Starting phenix.real_space_refine on Sat Dec 16 16:18:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of0_12865/12_2023/7of0_12865.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of0_12865/12_2023/7of0_12865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of0_12865/12_2023/7of0_12865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of0_12865/12_2023/7of0_12865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of0_12865/12_2023/7of0_12865.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of0_12865/12_2023/7of0_12865.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1432 5.49 5 Mg 61 5.21 5 S 305 5.16 5 C 57703 2.51 5 N 18030 2.21 5 O 21942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "7 PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 99476 Number of models: 1 Model: "" Number of chains: 62 Chain: "0" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 880 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "1" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "3" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 831 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "4" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 333 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "5" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3199 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 359} Chain: "6" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2723 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 28, 'TRANS': 295} Chain breaks: 3 Chain: "7" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2334 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 17, 'TRANS': 269} Chain: "8" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 651 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "9" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 107} Chain breaks: 1 Chain: "A" Number of atoms: 29219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1376, 29219 Classifications: {'RNA': 1376} Modifications used: {'rna2p_pur': 143, 'rna2p_pyr': 112, 'rna3p_pur': 584, 'rna3p_pyr': 537} Link IDs: {'rna2p': 254, 'rna3p': 1121} Chain breaks: 18 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1191 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 29, 'rna3p_pyr': 26} Link IDs: {'rna2p': 1, 'rna3p': 54} Chain breaks: 4 Chain: "C" Number of atoms: 2595 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2590 Classifications: {'peptide': 327} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 311} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2590 Classifications: {'peptide': 327} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 311} Chain breaks: 1 bond proxies already assigned to first conformer: 2641 Chain: "D" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1872 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 13, 'TRANS': 226} Chain: "E" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2427 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 24, 'TRANS': 283} Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "G" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1943 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1228 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 11, 'TRANS': 139} Chain breaks: 1 Chain: "J" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1061 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain: "K" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1451 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 889 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "M" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2305 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 26, 'TRANS': 260} Chain: "N" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1494 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 13, 'TRANS': 169} Chain breaks: 2 Chain: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1245 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain: "P" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1148 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 134} Chain: "Q" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1805 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 14, 'TRANS': 202} Chain: "R" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 971 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "S" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "T" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1368 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 12, 'TRANS': 153} Chain: "U" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1154 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain breaks: 1 Chain: "V" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 395 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "W" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 801 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "X" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2035 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} Chain: "Y" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1517 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "Z" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 937 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 10, 'TRANS': 104} Chain: "a" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 597 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 8, 'TRANS': 62} Chain breaks: 1 Chain: "b" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1178 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "c" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2217 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 258} Chain breaks: 1 Chain: "d" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1653 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 18, 'TRANS': 180} Chain breaks: 4 Chain: "e" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1599 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 9, 'TRANS': 187} Chain breaks: 2 Chain: "f" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 857 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 113} Chain: "h" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 862 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain breaks: 1 Chain: "i" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 827 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "j" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain: "k" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 627 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "m" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 245 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "o" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 676 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "p" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1058 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 3 Chain: "q" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1076 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 14, 'TRANS': 113} Chain: "r" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1203 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 16, 'TRANS': 129} Chain breaks: 2 Chain: "s" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3036 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain breaks: 1 Chain: "u" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 927 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 588 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "w" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Unusual residues: {' MG': 59} Classifications: {'undetermined': 59} Link IDs: {None: 58} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 264 SG CYS 0 110 143.883 38.009 126.810 1.00 91.34 S ATOM 286 SG CYS 0 113 147.131 38.651 125.259 1.00 97.52 S ATOM 366 SG CYS 0 123 144.395 41.340 124.846 1.00 78.86 S ATOM 389 SG CYS 0 126 144.698 38.147 122.829 1.00 84.94 S ATOM 2605 SG CYS 4 76 65.118 106.248 169.625 1.00134.76 S ATOM 2628 SG CYS 4 79 68.843 106.203 168.857 1.00121.78 S ATOM 2752 SG CYS 4 92 66.618 103.037 168.534 1.00116.10 S ATOM 54974 SG CYS I 64 91.987 112.198 197.480 1.00136.36 S ATOM 93255 SG CYS r 70 90.546 108.771 199.126 1.00117.98 S ATOM 93276 SG CYS r 73 92.520 110.697 199.919 1.00117.44 S ATOM 93570 SG CYS r 108 89.445 110.307 196.939 1.00105.25 S Time building chain proxies: 43.07, per 1000 atoms: 0.43 Number of scatterers: 99476 At special positions: 0 Unit cell: (235.2, 236.25, 227.