102 Evaluate side-chains 470 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 434 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain G residue 432 ARG Chi-restraints excluded: chain G residue 435 SER Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain G residue 621 GLU Chi-restraints excluded: chain t residue 6 GLN Chi-restraints excluded: chain t residue 92 SER Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 41 LYS Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain N residue 426 TYR Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 332 GLU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain R residue 38 ASP Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 198 GLN Chi-restraints excluded: chain L residue 402 LEU Chi-restraints excluded: chain L residue 405 LEU Chi-restraints excluded: chain L residue 487 MET Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain L residue 700 ARG Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 368 GLU Chi-restraints excluded: chain M residue 452 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 394 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 349 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 chunk 308 optimal weight: 0.0670 chunk 295 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 322 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 357 optimal weight: 1.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 520 GLN I 157 GLN E 36 GLN M 499 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.101580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.079040 restraints weight = 38066.436| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.03 r_work: 0.2902 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 42481 Z= 0.293 Angle : 1.830 50.684 57482 Z= 1.050 Chirality : 0.324 6.488 6232 Planarity : 0.004 0.053 7186 Dihedral : 12.825 178.917 6740 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.48 % Allowed : 9.75 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.12), residues: 5089 helix: 1.72 (0.10), residues: 2782 sheet: 0.35 (0.26), residues: 408 loop : -0.09 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 85 TYR 0.023 0.001 TYR M 433 PHE 0.032 0.001 PHE L 350 TRP 0.023 0.001 TRP L 594 HIS 0.006 0.001 HIS N 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00835 / 0.29 (42445) covalent geometry : angle 1.60327 / 1.05 (57398) hydrogen bonds : bond 0.04870 / 3.24 ( 2277) hydrogen bonds : angle 4.74242 / 3.38 ( 6465) metal coordination : bond 0.03690 / 2.47 ( 36) metal coordination : angle 23.13766 / 16.18 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 461 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 309 ARG cc_start: 0.8534 (mtm-85) cc_final: 0.8136 (mtm110) REVERT: G 312 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7974 (mmtm) REVERT: G 454 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7511 (mm-30) REVERT: I 41 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.7924 (mmtp) REVERT: N 352 VAL cc_start: 0.9129 (p) cc_final: 0.8779 (m) REVERT: H 252 TYR cc_start: 0.9348 (OUTLIER) cc_final: 0.8267 (t80) REVERT: H 332 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8373 (mt-10) REVERT: D 161 TYR cc_start: 0.9223 (OUTLIER) cc_final: 0.8766 (m-80) REVERT: D 296 GLN cc_start: 0.7845 (tm130) cc_final: 0.7596 (tm-30) REVERT: Q 19 ARG cc_start: 0.7988 (mmm-85) cc_final: 0.7456 (mmp80) REVERT: Q 73 GLU cc_start: 0.7860 (pt0) cc_final: 0.7517 (pt0) REVERT: C 64 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8395 (p0) REVERT: B 34 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7997 (mt-10) REVERT: B 166 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8518 (ttt-90) REVERT: L 208 GLN cc_start: 0.7955 (mt0) cc_final: 0.7646 (mt0) REVERT: L 278 MET cc_start: 0.8883 (mmm) cc_final: 0.8640 (mmm) REVERT: L 282 TYR cc_start: 0.8432 (m-80) cc_final: 0.8151 (m-80) REVERT: L 700 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6998 (tpm170) REVERT: M 112 GLU cc_start: 0.8565 (mp0) cc_final: 0.8349 (mp0) REVERT: M 368 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7574 (mp0) outliers start: 61 outliers final: 19 residues processed: 500 average time/residue: 0.9266 time to fit residues: 552.7497 Evaluate side-chains 467 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 438 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 435 SER Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain t residue 6 GLN Chi-restraints excluded: chain I residue 41 