Starting phenix.real_space_refine on Tue Aug 26 21:49:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qby_18324/08_2025/8qby_18324.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qby_18324/08_2025/8qby_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_18324/08_2025/8qby_18324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qby_18324/08_2025/8qby_18324.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qby_18324/08_2025/8qby_18324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qby_18324/08_2025/8qby_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-2.0-5787/lib/python3.9/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, 21 Unusual residues: {' NA': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Unusual residues: {' CA': 1, '3PH': 1, 'SF4': 2} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} 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, 218 Unusual residues: {' CA': 1, '3PE': 3, '3PH': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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, 43 Unusual residues: {' CA': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 27 Planarities with less than four sites: {'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 28 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, 306 Unusual residues: {' CA': 1, '3PE': 3, '3PH': 4, 'CDL': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 9.94, per 1000 atoms: 0.23 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: 4.24 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.54 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: 10.35 Time building geometry restraints manager: 5.32 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=" C3 U10 B 401 " pdb=" O3 U10 B 401 " ideal model delta sigma weight residual 1.230 1.399 -0.169 2.00e-02 2.50e+03 7.12e+01 bond pdb=" C4 U10 B 401 " pdb=" O4 U10 B 401 " ideal model delta sigma weight residual 1.230 1.399 -0.169 2.00e-02 2.50e+03 7.10e+01 bond pdb=" C5 U10 B 401 " pdb=" C6 U10 B 401 " ideal model delta sigma weight residual 1.390 1.532 -0.142 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C4 U10 B 401 " pdb=" C5 U10 B 401 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C1 U10 B 401 " pdb=" C2 U10 B 401 " ideal model delta sigma weight residual 1.390 1.524 -0.134 2.00e-02 2.50e+03 4.52e+01 ... (remaining 42440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 56163 1.76 - 3.51: 969 3.51 - 5.27: 231 5.27 - 7.03: 31 7.03 - 8.78: 4 Bond angle restraints: 57398 Sorted by residual: angle pdb=" C GLY L 376 " pdb=" N LEU L 377 " pdb=" CA LEU L 377 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.97e+00 angle pdb=" CA CYS B 54 " pdb=" C CYS B 54 " pdb=" N CYS B 55 " ideal model delta sigma weight residual 116.84 121.92 -5.08 1.71e+00 3.42e-01 8.83e+00 angle pdb=" CZ 2MR D 65 " pdb=" NH1 2MR D 65 " pdb=" CQ1 2MR D 65 " ideal model delta sigma weight residual 118.62 127.40 -8.78 3.00e+00 1.11e-01 8.57e+00 angle pdb=" CA CYS B 54 " pdb=" CB CYS B 54 " pdb=" SG CYS B 54 " ideal model delta sigma weight residual 114.40 120.90 -6.50 2.30e+00 1.89e-01 7.99e+00 angle pdb=" C LEU L 217 " pdb=" CA LEU L 217 " pdb=" CB LEU L 217 " ideal model delta sigma weight residual 110.42 115.70 -5.28 1.99e+00 2.53e-01 7.03e+00 ... (remaining 57393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 24331 34.18 - 68.36: 887 68.36 - 102.55: 92 102.55 - 136.73: 11 136.73 - 170.91: 5 Dihedral angle restraints: 25326 sinusoidal: 10642 harmonic: 14684 Sorted by residual: dihedral pdb=" C3M U10 B 401 " pdb=" C3 U10 B 401 " pdb=" O3 U10 B 401 " pdb=" C4 U10 B 401 " ideal model delta sinusoidal sigma weight residual 244.38 122.11 122.26 1 2.00e+01 2.50e-03 3.68e+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=" CA5 CDL M 606 " pdb=" CA4 CDL M 606 " pdb=" OA6 CDL M 606 " pdb=" CA6 CDL M 606 " ideal model delta sinusoidal sigma weight residual 168.24 -38.45 -153.31 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 25323 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=" C18 U10 B 401 " 0.095 2.00e-02 2.50e+03 1.63e-01 2.66e+02 pdb=" C19 U10 B 401 " -0.283 2.00e-02 2.50e+03 pdb=" C20 U10 B 401 " 0.094 2.00e-02 2.50e+03 pdb=" C21 U10 B 401 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 U10 B 401 " -0.082 2.00e-02 2.50e+03 1.45e-01 2.09e+02 pdb=" C11 U10 B 401 " -0.084 2.00e-02 2.50e+03 pdb=" C8 U10 B 401 " -0.084 2.00e-02 2.50e+03 pdb=" C9 U10 B 401 " 0.250 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 U10 B 401 " -0.074 2.00e-02 2.50e+03 1.27e-01 1.61e+02 pdb=" C14 U10 B 401 " 0.220 2.00e-02 2.50e+03 pdb=" C15 U10 B 401 " -0.074 2.00e-02 2.50e+03 pdb=" C16 U10 B 401 " -0.072 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 2.510 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: 24.