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 305 16.00 P 1432 15.00 Mg 61 11.99 O 21942 8.00 N 18030 7.00 C 57703 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 - 3.50 Amino acid : False - 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: 35.51 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb=" ZN 4 200 " pdb="ZN ZN 4 200 " - pdb=" ND1 HIS 4 98 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 76 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 92 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 79 " pdb=" ZN r 301 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 73 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 108 " pdb="ZN ZN r 301 " - pdb=" SG CYS I 64 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 70 " Number of angles added : 15 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15960 Finding SS restraints... Secondary structure from input PDB file: 337 helices and 84 sheets defined 42.8% alpha, 15.0% beta 383 base pairs and 746 stacking pairs defined. Time for finding SS restraints: 31.75 Creating SS restraints... Processing helix chain '0' and resid 86 through 95 Processing helix chain '0' and resid 123 through 146 Processing helix chain '2' and resid 56 through 65 Processing helix chain '2' and resid 65 through 71 Processing helix chain '2' and resid 72 through 86 Processing helix chain '3' and resid 107 through 112 removed outlier: 3.679A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 136 Processing helix chain '3' and resid 137 through 145 Processing helix chain '3' and resid 151 through 162 Processing helix chain '3' and resid 163 through 168 removed outlier: 3.683A pdb=" N ARG 3 168 " --> pdb=" O PHE 3 165 " (cutoff:3.500A) Processing helix chain '3' and resid 178 through 182 removed outlier: 3.807A pdb=" N ASP 3 182 " --> pdb=" O LYS 3 179 " (cutoff:3.500A) Processing helix chain '4' and resid 95 through 98 Processing helix chain '5' and resid 47 through 52 Processing helix chain '5' and resid 84 through 88 removed outlier: 3.877A pdb=" N TYR 5 88 " --> pdb=" O PRO 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 92 through 96 Processing helix chain '5' and resid 116 through 125 Processing helix chain '5' and resid 133 through 138 Processing helix chain '5' and resid 139 through 141 No H-bonds generated for 'chain '5' and resid 139 through 141' Processing helix chain '5' and resid 149 through 163 Processing helix chain '5' and resid 172 through 190 Proline residue: 5 178 - end of helix Processing helix chain '5' and resid 191 through 193 No H-bonds generated for 'chain '5' and resid 191 through 193' Processing helix chain '5' and resid 195 through 199 Processing helix chain '5' and resid 241 through 248 Processing helix chain '5' and resid 305 through 329 Processing helix chain '5' and resid 407 through 420 removed outlier: 3.940A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 67 removed outlier: 3.818A pdb=" N TYR 6 57 " --> pdb=" O SER 6 53 " (cutoff:3.500A) Processing helix chain '6' and resid 73 through 79 removed outlier: 3.844A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 100 through 116 Processing helix chain '6' and resid 116 through 125 Processing helix chain '6' and resid 131 through 143 Processing helix chain '6' and resid 143 through 155 Processing helix chain '6' and resid 156 through 162 Processing helix chain '6' and resid 292 through 296 Processing helix chain '6' and resid 299 through 306 Processing helix chain '6' and resid 324 through 334 removed outlier: 3.573A pdb=" N THR 6 328 " --> pdb=" O ASP 6 324 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU 6 334 " --> pdb=" O ILE 6 330 " (cutoff:3.500A) Processing helix chain '6' and resid 363 through 370 removed outlier: 4.268A pdb=" N ASP 6 367 " --> pdb=" O LEU 6 363 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 59 Processing helix chain '7' and resid 87 through 96 Processing helix chain '7' and resid 96 through 103 Processing helix chain '7' and resid 135 through 158 removed outlier: 4.021A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 173 through 177 Processing helix chain '7' and resid 186 through 190 Processing helix chain '7' and resid 195 through 213 Processing helix chain '7' and resid 223 through 230 Processing helix chain '7' and resid 233 through 247 Processing helix chain '7' and resid 271 through 273 No H-bonds generated for 'chain '7' and resid 271 through 273' Processing helix chain '7' and resid 305 through 307 No H-bonds generated for 'chain '7' and resid 305 through 307' Processing helix chain '7' and resid 309 through 321 Processing helix chain '8' and resid 107 through 154 Processing helix chain '8' and resid 157 through 162 removed outlier: 3.642A pdb=" N ILE 8 162 " --> pdb=" O HIS 8 158 " (cutoff:3.500A) Processing helix chain '9' and resid 27 through 34 Processing helix chain '9' and resid 46 through 48 No H-bonds generated for 'chain '9' and resid 46 through 48' Processing helix chain '9' and resid 54 through 57 Processing helix chain '9' and resid 87 through 96 Processing helix chain '9' and resid 96 through 106 removed outlier: 3.576A pdb=" N ASP 9 106 " --> pdb=" O LYS 9 102 " (cutoff:3.500A) Processing helix chain '9' and resid 114 through 118 Processing helix chain 'C' and resid 39 through 57 removed outlier: 3.829A pdb=" N SER C 53 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL C 54 " --> pdb=" O MET C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.627A pdb=" N ILE C 103 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N HIS C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 162 Processing helix chain 'C' and resid 163 through 170 removed outlier: 3.947A pdb=" N GLY C 170 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 193 Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 222 through 228 removed outlier: 3.739A pdb=" N GLY C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 245 removed outlier: 4.095A pdb=" N GLY C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 267 Processing helix chain 'C' and resid 274 through 276 No H-bonds generated for 'chain 'C' and resid 274 through 276' Processing helix chain 'C' and resid 277 through 298 Proline residue: C 285 - end of helix Processing helix chain 'C' and resid 313 through 331 removed outlier: 3.783A pdb=" N TYR C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL C 320 " --> pdb=" O GLN C 316 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 348 Processing helix chain 'D' and resid 185 through 187 No H-bonds generated for 'chain 'D' and resid 185 through 187' Processing helix chain 'D' and resid 249 through 255 removed outlier: 4.296A pdb=" N ASN D 253 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 255 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 267 removed outlier: 3.798A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 296 removed outlier: 4.143A pdb=" N SER D 294 " --> pdb=" O PRO D 291 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 296 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 75 removed outlier: 3.734A pdb=" N PHE E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 77 No H-bonds generated for 'chain 'E' and resid 76 through 77' Processing helix chain 'E' and resid 78 through 82 Processing helix chain 'E' and resid 153 through 157 removed outlier: 3.511A pdb=" N ARG E 156 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS E 157 " --> pdb=" O ARG E 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 157' Processing helix chain 'E' and resid 158 through 169 Processing helix chain 'E' and resid 182 through 186 Processing helix chain 'E' and resid 194 through 198 Processing helix chain 'E' and resid 217 through 223 Processing helix chain 'E' and resid 304 through 308 Processing helix chain 'E' and resid 320 through 324 Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 107 removed outlier: 4.662A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 184 Processing helix chain 'F' and resid 199 through 210 removed outlier: 3.621A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 236 removed outlier: 3.912A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 248 No H-bonds generated for 'chain 'F' and resid 246 through 248' Processing helix chain 'F' and resid 249 through 256 Processing helix chain 'F' and resid 263 through 277 removed outlier: 3.753A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 101 Processing helix chain 'G' and resid 105 through 116 Processing helix chain 'G' and resid 120 through 134 Processing helix chain 'G' and resid 137 through 148 Processing helix chain 'G' and resid 149 through 154 Processing helix chain 'G' and resid 155 through 170 Processing helix chain 'G' and resid 174 through 183 removed outlier: 4.293A pdb=" N ARG G 178 " --> pdb=" O GLY G 174 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL G 179 " --> pdb=" O LYS G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 188 removed outlier: 4.165A pdb=" N PHE G 187 " --> pdb=" O PRO G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 203 Processing helix chain 'G' and resid 208 through 219 Processing helix chain 'G' and resid 220 through 225 removed outlier: 3.926A pdb=" N ARG G 224 " --> pdb=" O PRO G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 239 Processing helix chain 'G' and resid 244 through 251 Processing helix chain 'G' and resid 252 through 256 Processing helix chain 'G' and resid 257 through 271 removed outlier: 3.514A pdb=" N TYR G 267 " --> pdb=" O GLN