LYS Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain N residue 426 TYR Chi-restraints excluded: chain H residue 252 TYR Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 332 GLU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain R residue 38 ASP Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain L residue 700 ARG Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 368 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 469 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 269 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 359 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 397 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 201 GLN I 157 GLN L 366 HIS M 499 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.076360 restraints weight = 38796.105| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.00 r_work: 0.2858 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.251 42481 Z= 0.336 Angle : 1.849 50.621 57482 Z= 1.059 Chirality : 0.330 6.621 6232 Planarity : 0.005 0.059 7186 Dihedral : 13.170 175.891 6740 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.55 % Allowed : 10.01 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.12), residues: 5089 helix: 1.52 (0.10), residues: 2789 sheet: 0.34 (0.26), residues: 398 loop : -0.12 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 85 TYR 0.025 0.002 TYR J 60 PHE 0.029 0.002 PHE L 350 TRP 0.024 0.002 TRP L 594 HIS 0.008 0.001 HIS R 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00918 / 0.33 (42445) covalent geometry : angle 1.62891 / 1.06 (57398) hydrogen bonds : bond 0.05937 / 3.95 ( 2277) hydrogen bonds : angle 4.92675 / 3.51 ( 6465) metal coordination : bond 0.05621 / 3.84 ( 36) metal coordination : angle 22.93973 / 15.99 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 441 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 312 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8023 (mmtm) REVERT: G 454 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: I 41 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.7950 (mmtp) REVERT: N 1 MET cc_start: 0.8351 (ttm) cc_final: 0.8084 (ttt) REVERT: H 332 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: D 161 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.8840 (m-80) REVERT: D 296 GLN cc_start: 0.7889 (tm130) cc_final: 0.7657 (tm-30) REVERT: q 84 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8285 (mptt) REVERT: A 50 ASN cc_start: 0.9025 (m-40) cc_final: 0.8702 (m-40) REVERT: J 146 MET cc_start: 0.8883 (mmp) cc_final: 0.8538 (mmp) REVERT: Q 19 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7510 (mmp80) REVERT: B 34 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8086 (mt-10) REVERT: B 102 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.8535 (tppp) REVERT: B 166 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8542 (ttt-90) REVERT: L 198 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: L 700 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7070 (tpm170) REVERT: M 1 MET cc_start: 0.5792 (OUTLIER) cc_final: 0.5043 (tpp) REVERT: M 112 GLU cc_start: 0.8637 (mp0) cc_final: 0.8383 (mp0) REVERT: M 368 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: M 495 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8139 (tt0) outliers start: 64 outliers final: 31 residues processed: 486 average time/residue: 0.9578 time to fit residues: 554.4196 Evaluate side-chains 477 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 433 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 435 SER Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain t residue 6 GLN Chi-restraints excluded: chain t residue 92 SER Chi-restraints excluded: chain I residue 41 LYS Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 426 TYR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 332 GLU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 84 LYS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain R residue 38 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 198 GLN Chi-restraints excluded: chain L residue 355 PHE Chi-restraints excluded: chain L residue 487 MET Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain L residue 700 ARG Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 368 GLU Chi-restraints excluded: chain M residue 495 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 475 optimal weight: 2.9990 chunk 476 optimal weight: 0.9990 chunk 436 optimal weight: 10.0000 chunk 380 optimal weight: 0.6980 chunk 321 optimal weight: 0.9990 chunk 353 optimal weight: 1.9990 chunk 369 optimal weight: 0.6980 chunk 300 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 336 optimal weight: 4.9990 chunk 230 optimal weight: 8.