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.890 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 52.980 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 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 0.169 42481 Z= 0.271 Angle : 0.676 17.018 57482 Z= 0.326 Chirality : 1.079 21.360 6232 Planarity : 0.005 0.163 7186 Dihedral : 17.191 170.912 15934 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 aren 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 covalent geometry : bond 0.00607 (42445) covalent geometry : angle 0.62867 (57398) hydrogen bonds : bond 0.21429 ( 2277) hydrogen bonds : angle 7.39594 ( 6465) metal coordination : bond 0.03960 ( 36) metal coordination : angle 6.54634 ( 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 : 1.722 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: 1.0312 time to fit residues: 599.0525 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 : 1.750 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 520 GLN N 136 GLN F 343 HIS q 122 GLN C 147 HIS L 29 GLN L 505 HIS M 33 ASN M 499 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.078847 restraints weight = 39989.430| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.07 r_work: 0.2897 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.295 42481 Z= 0.310 Angle : 1.843 50.922 57482 Z= 1.056 Chirality : 0.322 6.439 6232 Planarity : 0.004 0.050 7186 Dihedral : 14.469 179.706 6875 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.31 % Allowed : 7.88 % Favored : 90.81 % 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 aren not related in a simple way. whole: 1.12 (0.12), residues: 5089 helix: 1.43 (0.10), residues: 2776 sheet: 0.45 (0.26), residues: 398 loop : -0.11 (0.14), residues: 1915 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 0.001 PHE L 350 TRP 0.020 0.001 TRP L 594 HIS 0.006 0.001 HIS N 224 Details of bonding type rmsd covalent geometry : bond 0.00880 (42445) covalent geometry : angle 1.61744 (57398) hydrogen bonds : bond 0.05356 ( 2277) hydrogen bonds : angle 5.08490 ( 6465) metal coordination : bond 0.03656 ( 36) metal coordination : angle 23.18395 ( 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 530 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 476 time to evaluate : 1.801 Fit side-chains REVERT: G 311 MET cc_start: 0.8991 (mtp) cc_final: 0.8562 (mtp) REVERT: t 3 ASP cc_start: 0.7551 (t0) cc_final: 0.6363 (t70) REVERT: t 6 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7698 (mp10) REVERT: I 157 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8249 (mt0) REVERT: E 219 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8299 (tttm) REVERT: N 146 MET cc_start: 0.8265 (ptm) cc_final: 0.7909 (ptt) REVERT: N 376 MET cc_start: 0.9241 (mmp) cc_final: 0.8851 (mmp) REVERT: N 438 THR cc_start: 0.8462 (p) cc_final: 0.8181 (t) REVERT: H 224 GLU cc_start: 0.7813 (mp0) cc_final: 0.7321 (mp0) REVERT: D 161 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.8469 (m-80) REVERT: Q 19 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7296 (mmp80) REVERT: Q 67 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7663 (mp0) REVERT: C 64 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8180 (p0) REVERT: B 34 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7799 (mp0) REVERT: L 700 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6830 (tpm170) REVERT: M 26 GLN cc_start: 0.6770 (mp-120) cc_final: 0.6396 (mt0) REVERT: M 112 GLU cc_start: 0.8586 (mp0) cc_final: 0.8323 (mp0) REVERT: M 368 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7482 (mp0) outliers start: 54 outliers final: 11 residues processed: 510 average time/residue: 1.0393 time to fit residues: 627.2664 Evaluate side-chains 452 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 435 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 168 ILE 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: 0.7980 chunk 275 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 450 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 426 optimal weight: 0.0980 chunk 375 optimal weight: 4.9990 chunk 444 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 329 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 520 GLN I 157 GLN N 100 ASN ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 GLN q 122 GLN M 499 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.101788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.078957 restraints weight = 38622.688| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 0.99 r_work: 0.2903 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.257 42481 Z= 0.296 Angle : 1.830 50.797 57482 Z= 1.050 Chirality : 0.323 6.478 6232 Planarity : 0.004 0.049 7186 Dihedral : 13.713 179.009 6862 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.41 % Allowed : 8.53 % Favored : 90.06 % 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 aren not related in a simple way. whole: 1.44 (0.12), residues: 5089 helix: 1.73 (0.10), residues: 2781 sheet: 0.50 (0.26), residues: 398 loop : -0.03 (0.15), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 605 TYR 0.024 0.001 TYR L 441 PHE 0.031 0.001 PHE L 350 TRP 0.021 0.001 TRP L 594 HIS 0.007 0.001 HIS N 224 Details of bonding type rmsd covalent geometry : bond 0.00842 (42445) covalent geometry : angle 1.60428 (57398) hydrogen bonds : bond 0.05061 ( 2277) hydrogen bonds : angle 4.79448 ( 6465) metal coordination : bond 0.04361 ( 36) metal coordination : angle 23.06149 ( 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 520 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 462 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: G 312 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7870 (mmtm) REVERT: G 374 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8522 (mtm) REVERT: G 454 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: G 621 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: I 41 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.7945 (mmtp) REVERT: E 219 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8349 (tttm) REVERT: N 146 MET cc_start: 0.8191 (ptm) cc_final: 0.7963 (ptt) REVERT: N 376 MET cc_start: 0.9176 (mmp) cc_final: 0.8860 (mmp) REVERT: N 438 THR cc_start: 0.8448 (p) cc_final: 