G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 294 Processing helix chain 'G' and resid 297 through 304 Processing helix chain 'G' and resid 309 through 328 Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 116 through 122 Processing helix chain 'H' and resid 133 through 147 Processing helix chain 'I' and resid 41 through 51 Processing helix chain 'I' and resid 78 through 93 removed outlier: 3.700A pdb=" N GLN I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 118 Processing helix chain 'I' and resid 127 through 138 Proline residue: I 133 - end of helix removed outlier: 3.859A pdb=" N GLU I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 147 removed outlier: 3.823A pdb=" N PHE I 147 " --> pdb=" O LEU I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 170 removed outlier: 3.718A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 197 Processing helix chain 'J' and resid 35 through 41 removed outlier: 3.887A pdb=" N GLN J 41 " --> pdb=" O PRO J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 60 Processing helix chain 'J' and resid 87 through 95 Processing helix chain 'J' and resid 114 through 123 removed outlier: 4.199A pdb=" N ILE J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 151 removed outlier: 4.030A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER J 143 " --> pdb=" O SER J 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 27 through 41 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 92 through 99 Processing helix chain 'K' and resid 101 through 112 Processing helix chain 'K' and resid 117 through 124 Processing helix chain 'K' and resid 134 through 141 Processing helix chain 'K' and resid 159 through 166 Processing helix chain 'L' and resid 44 through 49 Processing helix chain 'L' and resid 124 through 128 Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'M' and resid 11 through 19 Processing helix chain 'M' and resid 55 through 60 Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.540A pdb=" N ILE M 78 " --> pdb=" O PHE M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'M' and resid 98 through 107 Processing helix chain 'M' and resid 117 through 124 Processing helix chain 'M' and resid 130 through 133 Processing helix chain 'M' and resid 144 through 148 Processing helix chain 'M' and resid 160 through 170 Processing helix chain 'M' and resid 180 through 189 Processing helix chain 'M' and resid 189 through 196 removed outlier: 3.628A pdb=" N PHE M 193 " --> pdb=" O LYS M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 216 Processing helix chain 'M' and resid 225 through 227 No H-bonds generated for 'chain 'M' and resid 225 through 227' Processing helix chain 'M' and resid 228 through 241 Processing helix chain 'M' and resid 246 through 250 Processing helix chain 'M' and resid 252 through 258 Processing helix chain 'M' and resid 287 through 296 Processing helix chain 'N' and resid 99 through 112 removed outlier: 4.053A pdb=" N SER N 112 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 183 removed outlier: 3.821A pdb=" N VAL N 172 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 209 Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 223 through 229 removed outlier: 6.003A pdb=" N ARG N 227 " --> pdb=" O LEU N 224 " (cutoff:3.500A) Processing helix chain 'N' and resid 231 through 238 removed outlier: 3.841A pdb=" N LEU N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR N 236 " --> pdb=" O PRO N 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 40 Processing helix chain 'O' and resid 46 through 66 removed outlier: 4.419A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 80 Processing helix chain 'O' and resid 84 through 92 removed outlier: 3.884A pdb=" N LYS O 88 " --> pdb=" O ASP O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 98 Processing helix chain 'O' and resid 143 through 160 Processing helix chain 'P' and resid 54 through 59 Processing helix chain 'P' and resid 109 through 114 Processing helix chain 'P' and resid 121 through 140 Processing helix chain 'P' and resid 149 through 155 Processing helix chain 'P' and resid 155 through 169 Processing helix chain 'Q' and resid 77 through 81 Processing helix chain 'Q' and resid 88 through 104 removed outlier: 3.798A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 146 removed outlier: 3.922A pdb=" N GLY Q 146 " --> pdb=" O ARG Q 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 143 through 146' Processing helix chain 'Q' and resid 187 through 192 Processing helix chain 'Q' and resid 194 through 198 Processing helix chain 'Q' and resid 244 through 249 removed outlier: 3.860A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 258 Processing helix chain 'Q' and resid 259 through 261 No H-bonds generated for 'chain 'Q' and resid 259 through 261' Processing helix chain 'Q' and resid 262 through 267 removed outlier: 3.616A pdb=" N GLU Q 266 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 268 through 272 removed outlier: 3.533A pdb=" N GLU Q 272 " --> pdb=" O MET Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 290 Processing helix chain 'R' and resid 16 through 29 removed outlier: 3.946A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 37 removed outlier: 3.686A pdb=" N LYS R 35 " --> pdb=" O ARG R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 78 removed outlier: 4.079A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS R 61 " --> pdb=" O ARG R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing helix chain 'R' and resid 98 through 109 Processing helix chain 'R' and resid 109 through 125 Processing helix chain 'S' and resid 68 through 90 Processing helix chain 'T' and resid 49 through 54 removed outlier: 3.704A pdb=" N LYS T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 57 No H-bonds generated for 'chain 'T' and resid 55 through 57' Processing helix chain 'T' and resid 83 through 95 removed outlier: 4.083A pdb=" N TYR T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 108 removed outlier: 3.800A pdb=" N PHE T 108 " --> pdb=" O ALA T 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 132 removed outlier: 4.192A pdb=" N LYS T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 205 Processing helix chain 'U' and resid 49 through 61 Processing helix chain 'U' and resid 127 through 136 Processing helix chain 'U' and resid 141 through 145 Processing helix chain 'V' and resid 178 through 184 Processing helix chain 'V' and resid 193 through 203 Processing helix chain 'W' and resid 110 through 119 Processing helix chain 'X' and resid 7 through 9 No H-bonds generated for 'chain 'X' and resid 7 through 9' Processing helix chain 'X' and resid 10 through 17 Processing helix chain 'X' and resid 19 through 24 Processing helix chain 'X' and resid 25 through 34 Processing helix chain 'X' and resid 72 through 78 Processing helix chain 'X' and resid 93 through 95 No H-bonds generated for 'chain 'X' and resid 93 through 95' Processing helix chain 'X' and resid 129 through 139 Processing helix chain 'X' and resid 140 through 148 Processing helix chain 'X' and resid 149 through 154 Processing helix chain 'X' and resid 155 through 172 Processing helix chain 'X' and resid 180 through 191 Processing helix chain 'X' and resid 192 through 195 Processing helix chain 'X' and resid 197 through 202 Processing helix chain 'X' and resid 207 through 220 Processing helix chain 'X' and resid 225 through 244 removed outlier: 3.583A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 68 Processing helix chain 'Y' and resid 70 through 74 Processing helix chain 'Y' and resid 86 through 92 removed outlier: 3.735A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 123 removed outlier: 3.657A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 129 through 159 removed outlier: 3.865A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 197 removed outlier: 3.697A pdb=" N LYS Y 197 " --> pdb=" O ARG Y 193 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 204 No H-bonds generated for 'chain 'Y' and resid 202 through 204' Processing helix chain 'Y' and resid 205 through 238 Processing helix chain 'Z' and resid 42 through 47 Processing helix chain 'Z' and resid 49 through 57 Processing helix chain 'Z' and resid 79 through 90 Processing helix chain 'Z' and resid 103 through 113 Processing helix chain 'a' and resid 68 through 72 Processing helix chain 'a' and resid 105 through 117 Processing helix chain 'a' and resid 119 through 124 removed outlier: 3.754A pdb=" N ARG a 122 " --> pdb=" O THR a 119 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR a 124 " --> pdb=" O HIS a 121 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 134 Processing helix chain 'b' and resid 37 through 39 No H-bonds generated for 'chain 'b' and resid 37 through 39' Processing helix chain 'b' and resid 40 through 50 Processing helix chain 'b' and resid 50 through 58 Processing helix chain 'b' and resid 93 through 107 Processing helix chain 'b' and resid 139 through 143 Processing helix chain 'c' and resid 35 through 