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 146 ASN G 520 GLN I 157 GLN N 323 ASN N 335 ASN D 39 HIS C 147 HIS L 366 HIS M 499 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.079521 restraints weight = 38606.794| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 0.98 r_work: 0.2917 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 42481 Z= 0.288 Angle : 1.828 50.644 57482 Z= 1.048 Chirality : 0.324 6.447 6232 Planarity : 0.004 0.054 7186 Dihedral : 12.615 177.352 6740 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.55 % Allowed : 10.47 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.12), residues: 5089 helix: 1.78 (0.10), residues: 2784 sheet: 0.30 (0.26), residues: 400 loop : -0.05 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 421 TYR 0.024 0.001 TYR M 433 PHE 0.033 0.001 PHE L 350 TRP 0.026 0.001 TRP L 594 HIS 0.007 0.001 HIS N 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00825 / 0.29 (42445) covalent geometry : angle 1.59958 / 1.05 (57398) hydrogen bonds : bond 0.04588 / 3.05 ( 2277) hydrogen bonds : angle 4.67365 / 3.33 ( 6465) metal coordination : bond 0.03115 / 2.06 ( 36) metal coordination : angle 23.18647 / 16.17 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 458 time to evaluate : 1.359 Fit side-chains revert: symmetry clash REVERT: G 281 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7970 (mtp85) REVERT: G 309 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.8115 (mtm110) REVERT: G 312 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.8011 (mmtm) REVERT: G 636 ARG cc_start: 0.7651 (mtm-85) cc_final: 0.7341 (mpp80) REVERT: I 41 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.7942 (mmtp) REVERT: H 252 TYR cc_start: 0.9318 (OUTLIER) cc_final: 0.8305 (t80) REVERT: H 332 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: D 161 TYR cc_start: 0.9199 (OUTLIER) cc_final: 0.8760 (m-80) REVERT: D 296 GLN cc_start: 0.7870 (tm130) cc_final: 0.7628 (tm-30) REVERT: q 4 LEU cc_start: 0.7786 (mm) cc_final: 0.7490 (tp) REVERT: A 50 ASN cc_start: 0.9009 (m-40) cc_final: 0.8688 (m-40) REVERT: Q 19 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7388 (mmp80) REVERT: Q 73 GLU cc_start: 0.7856 (pt0) cc_final: 0.7522 (pt0) REVERT: B 34 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8028 (mt-10) REVERT: B 102 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.8493 (tppp) REVERT: L 208 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7659 (mt0) REVERT: L 214 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7385 (ptm) REVERT: L 278 MET cc_start: 0.8914 (mmm) cc_final: 0.8506 (mmm) REVERT: L 700 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7045 (tpm170) REVERT: M 112 GLU cc_start: 0.8545 (mp0) cc_final: 0.8343 (mp0) REVERT: M 368 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7642 (mp0) outliers start: 64 outliers final: 25 residues processed: 502 average time/residue: 0.9234 time to fit residues: 553.6186 Evaluate side-chains 471 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 435 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain G residue 281 ARG Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain t residue 6 GLN Chi-restraints excluded: chain t residue 92 SER Chi-restraints excluded: chain I residue 41 LYS Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain N residue 426 TYR Chi-restraints excluded: chain H residue 252 TYR Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 332 GLU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain R residue 38 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 405 LEU Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain L residue 700 ARG Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 368 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 100 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 338 optimal weight: 0.7980 chunk 293 optimal weight: 5.9990 chunk 239 optimal weight: 0.7980 chunk 261 optimal weight: 0.3980 chunk 166 optimal weight: 4.9990 chunk 484 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 446 optimal weight: 9.