0.8135 (t) REVERT: H 332 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8252 (mt-10) REVERT: J 54 MET cc_start: 0.8689 (mpp) cc_final: 0.7585 (mpp) REVERT: Q 19 ARG cc_start: 0.7964 (mmm-85) cc_final: 0.7338 (mmp80) REVERT: Q 67 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7641 (mp0) REVERT: Q 73 GLU cc_start: 0.7881 (pt0) cc_final: 0.7583 (pt0) REVERT: C 64 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8158 (p0) REVERT: B 34 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7800 (mp0) REVERT: L 282 TYR cc_start: 0.8269 (m-80) cc_final: 0.7999 (m-80) REVERT: L 700 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6879 (tpm170) REVERT: M 26 GLN cc_start: 0.6757 (mp-120) cc_final: 0.6391 (mt0) REVERT: M 112 GLU cc_start: 0.8568 (mp0) cc_final: 0.8318 (mp0) REVERT: M 368 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: M 452 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7574 (mptt) outliers start: 58 outliers final: 15 residues processed: 496 average time/residue: 0.8885 time to fit residues: 523.4780 Evaluate side-chains 463 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 438 time to evaluate : 1.496 ------------------------------------------------------------------------------- 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 435 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 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 414 SER Chi-restraints excluded: chain H residue 332 GLU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain R residue 38 ASP Chi-restraints excluded: chain R residue 60 ASP 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 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: 5.9990 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 363 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 408 optimal weight: 5.9990 chunk 431 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 465 optimal weight: 6.9990 chunk 471 optimal weight: 1.9990 chunk 400 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 520 GLN I 157 GLN N 271 GLN q 12 ASN q 83 HIS Q 22 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 = 0.3358 r_free = 0.3358 target = 0.100199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.077083 restraints weight = 38244.882| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.06 r_work: 0.2862 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.247 42481 Z= 0.312 Angle : 1.840 50.642 57482 Z= 1.055 Chirality : 0.327 6.562 6232 Planarity : 0.004 0.055 7186 Dihedral : 13.689 177.613 6860 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.67 % Allowed : 9.04 % Favored : 89.28 % 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 aren not related in a simple way. whole: 1.33 (0.12), residues: 5089 helix: 1.65 (0.10), residues: 2786 sheet: 0.38 (0.26), residues: 406 loop : -0.07 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 85 TYR 0.022 0.002 TYR L 597 PHE 0.029 0.002 PHE L 350 TRP 0.022 0.001 TRP L 594 HIS 0.007 0.001 HIS R 28 Details of bonding type rmsd covalent geometry : bond 0.00870 (42445) covalent geometry : angle 1.61766 (57398) hydrogen bonds : bond 0.05513 ( 2277) hydrogen bonds : angle 4.86544 ( 6465) metal coordination : bond 0.04811 ( 36) metal coordination : angle 23.01485 ( 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 517 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 448 time to evaluate : 1.326 Fit side-chains REVERT: G 309 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.8127 (mtm110) REVERT: G 312 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7997 (mmtm) REVERT: G 454 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: G 636 ARG cc_start: 0.7782 (ttm-80) cc_final: 0.7415 (mtp-110) REVERT: t 6 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: I 41 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.7989 (mmtp) REVERT: E 219 LYS cc_start: 0.8638 (ttpp) cc_final: 0.8425 (tttm) REVERT: N 146 MET cc_start: 0.8236 (ptm) cc_final: 0.8021 (ptt) REVERT: H 332 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: D 161 TYR cc_start: 0.9284 (OUTLIER) cc_final: 0.8824 (m-80) REVERT: D 196 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8335 (mm-30) REVERT: D 296 GLN cc_start: 0.7859 (tm130) cc_final: 0.7592 (tm-30) REVERT: Q 19 ARG cc_start: 0.8000 (mmm-85) cc_final: 0.7450 (mmp80) REVERT: Q 73 GLU cc_start: 0.7946 (pt0) cc_final: 0.7629 (pt0) REVERT: B 34 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8008 (mt-10) REVERT: B 102 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.8556 (tppp) REVERT: B 166 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8557 (ttt-90) REVERT: L 198 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: L 208 GLN cc_start: 0.8002 (mt0) cc_final: 0.7787 (mt0) REVERT: L 282 TYR cc_start: 0.8473 (m-80) cc_final: 0.8212 (m-80) REVERT: L 700 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7003 (tpm170) REVERT: M 112 GLU cc_start: 0.8612 (mp0) cc_final: 0.8371 (mp0) REVERT: M 368 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7595 (mp0) outliers start: 69 outliers final: 21 residues processed: 491 average time/residue: 0.8705 time to fit residues: 508.1293 Evaluate side-chains 470 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 437 time to evaluate : 1.623 ------------------------------------------------------------------------------- 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 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 19 LYS 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 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 196 GLU 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 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: 0.0470 chunk 254 optimal weight: 1.9990 chunk 349 optimal weight: 5.9990 chunk 303 optimal weight: 7.9990 chunk 308 optimal weight: 6.9990 chunk 295 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 322 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 357 optimal weight: 1.