53 Processing helix chain 'c' and resid 59 through 63 Processing helix chain 'c' and resid 67 through 80 removed outlier: 3.630A pdb=" N GLY c 76 " --> pdb=" O ILE c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 92 Processing helix chain 'c' and resid 94 through 107 removed outlier: 3.775A pdb=" N GLN c 107 " --> pdb=" O ALA c 103 " (cutoff:3.500A) Processing helix chain 'c' and resid 122 through 145 Processing helix chain 'c' and resid 149 through 161 Processing helix chain 'c' and resid 162 through 173 Processing helix chain 'c' and resid 174 through 179 removed outlier: 3.535A pdb=" N LEU c 178 " --> pdb=" O ALA c 174 " (cutoff:3.500A) Processing helix chain 'c' and resid 187 through 207 Processing helix chain 'c' and resid 207 through 219 Processing helix chain 'c' and resid 220 through 224 Processing helix chain 'c' and resid 227 through 232 Processing helix chain 'c' and resid 236 through 248 Processing helix chain 'c' and resid 288 through 306 Processing helix chain 'd' and resid 48 through 52 Processing helix chain 'd' and resid 118 through 130 removed outlier: 4.386A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 136 through 155 removed outlier: 3.759A pdb=" N LYS d 140 " --> pdb=" O ASP d 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN d 153 " --> pdb=" O HIS d 149 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 164 removed outlier: 3.999A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 168 through 174 Processing helix chain 'e' and resid 64 through 82 Processing helix chain 'e' and resid 117 through 131 removed outlier: 3.864A pdb=" N PHE e 131 " --> pdb=" O LYS e 127 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 195 removed outlier: 4.065A pdb=" N ALA e 193 " --> pdb=" O GLU e 189 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU e 195 " --> pdb=" O THR e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 258 through 264 removed outlier: 4.140A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 271 removed outlier: 3.689A pdb=" N GLN e 271 " --> pdb=" O LYS e 267 " (cutoff:3.500A) Processing helix chain 'e' and resid 272 through 275 Processing helix chain 'f' and resid 59 through 63 Processing helix chain 'f' and resid 99 through 117 Processing helix chain 'f' and resid 163 through 178 removed outlier: 3.730A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 50 Processing helix chain 'g' and resid 116 through 133 Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 153 through 165 Processing helix chain 'h' and resid 65 through 78 Processing helix chain 'h' and resid 85 through 89 Processing helix chain 'h' and resid 93 through 109 Processing helix chain 'h' and resid 113 through 118 removed outlier: 4.297A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 131 Processing helix chain 'h' and resid 138 through 145 Processing helix chain 'i' and resid 48 through 53 Processing helix chain 'i' and resid 59 through 64 Processing helix chain 'i' and resid 69 through 74 Processing helix chain 'i' and resid 77 through 81 removed outlier: 3.986A pdb=" N ARG i 81 " --> pdb=" O ILE i 78 " (cutoff:3.500A) Processing helix chain 'i' and resid 86 through 99 Processing helix chain 'i' and resid 100 through 102 No H-bonds generated for 'chain 'i' and resid 100 through 102' Processing helix chain 'i' and resid 103 through 124 Processing helix chain 'j' and resid 25 through 31 Processing helix chain 'j' and resid 41 through 46 Processing helix chain 'j' and resid 60 through 105 Processing helix chain 'k' and resid 27 through 37 removed outlier: 3.679A pdb=" N ARG k 31 " --> pdb=" O VAL k 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 44 Processing helix chain 'k' and resid 82 through 96 Processing helix chain 'o' and resid 28 through 50 Processing helix chain 'o' and resid 55 through 60 removed outlier: 3.534A pdb=" N ARG o 60 " --> pdb=" O ARG o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 80 Processing helix chain 'o' and resid 87 through 94 removed outlier: 4.081A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) Processing helix chain 'o' and resid 95 through 99 Processing helix chain 'p' and resid 44 through 49 Processing helix chain 'p' and resid 54 through 59 Processing helix chain 'p' and resid 112 through 123 Processing helix chain 'p' and resid 124 through 127 Processing helix chain 'p' and resid 142 through 163 Processing helix chain 'p' and resid 175 through 189 Processing helix chain 'q' and resid 48 through 52 Processing helix chain 'q' and resid 53 through 65 removed outlier: 3.565A pdb=" N ALA q 57 " --> pdb=" O GLY q 53 " (cutoff:3.500A) Processing helix chain 'q' and resid 66 through 69 Processing helix chain 'q' and resid 71 through 76 removed outlier: 3.560A pdb=" N TRP q 76 " --> pdb=" O GLY q 73 " (cutoff:3.500A) Processing helix chain 'q' and resid 78 through 93 Processing helix chain 'q' and resid 95 through 152 Proline residue: q 129 - end of helix Processing helix chain 'r' and resid 70 through 75 Processing helix chain 'r' and resid 85 through 90 Processing helix chain 'r' and resid 91 through 93 No H-bonds generated for 'chain 'r' and resid 91 through 93' Processing helix chain 'r' and resid 101 through 106 Processing helix chain 'r' and resid 108 through 125 Processing helix chain 'r' and resid 155 through 159 removed outlier: 4.053A pdb=" N VAL r 159 " --> pdb=" O PRO r 156 " (cutoff:3.500A) Processing helix chain 'r' and resid 167 through 171 removed outlier: 3.974A pdb=" N ARG r 171 " --> pdb=" O ARG r 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 178 through 184 removed outlier: 4.547A pdb=" N ASP r 183 " --> pdb=" O LEU r 180 " (cutoff:3.500A) Processing helix chain 's' and resid 55 through 73 Processing helix chain 's' and resid 75 through 85 Processing helix chain 's' and resid 101 through 111 Processing helix chain 's' and resid 141 through 155 Processing helix chain 's' and resid 167 through 189 removed outlier: 4.472A pdb=" N LEU s 174 " --> pdb=" O GLU s 170 " (cutoff:3.500A) Proline residue: s 175 - end of helix Processing helix chain 's' and resid 192 through 197 removed outlier: 3.611A pdb=" N ALA s 196 " --> pdb=" O ASN s 192 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA s 197 " --> pdb=" O PRO s 193 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 192 through 197' Processing helix chain 's' and resid 303 through 306 Processing helix chain 's' and resid 307 through 315 Processing helix chain 's' and resid 317 through 344 removed outlier: 4.177A pdb=" N GLU s 321 " --> pdb=" O ALA s 317 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 385 Processing helix chain 's' and resid 414 through 427 removed outlier: 3.827A pdb=" N LEU s 418 " --> pdb=" O ASN s 414 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 104 Processing helix chain 'u' and resid 131 through 150 removed outlier: 4.144A pdb=" N LYS u 150 " --> pdb=" O TYR u 146 " (cutoff:3.500A) Processing helix chain 'u' and resid 181 through 189 Processing helix chain 'u' and resid 189 through 196 Processing helix chain 'v' and resid 5 through 22 removed outlier: 4.090A pdb=" N VAL v 9 " --> pdb=" O SER v 5 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU v 10 " --> pdb=" O ARG v 6 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 41 Processing helix chain 'v' and resid 49 through 64 removed outlier: 4.140A pdb=" N ARG v 53 " --> pdb=" O GLU v 49 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 90 removed outlier: 3.522A pdb=" N TYR w 90 " --> pdb=" O VAL w 86 " (cutoff:3.500A) Processing helix chain 'w' and resid 111 through 124 Processing helix chain 'w' and resid 131 through 139 removed outlier: 4.360A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N MET w 139 " --> pdb=" O ALA w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 140 through 152 Processing sheet with id=AA1, first strand: chain '0' and resid 107 through 109 Processing sheet with id=AA2, first strand: chain '0' and resid 156 through 159 Processing sheet with id=AA3, first strand: chain '1' and resid 29 through 35 removed outlier: 7.383A pdb=" N LEU 1 17 " --> pdb=" O LYS 1 61 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LYS 1 61 " --> pdb=" O LEU 1 17 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ARG 1 19 " --> pdb=" O LYS 1 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 115 through 116 Processing sheet with id=AA5, first strand: chain '4' and resid 67 through 68 removed outlier: 6.033A pdb=" N LYS 4 67 " --> pdb=" O ARG 4 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 209 through 215 removed outlier: 10.340A pdb=" N LEU 5 219 " --> pdb=" O ASP 5 101 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA 5 103 " --> pdb=" O LEU 5 219 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN 5 221 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR 5 105 " --> pdb=" O GLN 5 221 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG 5 223 " --> pdb=" O TYR 5 105 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE 5 107 " --> pdb=" O