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 157 GLN N 335 ASN L 366 HIS M 33 ASN M 499 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.103348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.080675 restraints weight = 38622.247| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 0.98 r_work: 0.2939 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.251 42481 Z= 0.287 Angle : 1.828 50.691 57482 Z= 1.046 Chirality : 0.324 6.428 6232 Planarity : 0.004 0.052 7186 Dihedral : 12.193 176.302 6740 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.26 % Allowed : 10.96 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.12), residues: 5089 helix: 1.88 (0.10), residues: 2784 sheet: 0.33 (0.26), residues: 402 loop : -0.01 (0.15), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 58 TYR 0.023 0.001 TYR M 433 PHE 0.033 0.001 PHE L 350 TRP 0.027 0.001 TRP L 594 HIS 0.007 0.001 HIS N 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00826 / 0.29 (42445) covalent geometry : angle 1.59603 / 1.04 (57398) hydrogen bonds : bond 0.04327 / 2.88 ( 2277) hydrogen bonds : angle 4.57129 / 3.26 ( 6465) metal coordination : bond 0.03201 / 2.17 ( 36) metal coordination : angle 23.34691 / 16.27 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 459 time to evaluate : 1.706 Fit side-chains revert: symmetry clash REVERT: G 281 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7968 (mtp85) REVERT: G 309 ARG cc_start: 0.8526 (mtm-85) cc_final: 0.8106 (mtm110) REVERT: G 312 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7972 (mmtm) REVERT: G 636 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7375 (mpp80) REVERT: E 1 MET cc_start: 0.6798 (ttt) cc_final: 0.5857 (tpt) REVERT: E 156 ASP cc_start: 0.8271 (m-30) cc_final: 0.7915 (m-30) REVERT: N 147 ARG cc_start: 0.8273 (ttt90) cc_final: 0.7774 (ttt180) REVERT: H 332 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8329 (mt-10) REVERT: F 321 MET cc_start: 0.8547 (mtm) cc_final: 0.8092 (ptp) REVERT: F 326 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: F 415 ASP cc_start: 0.8110 (m-30) cc_final: 0.7793 (m-30) REVERT: D 161 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: q 4 LEU cc_start: 0.7773 (mm) cc_final: 0.7478 (tp) REVERT: A 50 ASN cc_start: 0.8993 (m-40) cc_final: 0.8669 (m-40) REVERT: Q 19 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7364 (mmp80) REVERT: Q 73 GLU cc_start: 0.7731 (pt0) cc_final: 0.7406 (pt0) REVERT: B 34 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8015 (mt-10) REVERT: B 102 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8509 (tppp) REVERT: L 208 GLN cc_start: 0.7966 (mt0) cc_final: 0.7664 (mt0) REVERT: L 214 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7353 (ptm) REVERT: L 278 MET cc_start: 0.8895 (mmm) cc_final: 0.8535 (mmm) REVERT: L 282 TYR cc_start: 0.8477 (m-80) cc_final: 0.8242 (m-80) REVERT: L 453 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6739 (tppt) REVERT: L 601 PRO cc_start: 0.7235 (Cg_exo) cc_final: 0.6852 (Cg_endo) REVERT: L 700 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7032 (tpm170) REVERT: M 112 GLU cc_start: 0.8533 (mp0) cc_final: 0.8331 (mp0) REVERT: M 368 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: M 452 LYS cc_start: 0.7845 (mptt) cc_final: 0.7610 (mptt) outliers start: 52 outliers final: 19 residues processed: 496 average time/residue: 0.9262 time to fit residues: 547.8221 Evaluate side-chains 472 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 443 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain G residue 281 ARG Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain t residue 6 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain N residue 426 TYR Chi-restraints excluded: chain H residue 332 GLU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 326 GLN Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain R residue 38 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 453 LYS Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain L residue 700 ARG Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 368 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 56 optimal weight: 7.9990 chunk 343 optimal weight: 0.7980 chunk 296 optimal weight: 0.9980 chunk 250 optimal weight: 0.8980 chunk 471 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 362 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 520 GLN I 157 GLN N 271 GLN N 335 ASN L 366 HIS M 499 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.103296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.080588 restraints weight = 38442.857| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 0.98 r_work: 0.2938 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 42481 Z= 0.288 Angle : 1.827 50.731 57482 Z= 1.047 Chirality : 0.324 6.464 