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 520 GLN N 271 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 = 0.3353 r_free = 0.3353 target = 0.099903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.076817 restraints weight = 37969.175| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.05 r_work: 0.2857 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.2233 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= 0.314 Angle : 1.840 50.644 57482 Z= 1.055 Chirality : 0.328 6.572 6232 Planarity : 0.004 0.057 7186 Dihedral : 13.655 176.907 6858 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.55 % Allowed : 9.70 % Favored : 88.75 % 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 aren not related in a simple way. whole: 1.26 (0.12), residues: 5089 helix: 1.59 (0.10), residues: 2789 sheet: 0.33 (0.26), residues: 406 loop : -0.09 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 640 TYR 0.021 0.002 TYR L 597 PHE 0.030 0.002 PHE L 350 TRP 0.024 0.002 TRP L 594 HIS 0.007 0.001 HIS R 28 Details of bonding type rmsd covalent geometry : bond 0.00874 (42445) covalent geometry : angle 1.61770 (57398) hydrogen bonds : bond 0.05575 ( 2277) hydrogen bonds : angle 4.86907 ( 6465) metal coordination : bond 0.04900 ( 36) metal coordination : angle 22.99888 ( 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 510 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 446 time to evaluate : 1.703 Fit side-chains revert: symmetry clash REVERT: G 312 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8009 (mmtm) REVERT: G 454 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: G 636 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7471 (ttm110) REVERT: t 6 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: I 41 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.7963 (mmtp) REVERT: E 219 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8468 (tttm) REVERT: N 146 MET cc_start: 0.8252 (ptm) cc_final: 0.8046 (ptt) REVERT: H 332 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: D 161 TYR cc_start: 0.9283 (OUTLIER) cc_final: 0.8818 (m-80) REVERT: D 196 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8329 (mm-30) REVERT: D 296 GLN cc_start: 0.7870 (tm130) cc_final: 0.7600 (tm-30) REVERT: A 50 ASN cc_start: 0.9020 (m-40) cc_final: 0.8711 (m-40) REVERT: J 146 MET cc_start: 0.8861 (mmp) cc_final: 0.8506 (mmp) REVERT: Q 19 ARG cc_start: 0.7973 (mmm-85) cc_final: 0.7371 (mmp80) REVERT: C 64 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8424 (p0) REVERT: B 34 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8014 (mt-10) REVERT: B 102 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.8510 (tppp) REVERT: B 166 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8561 (ttt-90) REVERT: L 198 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: L 208 GLN cc_start: 0.8048 (mt0) cc_final: 0.7818 (mt0) REVERT: L 282 TYR cc_start: 0.8488 (m-80) cc_final: 0.8199 (m-80) REVERT: L 700 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6995 (tpm170) REVERT: M 112 GLU cc_start: 0.8603 (mp0) cc_final: 0.8358 (mp0) REVERT: M 368 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7608 (mp0) outliers start: 64 outliers final: 28 residues processed: 490 average time/residue: 0.9316 time to fit residues: 543.1481 Evaluate side-chains 478 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 437 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 430 SER 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 19 LYS 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 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 196 GLU Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 313 THR 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 R residue 60 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 469 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 269 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 359 optimal weight: 2.9990 chunk 195 optimal weight: 0.4980 chunk 63 optimal weight: 8.9990 chunk 397 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 201 GLN N 323 ASN 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 = 0.3379 r_free = 0.3379 target = 0.101537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.078714 restraints weight = 38490.873| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 0.98 r_work: 0.2901 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2374 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= 0.293 Angle : 1.829 50.616 57482 Z= 1.049 Chirality : 0.325 6.483 6232 Planarity : 0.004 0.054 7186 Dihedral : 13.285 177.160 6858 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.38 % Allowed : 10.35 % Favored : 88.27 % 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 aren not related in a simple way. whole: 1.40 (0.12), residues: 5089 helix: 1.74 (0.10), residues: 2784 sheet: 0.39 (0.26), residues: 400 loop : -0.08 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 640 TYR 0.024 0.001 TYR L 426 PHE 0.031 0.001 PHE L 350 TRP 0.024 0.001 TRP L 594 HIS 0.006 0.001 HIS N 224 