ARG 5 223 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N GLN 5 102 " --> pdb=" O ILE 5 270 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE 5 270 " --> pdb=" O GLN 5 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '5' and resid 126 through 130 removed outlier: 6.059A pdb=" N LYS 5 127 " --> pdb=" O ALA 5 374 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL 5 376 " --> pdb=" O LYS 5 127 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE 5 129 " --> pdb=" O VAL 5 376 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N SER 5 378 " --> pdb=" O ILE 5 129 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N PHE 5 352 " --> pdb=" O ASP 5 379 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR 5 361 " --> pdb=" O GLN 5 338 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N GLN 5 338 " --> pdb=" O THR 5 361 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N TYR 5 287 " --> pdb=" O VAL 5 341 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N GLN 5 343 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N HIS 5 289 " --> pdb=" O GLN 5 343 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL 5 345 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU 5 291 " --> pdb=" O VAL 5 345 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR 5 347 " --> pdb=" O LEU 5 291 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU 5 293 " --> pdb=" O THR 5 347 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N THR 5 232 " --> pdb=" O PRO 5 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '5' and resid 385 through 387 Processing sheet with id=AA9, first strand: chain '5' and resid 391 through 393 removed outlier: 6.971A pdb=" N VAL 5 391 " --> pdb=" O VAL 5 398 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '6' and resid 183 through 187 removed outlier: 3.729A pdb=" N ASP 6 183 " --> pdb=" O VAL 6 179 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '6' and resid 191 through 192 removed outlier: 6.653A pdb=" N ASN 6 191 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU 6 316 " --> pdb=" O PHE 6 270 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE 6 270 " --> pdb=" O LEU 6 316 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE 6 318 " --> pdb=" O LEU 6 268 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU 6 268 " --> pdb=" O PHE 6 318 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN 6 320 " --> pdb=" O HIS 6 266 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS 6 266 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU 6 216 " --> pdb=" O THR 6 238 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N THR 6 238 " --> pdb=" O LEU 6 216 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU 6 218 " --> pdb=" O LEU 6 236 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU 6 236 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N SER 6 220 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N HIS 6 234 " --> pdb=" O SER 6 220 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU 6 236 " --> pdb=" O THR 6 251 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR 6 251 " --> pdb=" O LEU 6 236 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '6' and resid 191 through 192 removed outlier: 6.653A pdb=" N ASN 6 191 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU 6 316 " --> pdb=" O PHE 6 270 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE 6 270 " --> pdb=" O LEU 6 316 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE 6 318 " --> pdb=" O LEU 6 268 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU 6 268 " --> pdb=" O PHE 6 318 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN 6 320 " --> pdb=" O HIS 6 266 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS 6 266 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU 6 216 " --> pdb=" O THR 6 238 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N THR 6 238 " --> pdb=" O LEU 6 216 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU 6 218 " --> pdb=" O LEU 6 236 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU 6 236 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N SER 6 220 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N HIS 6 234 " --> pdb=" O SER 6 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '6' and resid 339 through 345 removed outlier: 5.338A pdb=" N GLU 6 339 " --> pdb=" O MET W 147 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N MET W 147 " --> pdb=" O GLU 6 339 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL 6 341 " --> pdb=" O VAL W 145 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE W 142 " --> pdb=" O PHE P 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '7' and resid 111 through 114 removed outlier: 8.891A pdb=" N CYS 7 123 " --> pdb=" O LYS 7 64 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU 7 66 " --> pdb=" O CYS 7 123 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE 7 125 " --> pdb=" O GLU 7 66 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LYS 7 68 " --> pdb=" O ILE 7 125 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N PHE 7 127 " --> pdb=" O LYS 7 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '7' and resid 165 through 168 removed outlier: 5.285A pdb=" N LEU 7 166 " --> pdb=" O VAL 7 184 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL 7 184 " --> pdb=" O LEU 7 166 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL 7 300 " --> pdb=" O VAL 7 280 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL 7 280 " --> pdb=" O VAL 7 300 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU 7 302 " --> pdb=" O TYR 7 278 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TYR 7 278 " --> pdb=" O LEU 7 302 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '7' and resid 217 through 222 Processing sheet with id=AB8, first strand: chain '9' and resid 42 through 44 Processing sheet with id=AB9, first strand: chain '9' and resid 59 through 60 removed outlier: 5.971A pdb=" N GLU 9 59 " --> pdb=" O VAL U 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain '9' and resid 73 through 74 removed outlier: 7.494A pdb=" N TYR 9 73 " --> pdb=" O THR V 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AC3, first strand: chain 'C' and resid 231 through 233 removed outlier: 6.370A pdb=" N VAL C 177 " --> pdb=" O ALA C 201 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 178 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASP C 255 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR C 249 " --> pdb=" O LYS C 300 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY C 302 " --> pdb=" O TYR C 249 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG C 251 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N HIS C 304 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU C 253 " --> pdb=" O HIS C 304 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL C 306 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP C 255 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER C 308 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ARG C 382 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N HIS C 304 " --> pdb=" O MET C 380 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N MET C 380 " --> pdb=" O HIS C 304 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL C 306 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N CYS C 378 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C 308 " --> pdb=" O TYR C 376 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR C 376 " --> pdb=" O SER C 308 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 231 through 233 removed outlier: 6.370A pdb=" N VAL C 177 " --> pdb=" O ALA C 201 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 178 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASP C 255 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR C 249 " --> pdb=" O LYS C 300 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY C 302 " --> pdb=" O TYR C 249 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG C 251 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N HIS C 304 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU C 253 " --> pdb=" O HIS C 304 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL C 306 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP C 255 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER C 308 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ARG C 382 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N HIS C 304 " --> pdb=" O MET C 380 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N MET C 380 " --> pdb=" O HIS C 304 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL C 306 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N CYS C 378 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C 308 " --> pdb=" O TYR C 376 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR C 376 " --> pdb=" O SER C 308 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU C 363 " --> pdb=" O PHE C 355 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS C 353 " --> pdb=" O ILE C 365 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 77 through 78 Processing sheet with id=AC6, first strand: chain 'D' and resid 147 through 152 removed outlier: 6.580A pdb=" N ILE D 139 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL D 129 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.016A pdb=" N LEU D 216 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN D 227 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 331 through 333 removed outlier: 4.975A pdb=" N LYS E 272 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR E 284 " --> pdb=" O TRP E 274 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE E 276 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE E 282 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N HIS E 117 " --> pdb=" O PRO E 108 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL E 119 " --> pdb=" O MET E 106 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N MET E 106 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU E 121 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU E 296 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LYS E 209 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL E 206 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR E 269 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ALA E 208 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR E 267 " --> pdb=" O ALA E 208 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 173 through 181 removed outlier: 6.387A pdb=" N LYS E 173 " --> pdb=" O THR E 151 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR E 151 " --> pdb=" O LYS E 173 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR E 175 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY E 148 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL E 129 " --> pdb=" O GLY E 148 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LYS E 150 " --> pdb=" O CYS E 127 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N CYS E 127 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 214 through 216 removed outlier: 3.567A pdb=" N GLY E 214 " --> pdb=" O MET E 261 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 47 through 49 removed outlier: 9.627A pdb=" N LEU F 187 " --> pdb=" O GLN F 63 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP F 65 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE F 189 " --> pdb=" O TRP F 65 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU F 217 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR F 262 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL F 219 " --> pdb=" O THR F 262 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL F 216 " --> pdb=" O ASN F 241 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE F 243 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU F 218 " --> pdb=" O ILE F 243 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 109 through 110 Processing sheet with id=AD4, first strand: chain 'H' and resid 54 through 58 removed outlier: 6.522A pdb=" N GLU H 57 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU H 82 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 111 through 115 Processing sheet with id=AD6, first strand: chain 'I' and resid 98 through 99 Processing sheet with id=AD7, first strand: chain 'I' and resid 179 through 181 Processing sheet with id=AD8, first strand: chain 'J' and resid 19 through 22 removed outlier: 3.642A pdb=" N ILE J 70 " --> pdb=" O ILE J 20 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA J 22 " --> pdb=" O THR J 68 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 110 through 113 removed outlier: 3.738A pdb=" N ARG J 154 " --> pdb=" O GLY J 110 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 125 through 127 removed outlier: 6.432A pdb=" N VAL K 57 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR K 19 " --> pdb=" O VAL K 58 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N MET K 60 " --> pdb=" O TYR K 19 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU K 21 " --> pdb=" O MET K 60 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP K 18 " --> pdb=" O GLU K 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'K' and resid 66 through 68 removed outlier: 3.503A pdb=" N TYR r 150 " --> pdb=" O PHE K 67 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 76 through 80 Processing sheet with id=AE4, first strand: chain 'L' and resid 39 through 40 removed outlier: 6.174A pdb=" N ARG L 39 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU L 107 " --> pdb=" O ARG L 39 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ASN L 104 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLN L 72 " --> pdb=" O VAL L 60 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL L 60 " --> pdb=" O GLN L 72 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU L 74 " --> pdb=" O ILE L 58 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG L 56 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 98 through 100 removed outlier: 6.521A pdb=" N ARG Q 152 " --> pdb=" O CYS Q 137 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N CYS Q 137 " --> pdb=" O ARG Q 152 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N VAL Q 154 " --> pdb=" O GLY Q 135 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N GLY Q 135 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS Q 129 " --> pdb=" O ASP Q 123 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA Q 122 " --> pdb=" O VAL Q 171 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL Q 171 " --> pdb=" O ALA Q 122 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 92 through 97 removed outlier: 7.022A pdb=" N GLN M 92 " --> pdb=" O TYR M 136 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL M 138 " --> pdb=" O GLN M 92 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LYS M 94 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU M 140 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU M 96 " --> pdb=" O LEU M 140 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 153 through 156 Processing sheet with id=AE8, first strand: chain 'M' and resid 274 through 276 Processing sheet with id=AE9, first strand: chain 'N' and resid 119 through 122 removed outlier: 6.524A pdb=" N ILE N 89 " --> pdb=" O VAL N 160 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU N 162 " --> pdb=" O PHE N 87 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE N 87 " --> pdb=" O GLU N 162 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 95 through 98 Processing sheet with id=AF2, first strand: chain 'N' and resid 241 through 242 Processing sheet with id=AF3, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.233A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 101 through 106 removed outlier: 6.073A pdb=" N VAL P 101 " --> pdb=" O HIS P 96 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N HIS P 96 " --> pdb=" O VAL P 101 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 181 through 182 removed outlier: 6.509A pdb=" N LYS Q 181 " --> pdb=" O ASN Q 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'S' and resid 104 through 109 removed outlier: 6.666A pdb=" N PHE S 96 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL S 136 " --> pdb=" O PHE S 96 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL S 98 " --> pdb=" O LEU S 134 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU S 134 " --> pdb=" O GLY S 145 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'b' and resid 119 through 120 removed outlier: 6.474A pdb=" N ARG S 194 " --> pdb=" O VAL S 160 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL S 160 " --> pdb=" O ARG S 194 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASN S 196 " --> pdb=" O ALA S 158 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA S 158 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE S 198 " --> pdb=" O VAL S 156 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL S 156 " --> pdb=" O ILE S 198 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE S 200 " --> pdb=" O VAL S 154 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL S 154 " --> pdb=" O ILE S 200 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 169 through 175 removed outlier: 3.924A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 72 through 80 removed outlier: 7.053A pdb=" N GLU T 72 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLU T 180 " --> pdb=" O GLU T 72 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR T 74 " --> pdb=" O LEU T 178 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU T 178 " --> pdb=" O TYR T 74 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N CYS T 76 " --> pdb=" O VAL T 176 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL T 176 " --> pdb=" O CYS T 76 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ARG T 78 " --> pdb=" O TYR T 174 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR T 174 " --> pdb=" O ARG T 78 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL T 179 