6232 Planarity : 0.004 0.052 7186 Dihedral : 12.021 175.247 6740 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.02 % Allowed : 11.39 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.12), residues: 5089 helix: 1.89 (0.10), residues: 2786 sheet: 0.29 (0.26), residues: 418 loop : 0.01 (0.15), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 58 TYR 0.023 0.001 TYR M 433 PHE 0.032 0.001 PHE L 350 TRP 0.028 0.001 TRP L 594 HIS 0.007 0.001 HIS N 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.29 (42445) covalent geometry : angle 1.59756 / 1.04 (57398) hydrogen bonds : bond 0.04365 / 2.90 ( 2277) hydrogen bonds : angle 4.55651 / 3.25 ( 6465) metal coordination : bond 0.03466 / 2.41 ( 36) metal coordination : angle 23.22617 / 16.19 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 442 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 281 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7985 (mtp85) REVERT: G 309 ARG cc_start: 0.8515 (mtm-85) cc_final: 0.8100 (mtm110) REVERT: G 312 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7920 (mmtm) REVERT: G 636 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7078 (mtp-110) REVERT: E 156 ASP cc_start: 0.8247 (m-30) cc_final: 0.7891 (m-30) REVERT: N 147 ARG cc_start: 0.8251 (ttt90) cc_final: 0.7743 (ttt180) REVERT: H 332 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8318 (mt-10) REVERT: F 321 MET cc_start: 0.8519 (mtm) cc_final: 0.8113 (ptp) REVERT: F 415 ASP cc_start: 0.8080 (m-30) cc_final: 0.7759 (m-30) REVERT: D 161 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.8829 (m-80) REVERT: q 4 LEU cc_start: 0.7782 (mm) cc_final: 0.7499 (tp) REVERT: A 50 ASN cc_start: 0.8995 (m-40) cc_final: 0.8672 (m-40) REVERT: J 54 MET cc_start: 0.8760 (mpp) cc_final: 0.7833 (mpp) REVERT: Q 19 ARG cc_start: 0.7964 (mmm-85) cc_final: 0.7374 (mmp80) REVERT: Q 73 GLU cc_start: 0.7723 (pt0) cc_final: 0.7406 (pt0) REVERT: C 64 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8194 (p0) REVERT: B 102 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.8516 (tppp) REVERT: L 208 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7695 (mt0) REVERT: L 214 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7361 (ptm) REVERT: L 278 MET cc_start: 0.8914 (mmm) cc_final: 0.8560 (mmm) REVERT: L 282 TYR cc_start: 0.8452 (m-80) cc_final: 0.8247 (m-80) REVERT: L 453 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6701 (tppt) REVERT: L 601 PRO cc_start: 0.7222 (Cg_exo) cc_final: 0.6839 (Cg_endo) REVERT: L 700 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7083 (tpt170) REVERT: M 368 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: M 452 LYS cc_start: 0.7851 (mptt) cc_final: 0.7609 (mptt) outliers start: 42 outliers final: 19 residues processed: 466 average time/residue: 0.9237 time to fit residues: 511.6311 Evaluate side-chains 470 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 440 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain G residue 281 ARG Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain t residue 6 GLN Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 378 SER Chi-restraints excluded: chain N residue 426 TYR Chi-restraints excluded: chain H residue 332 GLU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain R residue 38 ASP Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 453 LYS Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain L residue 700 ARG Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 368 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 37 optimal weight: 6.9990 chunk 458 optimal weight: 2.9990 chunk 370 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 159 optimal weight: 0.4980 chunk 498 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 419 optimal weight: 9.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 157 GLN N 271 GLN N 323 ASN N 335 ASN q 122 GLN L 366 HIS M 33 ASN M 499 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.077138 restraints weight = 38170.241| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 0.98 r_work: 0.2872 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.244 42481 Z= 0.321 Angle : 1.843 50.704 57482 Z= 1.056 Chirality : 0.329 6.595 6232 Planarity : 0.004 0.054 7186 Dihedral : 12.489 172.686 6740 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.95 % Allowed : 11.59 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.12), residues: 5089 helix: 1.69 (0.10), residues: 2781 sheet: 0.29 (0.26), residues: 409 loop : -0.05 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 