Details of bonding type rmsd covalent geometry : bond 0.00834 (42445) covalent geometry : angle 1.60246 (57398) hydrogen bonds : bond 0.04838 ( 2277) hydrogen bonds : angle 4.71840 ( 6465) metal coordination : bond 0.03655 ( 36) metal coordination : angle 23.09376 ( 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 510 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 453 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 1 MET cc_start: 0.6407 (tpp) cc_final: 0.6204 (tpt) REVERT: G 281 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7953 (mtp85) REVERT: G 312 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.8001 (mmtm) REVERT: G 454 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: G 636 ARG cc_start: 0.7651 (ttm-80) cc_final: 0.7445 (ttm110) REVERT: I 41 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.7933 (mmtp) REVERT: H 252 TYR cc_start: 0.9346 (OUTLIER) cc_final: 0.8389 (t80) REVERT: H 332 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8314 (mt-10) REVERT: D 161 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.8788 (m-80) REVERT: D 196 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8286 (mm-30) REVERT: D 296 GLN cc_start: 0.7859 (tm130) cc_final: 0.7610 (tm-30) REVERT: A 50 ASN cc_start: 0.9007 (m-40) cc_final: 0.8692 (m-40) REVERT: Q 19 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7399 (mmp80) REVERT: C 64 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8344 (p0) REVERT: B 34 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8026 (mt-10) REVERT: B 102 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.8506 (tppp) REVERT: B 166 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8517 (ttt-90) REVERT: L 208 GLN cc_start: 0.8089 (mt0) cc_final: 0.7888 (mt0) REVERT: L 214 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7395 (ptm) REVERT: L 278 MET cc_start: 0.8895 (mmm) cc_final: 0.8589 (mmm) REVERT: L 282 TYR cc_start: 0.8472 (m-80) cc_final: 0.8167 (m-80) REVERT: L 601 PRO cc_start: 0.7250 (Cg_exo) cc_final: 0.6881 (Cg_endo) REVERT: L 700 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7033 (tpm170) REVERT: M 1 MET cc_start: 0.5726 (tpp) cc_final: 0.4968 (tpp) REVERT: M 112 GLU cc_start: 0.8555 (mp0) cc_final: 0.8340 (mp0) REVERT: M 368 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7622 (mp0) outliers start: 57 outliers final: 20 residues processed: 491 average time/residue: 0.9901 time to fit residues: 579.1364 Evaluate side-chains 474 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 440 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 96 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 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 98 THR Chi-restraints excluded: chain N residue 59 VAL 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 196 GLU Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain A residue 75 LEU 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 B residue 166 ARG Chi-restraints excluded: chain L residue 36 LEU 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 212 THR Chi-restraints excluded: chain M residue 368 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 475 optimal weight: 6.9990 chunk 476 optimal weight: 0.9990 chunk 436 optimal weight: 7.9990 chunk 380 optimal weight: 3.9990 chunk 321 optimal weight: 0.9990 chunk 353 optimal weight: 8.9990 chunk 369 optimal weight: 5.9990 chunk 300 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 336 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 520 GLN E 36 GLN N 323 ASN L 366 HIS M 33 ASN M 499 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.100288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.077123 restraints weight = 38363.571| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.07 r_work: 0.2863 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2351 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= 0.310 Angle : 1.838 50.593 57482 Z= 1.054 Chirality : 0.327 6.556 6232 Planarity : 0.004 0.056 7186 Dihedral : 13.351 175.445 6858 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.58 % Allowed : 10.38 % Favored : 88.05 % 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 aren not related in a simple way. whole: 1.34 (0.12), residues: 5089 helix: 1.66 (0.10), residues: 2789 sheet: 0.38 (0.26), residues: 396 loop : -0.06 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 58 TYR 0.024 0.002 TYR J 60 PHE 0.030 0.002 PHE L 350 TRP 0.025 0.001 TRP L 594 HIS 0.007 0.001 HIS R 28 Details of bonding type rmsd covalent geometry : bond 0.00866 (42445) covalent geometry : angle 1.61475 (57398) hydrogen bonds : bond 0.05373 ( 2277) hydrogen bonds : angle 4.80402 ( 6465) metal coordination : bond 0.04689 ( 36) metal coordination : angle 23.00080 ( 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 509 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 444 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 1 MET cc_start: 0.6522 (tpp) cc_final: 0.6320 (tpt) REVERT: G 281 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8018 (mtp85) REVERT: G 312 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8014 (mmtm) REVERT: G 454 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: G 636 ARG cc_start: 0.7672 (ttm-80) cc_final: 0.7466 (ttm110) REVERT: I 41 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.7959 (mmtp) REVERT: H 252 TYR cc_start: 0.9367 (OUTLIER) cc_final: 0.8326 (t80) REVERT: H 332 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: D 161 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.8821 (m-80) REVERT: D 196 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8348 (mm-30) REVERT: D 296 GLN cc_start: 0.7888 (tm130) cc_final: 0.7619 (tm-30) REVERT: q 4 LEU cc_start: 0.7828 (mm) cc_final: 0.7516 (tp) REVERT: A 50 ASN cc_start: 0.9015 (m-40) cc_final: 0.8696 (m-40) REVERT: J 146 MET cc_start: 0.8864 (mmp) cc_final: 0.8514 (mmp) REVERT: Q 19 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7361 (mmp80) REVERT: C 64 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8443 (p0) REVERT: B 34 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8043 (mt-10) REVERT: B 102 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.8506 (tppp) REVERT: B 166 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8558 (ttt-90) REVERT: L 208 GLN cc_start: 0.8107 (mt0) cc_final: 0.7888 (mt0) REVERT: L 278 MET cc_start: 0.8938 (mmm) cc_final: 0.8577 (mmm) REVERT: L 282 TYR cc_start: 0.8487 (m-80) cc_final: 0.8242 (m-80) REVERT: L 453 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6717 (tppt) REVERT: L 601 PRO cc_start: 0.7264 (Cg_exo) cc_final: 0.6890 (Cg_endo) REVERT: L 700 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7010 (tpm170) REVERT: M 1 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.5189 (tmm) REVERT: M 112 GLU cc_start: 0.8583 (mp0) cc_final: 0.8340 (mp0) REVERT: M 368 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: M 495 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8087 (tt0) outliers start: 65 outliers final: 26 residues processed: 492 average time/residue: 0.9801 time to fit residues: 573.1373 Evaluate side-chains 476 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 434 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 96 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 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 19 LYS 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 59 VAL Chi-restraints excluded: chain N residue 426 TYR Chi-restraints excluded: chain H residue 66 LEU 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 196 GLU Chi-restraints excluded: chain D residue 269 ARG 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 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 B residue 166 ARG Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 355 PHE Chi-restraints excluded: chain L residue 405 LEU 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 1 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 100 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 338 optimal weight: 0.9990 chunk 293 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 166 optimal weight: 0.6980 chunk 484 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 446 optimal weight: 9.9990 chunk 13 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 323 ASN L 366 HIS M 33 ASN M 499 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.079854 restraints weight = 38378.505| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 0.98 r_work: 0.2923 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.253 42481 Z= 0.288 Angle : 1.829 50.778 57482 Z= 1.048 Chirality : 0.323 6.440 6232 Planarity : 0.004 0.053 7186 Dihedral : 12.942 175.925 6858 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.04 % Allowed : 10.96 % Favored : 88.00 % 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 aren not related in a simple way. whole: 1.51 (0.12), residues: 5089 helix: 1.84 (0.10), residues: 2779 sheet: 0.36 (0.26), residues: 396 loop : -0.04 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 163 TYR 0.023 0.001 TYR M 433 PHE 0.033 0.001 PHE L 350 TRP 0.025 0.001 TRP L 594 HIS 0.007 0.001 HIS N 224 Details of bonding type rmsd covalent geometry : bond 0.00825 (42445) covalent geometry : angle 1.59989 (57398) hydrogen bonds : bond 0.04516 ( 2277) hydrogen bonds : angle 4.63513 ( 6465) metal coordination : bond 0.03234 ( 36) metal coordination : angle 23.26433 ( 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 503 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 460 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 281 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7964 (mtp85) REVERT: G 312 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.8001 (mmtm) REVERT: G 454 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: H 252 TYR cc_start: 0.9290 (OUTLIER) cc_final: 0.8251 (t80) REVERT: H 332 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8357 (mt-10) REVERT: D 161 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8857 (m-80) REVERT: D 196 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8268 (mm-30) REVERT: q 4 LEU cc_start: 0.7811 (mm) cc_final: 0.7511 (tp) REVERT: A 50 ASN cc_start: 0.8996 (m-40) cc_final: 0.8673 (m-40) REVERT: Q 19 ARG cc_start: 0.7931 (mmm-85) cc_final: 0.7335 (mmp80) REVERT: C 64 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8317 (p0) REVERT: B 34 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 102 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.8497 (tppp) REVERT: B 166 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8504 (ttt-90) REVERT: L 278 MET cc_start: 0.8885 (mmm) cc_final: 0.8674 (mmm) REVERT: L 282 TYR cc_start: 0.8461 (m-80) cc_final: 0.8175 (m-80) REVERT: L 453 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6706 (tppt) REVERT: L 601 PRO cc_start: 0.7288 (Cg_exo) cc_final: 0.6917 (Cg_endo) REVERT: L 700 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7049 (tpm170) REVERT: M 368 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7639 (mp0) outliers start: 43 outliers final: 20 residues processed: 488 average time/residue: 0.9181 time to fit residues: 533.0495 Evaluate side-chains 477 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 444 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 96 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 G residue 454 GLU Chi-restraints excluded: chain t residue 6 GLN Chi-restraints excluded: chain t residue 92 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain N residue 59 VAL 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 196 GLU Chi-restraints excluded: chain D residue 269 ARG 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 B residue 166 ARG Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 405 LEU 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: 1.9990 chunk 250 optimal weight: 3.9990 chunk 471 optimal weight: 0.9980 chunk 10 optimal weight: 0.0060 chunk 19 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 362 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 366 HIS M 499 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.101575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.078706 restraints weight = 38176.809| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 0.98 r_work: 0.2901 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2484 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= 0.297 Angle : 1.832 50.735 57482 Z= 1.050 Chirality : 0.326 6.508 6232 Planarity : 0.004 0.053 7186 Dihedral : 12.928 174.828 6858 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.19 % Allowed : 11.32 % Favored : 87.49 % 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 aren not related in a simple way. whole: 1.46 (0.12), residues: 5089 helix: 1.79 (0.10), residues: 2786 sheet: 0.34 (0.26), residues: 407 loop : -0.04 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 421 TYR 0.023 0.002 TYR J 60 PHE 0.031 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 covalent geometry : bond 0.00843 (42445) covalent geometry : angle 1.60620 (57398) hydrogen bonds : bond 0.04873 ( 2277) hydrogen bonds : angle 4.67762 ( 6465) metal coordination : bond 0.04160 ( 36) metal coordination : angle 23.11466 ( 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 491 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 442 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 281 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8015 (mtp85) REVERT: G 309 ARG cc_start: 0.8538 (mtm-85) cc_final: 0.8120 (mtm110) REVERT: G 312 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8031 (mmtm) REVERT: G 454 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: I 41 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.7953 (mmtp) REVERT: H 252 TYR cc_start: 0.9335 (OUTLIER) cc_final: 0.8234 (t80) REVERT: H 332 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: D 161 TYR cc_start: 0.9244 (OUTLIER) cc_final: 0.8878 (m-80) REVERT: D 196 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8280 (mm-30) REVERT: D 296 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7943 (tm130) REVERT: q 4 LEU cc_start: 0.7834 (mm) cc_final: 0.7541 (tp) REVERT: A 50 ASN cc_start: 0.9007 (m-40) cc_final: 0.8691 (m-40) REVERT: J 146 MET cc_start: 0.8836 (mmp) cc_final: 0.8477 (mmp) REVERT: Q 19 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7333 (mmp80) REVERT: C 64 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8359 (p0) REVERT: B 102 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.8499 (tppp) REVERT: B 166 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8528 (ttt-90) REVERT: L 278 MET cc_start: 0.8902 (mmm) cc_final: 0.8583 (mmm) REVERT: L 282 TYR cc_start: 0.8480 (m-80) cc_final: 0.8199 (m-80) REVERT: L 453 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6717 (tppt) REVERT: L 601 PRO cc_start: 0.7276 (Cg_exo) cc_final: 0.6903 (Cg_endo) REVERT: L 700 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7080 (tpm170) REVERT: M 1 MET cc_start: 0.5597 (tpp) cc_final: 0.4778 (tmm) REVERT: M 368 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7654 (mp0) outliers start: 49 outliers final: 22 residues processed: 476 average time/residue: 0.7961 time to fit residues: 449.8291 Evaluate side-chains 473 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 437 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 96 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 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 98 THR Chi-restraints excluded: chain N residue 59 VAL 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 196 GLU Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 313 THR 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 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 B residue 166 ARG Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 355 PHE Chi-restraints excluded: chain L residue 405 LEU 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: 3.9990 chunk 370 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 498 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 138 optimal weight: 9.9990 chunk 214 optimal weight: 0.7980 chunk 419 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 271 GLN D 296 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 = 0.3364 r_free = 0.3364 target = 0.100608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.077639 restraints weight = 38175.875| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 0.98 r_work: 0.2881 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2449 