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE T 142 " --> pdb=" O VAL T 179 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'T' and resid 153 through 158 Processing sheet with id=AG2, first strand: chain 'U' and resid 27 through 29 removed outlier: 4.354A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR U 92 " --> pdb=" O VAL U 72 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL U 72 " --> pdb=" O TYR U 92 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL U 94 " --> pdb=" O THR U 70 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR U 70 " --> pdb=" O VAL U 94 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR U 96 " --> pdb=" O VAL U 68 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL U 68 " --> pdb=" O TYR U 96 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN U 98 " --> pdb=" O ALA U 66 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 214 through 216 Processing sheet with id=AG4, first strand: chain 'W' and resid 52 through 53 removed outlier: 6.609A pdb=" N LEU W 89 " --> pdb=" O ILE W 67 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 60 through 61 Processing sheet with id=AG6, first strand: chain 'X' and resid 50 through 52 Processing sheet with id=AG7, first strand: chain 'X' and resid 86 through 91 Processing sheet with id=AG8, first strand: chain 'X' and resid 109 through 116 Processing sheet with id=AG9, first strand: chain 'Y' and resid 166 through 170 Processing sheet with id=AH1, first strand: chain 'Z' and resid 98 through 101 Processing sheet with id=AH2, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AH3, first strand: chain 'a' and resid 73 through 74 removed outlier: 5.694A pdb=" N SER c 255 " --> pdb=" O TYR c 275 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR c 275 " --> pdb=" O SER c 255 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU c 257 " --> pdb=" O GLY c 273 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY c 273 " --> pdb=" O LEU c 257 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR c 270 " --> pdb=" O PRO c 285 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL c 272 " --> pdb=" O GLU c 283 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU c 283 " --> pdb=" O VAL c 272 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU c 274 " --> pdb=" O ILE c 281 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 8 through 9 Processing sheet with id=AH5, first strand: chain 'b' and resid 84 through 88 removed outlier: 6.218A pdb=" N ILE b 63 " --> pdb=" O LYS h 153 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'd' and resid 184 through 198 removed outlier: 10.999A pdb=" N GLU d 187 " --> pdb=" O THR d 221 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N THR d 221 " --> pdb=" O GLU d 187 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU d 189 " --> pdb=" O ARG d 219 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ARG d 219 " --> pdb=" O LEU d 189 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N HIS d 217 " --> pdb=" O PRO d 191 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS d 193 " --> pdb=" O ARG d 215 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR d 213 " --> pdb=" O VAL d 195 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL d 197 " --> pdb=" O GLN d 211 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLN d 211 " --> pdb=" O VAL d 197 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR d 245 " --> pdb=" O ILE d 265 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLU d 249 " --> pdb=" O MET d 261 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N MET d 261 " --> pdb=" O GLU d 249 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'd' and resid 224 through 225 removed outlier: 6.543A pdb=" N ILE d 224 " --> pdb=" O MET d 232 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'e' and resid 175 through 177 removed outlier: 3.540A pdb=" N LYS e 230 " --> pdb=" O ARG e 46 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE e 232 " --> pdb=" O LEU e 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'e' and resid 52 through 54 removed outlier: 6.704A pdb=" N CYS e 52 " --> pdb=" O ALA e 236 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LEU e 238 " --> pdb=" O CYS e 52 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLN e 54 " --> pdb=" O LEU e 238 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N THR e 240 " --> pdb=" O GLN e 54 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU e 238 " --> pdb=" O LYS e 203 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS e 203 " --> pdb=" O LEU e 238 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 161 through 164 removed outlier: 3.707A pdb=" N VAL e 161 " --> pdb=" O ILE e 172 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE e 172 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU e 163 " --> pdb=" O VAL e 170 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL e 170 " --> pdb=" O GLU e 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'f' and resid 91 through 97 Processing sheet with id=AI3, first strand: chain 'g' and resid 84 through 86 Processing sheet with id=AI4, first strand: chain 'g' and resid 96 through 101 Processing sheet with id=AI5, first strand: chain 'k' and resid 50 through 53 removed outlier: 3.556A pdb=" N HIS k 72 " --> pdb=" O PHE k 68 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE r 49 " --> pdb=" O ARG k 73 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE k 75 " --> pdb=" O ILE r 49 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N GLY r 51 " --> pdb=" O ILE k 75 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'm' and resid 64 through 68 Processing sheet with id=AI7, first strand: chain 'p' and resid 77 through 81 removed outlier: 7.332A pdb=" N SER p 97 " --> pdb=" O SER p 139 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER p 139 " --> pdb=" O SER p 97 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 's' and resid 206 through 216 removed outlier: 4.454A pdb=" N LEU s 229 " --> pdb=" O ARG s 212 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU s 214 " --> pdb=" O ASP s 227 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP s 227 " --> pdb=" O GLU s 214 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 's' and resid 112 through 116 removed outlier: 9.163A pdb=" N VAL s 356 " --> pdb=" O TYR s 294 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N HIS s 296 " --> pdb=" O VAL s 356 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY s 295 " --> pdb=" O ILE s 243 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE s 243 " --> pdb=" O GLY s 295 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR s 297 " --> pdb=" O ILE s 241 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 's' and resid 112 through 116 Processing sheet with id=AJ2, first strand: chain 's' and resid 404 through 406 Processing sheet with id=AJ3, first strand: chain 'u' and resid 167 through 171 removed outlier: 3.792A pdb=" N ASP u 108 " --> pdb=" O SER u 128 " (cutoff:3.500A) 2874 hydrogen bonds defined for protein. 7965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 934 hydrogen bonds 1604 hydrogen bond angles 0 basepair planarities 383 basepair parallelities 746 stacking parallelities Total time for adding SS restraints: 72.77 Time building geometry restraints manager: 38.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 17222 1.33 - 1.45: 33186 1.45 - 1.57: 50922 1.57 - 1.69: 2840 1.69 - 1.81: 479 Bond restraints: 104649 Sorted by residual: bond pdb=" O3' U A2634 " pdb=" P G A2635 " ideal model delta sigma weight residual 1.607 1.648 -0.041 1.50e-02 4.44e+03 7.35e+00 bond pdb=" O5' G A2635 " pdb=" C5' G A2635 " ideal model delta sigma weight residual 1.420 1.453 -0.033 1.50e-02 4.44e+03 4.93e+00 bond pdb=" P G A2635 " pdb=" OP2 G A2635 " ideal model delta sigma weight residual 1.485 1.528 -0.043 2.00e-02 2.50e+03 4.63e+00 bond pdb=" C3' C A2543 " pdb=" O3' C A2543 " ideal model delta sigma weight residual 1.417 1.448 -0.031 1.50e-02 4.44e+03 4.21e+00 bond pdb=" P G A2635 " pdb=" O5' G A2635 " ideal model delta sigma weight residual 1.593 1.621 -0.028 1.50e-02 4.44e+03 3.58e+00 ... (remaining 104644 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.59: 8625 105.59 - 112.73: 57884 112.73 - 119.87: 35835 119.87 - 127.01: 41649 127.01 - 134.15: 4298 Bond angle restraints: 148291 Sorted by residual: angle pdb=" O3' C A2543 " pdb=" C3' C A2543 " pdb=" C2' C A2543 " ideal model delta sigma weight residual 113.70 123.99 -10.29 1.50e+00 4.44e-01 4.70e+01 angle pdb=" C3' C A2543 " pdb=" C2' C A2543 " pdb=" O2' C A2543 " ideal model delta sigma weight residual 110.70 119.24 -8.54 1.50e+00 4.44e-01 3.24e+01 angle pdb=" O3' G A2635 " pdb=" C3' G A2635 " pdb=" C2' G A2635 " ideal model delta sigma weight residual 113.70 121.32 -7.62 1.50e+00 4.44e-01 2.58e+01 angle pdb=" C3' G A2635 " pdb=" C2' G A2635 " pdb=" O2' G A2635 " ideal model delta sigma weight residual 110.70 118.30 -7.60 1.50e+00 4.44e-01 2.57e+01 angle