58 TYR 0.033 0.002 TYR J 60 PHE 0.029 0.002 PHE L 350 TRP 0.028 0.002 TRP L 594 HIS 0.008 0.001 HIS R 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00886 / 0.32 (42445) covalent geometry : angle 1.62144 / 1.05 (57398) hydrogen bonds : bond 0.05534 / 3.68 ( 2277) hydrogen bonds : angle 4.79429 / 3.42 ( 6465) metal coordination : bond 0.05191 / 3.61 ( 36) metal coordination : angle 22.99531 / 16.02 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 439 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 1 MET cc_start: 0.6547 (tpp) cc_final: 0.6306 (tpt) REVERT: G 281 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8030 (mtp85) REVERT: G 309 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8120 (mtm110) REVERT: G 312 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8037 (mmtm) REVERT: G 454 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: G 636 ARG cc_start: 0.7722 (mtm-85) cc_final: 0.7409 (mpp80) REVERT: N 450 MET cc_start: 0.9168 (mmt) cc_final: 0.8782 (mmt) REVERT: H 332 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: D 161 TYR cc_start: 0.9300 (OUTLIER) cc_final: 0.8925 (m-80) REVERT: q 4 LEU cc_start: 0.7822 (mm) cc_final: 0.7537 (tp) REVERT: A 50 ASN cc_start: 0.9024 (m-40) cc_final: 0.8706 (m-40) REVERT: J 146 MET cc_start: 0.8858 (mmp) cc_final: 0.8510 (mmp) REVERT: Q 19 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7428 (mmp80) REVERT: Q 73 GLU cc_start: 0.7826 (pt0) cc_final: 0.7587 (pt0) REVERT: B 102 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.8496 (tppp) REVERT: L 208 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7665 (mt0) REVERT: L 282 TYR cc_start: 0.8503 (m-80) cc_final: 0.8228 (m-80) REVERT: L 453 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6723 (tppt) REVERT: L 601 PRO cc_start: 0.7293 (Cg_exo) cc_final: 0.6929 (Cg_endo) REVERT: L 700 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7533 (mtt-85) REVERT: M 1 MET cc_start: 0.5655 (tpp) cc_final: 0.5250 (tmm) REVERT: M 368 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7706 (mp0) outliers start: 39 outliers final: 17 residues processed: 463 average time/residue: 0.9392 time to fit residues: 516.9080 Evaluate side-chains 469 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 442 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 281 ARG Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain t residue 6 GLN Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 426 TYR Chi-restraints excluded: chain H residue 332 GLU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain R residue 38 ASP Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain L residue 453 LYS Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain L residue 700 ARG Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 368 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 476 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 441 optimal weight: 0.0870 chunk 305 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 343 optimal weight: 3.9990 chunk 468 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 302 optimal weight: 0.4980 chunk 310 optimal weight: 2.9990 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 157 GLN N 335 ASN D 296 GLN q 122 GLN L 366 HIS M 499 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.101141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.078214 restraints weight = 38339.161| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 0.98 r_work: 0.2891 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.245 42481 Z= 0.300 Angle : 1.836 50.702 57482 Z= 1.052 Chirality : 0.326 6.513 6232 Planarity : 0.004 0.054 7186 Dihedral : 12.380 176.888 6740 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.92 % Allowed : 11.73 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.12), residues: 5089 helix: 1.72 (0.10), residues: 2782 sheet: 0.29 (0.26), residues: 407 loop : -0.04 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 58 TYR 0.024 0.002 TYR J 60 PHE 0.031 0.002 PHE L 350 TRP 0.029 0.001 TRP L 594 HIS 0.006 0.001 HIS N 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00848 / 0.30 (42445) covalent geometry : angle 1.61101 / 1.05 (57398) hydrogen bonds : bond 0.05056 / 3.36 ( 2277) hydrogen bonds : angle 4.72795 / 3.38 ( 6465) metal coordination : bond 0.04277 / 2.95 ( 36) metal coordination : angle 23.08590 / 16.10 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21252.21 seconds wall clock time: 361 minutes 6.37 seconds (21666.37 seconds total)