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= 0.308 Angle : 1.840 50.703 57482 Z= 1.054 Chirality : 0.327 6.538 6232 Planarity : 0.004 0.054 7186 Dihedral : 13.070 173.240 6858 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.97 % Allowed : 11.59 % Favored : 87.44 % 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 aren not related in a simple way. whole: 1.38 (0.12), residues: 5089 helix: 1.71 (0.10), residues: 2785 sheet: 0.30 (0.26), residues: 407 loop : -0.06 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 421 TYR 0.029 0.002 TYR J 60 PHE 0.030 0.002 PHE L 350 TRP 0.029 0.001 TRP L 594 HIS 0.007 0.001 HIS R 28 Details of bonding type rmsd covalent geometry : bond 0.00863 (42445) covalent geometry : angle 1.61610 (57398) hydrogen bonds : bond 0.05284 ( 2277) hydrogen bonds : angle 4.76399 ( 6465) metal coordination : bond 0.04822 ( 36) metal coordination : angle 23.06227 ( 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 479 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 439 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 281 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7988 (mtp85) REVERT: G 309 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8119 (mtm110) REVERT: G 312 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8024 (mmtm) REVERT: G 454 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: G 636 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7522 (mtp85) REVERT: I 41 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.7956 (mmtp) REVERT: H 252 TYR cc_start: 0.9368 (OUTLIER) cc_final: 0.8324 (t80) REVERT: H 332 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: D 161 TYR cc_start: 0.9280 (OUTLIER) cc_final: 0.8915 (m-80) REVERT: D 196 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8294 (mm-30) REVERT: D 296 GLN cc_start: 0.8245 (tm130) cc_final: 0.7974 (tm130) REVERT: q 4 LEU cc_start: 0.7848 (mm) cc_final: 0.7545 (tp) REVERT: q 45 LYS cc_start: 0.9157 (tttm) cc_final: 0.8916 (tmtt) REVERT: A 50 ASN cc_start: 0.9017 (m-40) cc_final: 0.8698 (m-40) REVERT: J 146 MET cc_start: 0.8851 (mmp) cc_final: 0.8507 (mmp) REVERT: Q 19 ARG cc_start: 0.7956 (mmm-85) cc_final: 0.7383 (mmp80) REVERT: C 64 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8400 (p0) REVERT: B 102 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.8493 (tppp) REVERT: B 166 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8532 (ttt-90) REVERT: L 278 MET cc_start: 0.8942 (mmm) cc_final: 0.8591 (mmm) REVERT: L 282 TYR cc_start: 0.8483 (m-80) cc_final: 0.8249 (m-80) REVERT: L 453 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6717 (tppt) REVERT: L 601 PRO cc_start: 0.7297 (Cg_exo) cc_final: 0.6928 (Cg_endo) REVERT: L 700 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7083 (tpm170) REVERT: M 1 MET cc_start: 0.5597 (tpp) cc_final: 0.4824 (tmm) REVERT: M 112 GLU cc_start: 0.8544 (mp0) cc_final: 0.8324 (mp0) REVERT: M 368 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7726 (mp0) outliers start: 40 outliers final: 22 residues processed: 466 average time/residue: 0.8739 time to fit residues: 484.1777 Evaluate side-chains 476 residues out of total 4125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 440 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 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 19 LYS 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 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 196 GLU Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 313 THR 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 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 B residue 166 ARG Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 355 PHE Chi-restraints excluded: chain L residue 405 LEU 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: 6.9990 chunk 218 optimal weight: 9.9990 chunk 441 optimal weight: 7.9990 chunk 305 optimal weight: 7.9990 chunk 290 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 343 optimal weight: 6.9990 chunk 468 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 302 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 449 GLN I 157 GLN N 271 GLN N 323 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 = 0.3358 r_free = 0.3358 target = 0.100092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.077062 restraints weight = 38677.186| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.00 r_work: 0.2872 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2420 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= 0.320 Angle : 1.846 50.689 57482 Z= 1.057 Chirality : 0.328 6.571 6232 Planarity : 0.004 0.055 7186 Dihedral : 13.283 175.418 6858 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.07 % Allowed : 11.64 % Favored : 87.30 % 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 aren not related in a simple way. whole: 1.28 (0.12), residues: 5089 helix: 1.62 (0.10), residues: 2789 sheet: 0.33 (0.26), residues: 398 loop : -0.10 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 636 TYR 0.028 0.002 TYR J 60 PHE 0.029 0.002 PHE L 350 TRP 0.029 0.002 TRP L 594 HIS 0.007 0.001 HIS R 28 Details of bonding type rmsd covalent geometry : bond 0.00885 (42445) covalent geometry : angle 1.62401 (57398) hydrogen bonds : bond 0.05595 ( 2277) hydrogen bonds : angle 4.84886 ( 6465) metal coordination : bond 0.05263 ( 36) metal coordination : angle 23.00172 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21042.17 seconds wall clock time: 357 minutes 56.57 seconds (21476.57 seconds total)