pdb=" C3' A A1823 " pdb=" O3' A A1823 " pdb=" P U A1824 " ideal model delta sigma weight residual 120.20 126.74 -6.54 1.50e+00 4.44e-01 1.90e+01 ... (remaining 148286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 60008 35.99 - 71.97: 2777 71.97 - 107.96: 451 107.96 - 143.95: 20 143.95 - 179.94: 36 Dihedral angle restraints: 63292 sinusoidal: 38662 harmonic: 24630 Sorted by residual: dihedral pdb=" O4' C A2379 " pdb=" C1' C A2379 " pdb=" N1 C A2379 " pdb=" C2 C A2379 " ideal model delta sinusoidal sigma weight residual 200.00 21.43 178.57 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A3170 " pdb=" C1' C A3170 " pdb=" N1 C A3170 " pdb=" C2 C A3170 " ideal model delta sinusoidal sigma weight residual -160.00 17.83 -177.83 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1852 " pdb=" C1' C A1852 " pdb=" N1 C A1852 " pdb=" C2 C A1852 " ideal model delta sinusoidal sigma weight residual 200.00 24.68 175.32 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 63289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 15669 0.067 - 0.134: 1609 0.134 - 0.201: 97 0.201 - 0.268: 12 0.268 - 0.335: 5 Chirality restraints: 17392 Sorted by residual: chirality pdb=" C3' A A1823 " pdb=" C4' A A1823 " pdb=" O3' A A1823 " pdb=" C2' A A1823 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" P G A2635 " pdb=" OP1 G A2635 " pdb=" OP2 G A2635 " pdb=" O5' G A2635 " both_signs ideal model delta sigma weight residual True 2.41 -2.74 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C3' A A2457 " pdb=" C4' A A2457 " pdb=" O3' A A2457 " pdb=" C2' A A2457 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 17389 not shown) Planarity restraints: 13721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1671 " 0.042 2.00e-02 2.50e+03 1.81e-02 9.86e+00 pdb=" N9 G A1671 " -0.042 2.00e-02 2.50e+03 pdb=" C8 G A1671 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A1671 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A1671 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A1671 " 0.014 2.00e-02 2.50e+03 pdb=" O6 G A1671 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G A1671 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G A1671 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G A1671 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A1671 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A1671 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A2456 " 0.039 2.00e-02 2.50e+03 1.91e-02 8.21e+00 pdb=" N1 U A2456 " -0.037 2.00e-02 2.50e+03 pdb=" C2 U A2456 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U A2456 " -0.006 2.00e-02 2.50e+03 pdb=" N3 U A2456 " -0.000 2.00e-02 2.50e+03 pdb=" C4 U A2456 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U A2456 " 0.015 2.00e-02 2.50e+03 pdb=" C5 U A2456 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U A2456 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A3051 " -0.038 2.00e-02 2.50e+03 1.69e-02 7.90e+00 pdb=" N9 A A3051 " 0.039 2.00e-02 2.50e+03 pdb=" C8 A A3051 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A A3051 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A3051 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A A3051 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A A3051 " -0.011 2.00e-02 2.50e+03 pdb=" N1 A A3051 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A A3051 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A3051 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A A3051 " 0.007 2.00e-02 2.50e+03 ... (remaining 13718 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 459 2.46 - 3.07: 64961 3.07 - 3.68: 174485 3.68 - 4.29: 263849 4.29 - 4.90: 389688 Nonbonded interactions: 893442 Sorted by model distance: nonbonded pdb=" OP1 A A1961 " pdb="MG MG A3313 " model vdw 1.851 2.170 nonbonded pdb=" OP1 C A2915 " pdb="MG MG A3336 " model vdw 1.902 2.170 nonbonded pdb=" OP1 A A2430 " pdb="MG MG A3313 " model vdw 1.911 2.170 nonbonded pdb=" OP2 U A1950 " pdb="MG MG A3308 " model vdw 1.922 2.170 nonbonded pdb=" OP2 U A2660 " pdb="MG MG A3343 " model vdw 1.928 2.170 ... (remaining 893437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.48 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 12.610 Check model and map are aligned: 1.220 Set scattering table: 0.870 Process input model: 280.030 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.270 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:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 311.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 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 : 0.005 0.092 104649 Z= 0.340 Angle : 0.590 10.287 148291 Z= 0.307 Chirality : 0.041 0.335 17392 Planarity : 0.004 0.065 13721 Dihedral : 18.473 179.935 47332 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.08 % Allowed : 2.89 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.09), residues: 8285 helix: 1.75 (0.10), residues: 3034 sheet: -0.08 (0.16), residues: 1001 loop : 0.43 (0.10), residues: 4250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP 6 235 HIS 0.010 0.001 HIS S 76 PHE 0.018 0.002 PHE D 112 TYR 0.029 0.001 TYR E 284 ARG 0.008 0.001 ARG H 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1645 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1639 time to evaluate : 7.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 1644 average time/residue: 2.0240 time to fit residues: 4476.9820 Evaluate side-chains 1307 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1301 time to evaluate : 6.837 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 3 average time/residue: 0.7655 time to fit residues: 13.0291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 809 optimal weight: 2.9990 chunk 726 optimal weight: 6.9990 chunk 403 optimal weight: 0.6980 chunk 248 optimal weight: 20.0000 chunk 490 optimal weight: 2.9990 chunk 388 optimal weight: 0.9990 chunk 751 optimal weight: 3.9990 chunk 290 optimal weight: 20.0000 chunk 457 optimal weight: 2.9990 chunk 559 optimal weight: 30.0000 chunk 870 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 15 ASN 3 185 ASN 5 165 GLN ** 5 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 37 ASN 6 307 HIS 6 354 GLN ** 8 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN C 367 ASN D 195 ASN D 252 HIS D 253 ASN D 271 ASN E 125 GLN F 201 GLN F 241 ASN G 137 ASN G 195 ASN G 287 ASN H 93 ASN H 126 GLN J 54 ASN L 113 ASN L 142 GLN ** M 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 202 GLN P 87 GLN P 115 HIS Q 213 GLN Q 239 ASN S 118 ASN T 62 GLN T 133 ASN T 195 HIS U 23 ASN X 53 ASN X 239 GLN ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 76 GLN Y 88 GLN ** Y 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 122 GLN Y 183 GLN Y 195 ASN b 58 ASN ** b 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 ASN ** c 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 217 HIS e 67 GLN ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 96 ASN ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 147 GLN s 179 GLN s 315 ASN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 63 ASN w 103 HIS Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 104649 Z= 0.235 Angle : 0.584 11.297 148291 Z= 0.297 Chirality : 0.039 0.301 17392 Planarity : 0.004 0.052 13721 Dihedral : 19.915 179.569 29474 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.25 % Allowed : 11.59 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.09), residues: 8285 helix: 1.68 (0.10), residues: 3050 sheet: -0.03 (0.16), residues: 1025 loop : 0.47 (0.10), residues: 4210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 6 214 HIS 0.007 0.001 HIS P 115 PHE 0.023 0.001 PHE G 301 TYR 0.026 0.001 TYR C 376 ARG 0.012 0.001 ARG G 240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1552 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1384 time to evaluate : 6.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 168 outliers final: 63 residues processed: 1441 average time/residue: 1.9986 time to fit residues: 3916.4583 Evaluate side-chains 1364 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1301 time to evaluate : 6.792 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 25 residues processed: 40 average time/residue: 0.9309 time to fit residues: 74.1068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 483 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 724 optimal weight: 1.9990 chunk 593 optimal weight: 0.5980 chunk 240 optimal weight: 6.9990 chunk 872 optimal weight: 7.9990 chunk 942 optimal weight: 5.9990 chunk 776 optimal weight: 6.9990 chunk 865 optimal weight: 10.0000 chunk 297 optimal weight: 40.0000 chunk 699 optimal weight: 10.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 170 GLN 3 185 ASN 5 165 GLN 5 266 HIS ** 5 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 37 ASN ** 6 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN C 304 HIS E 202 GLN F 201 GLN G 137 ASN G 195 ASN H 93 ASN H 121 ASN H 126 GLN H 136 ASN J 54 ASN L 113 ASN L 142 GLN N 202 GLN N 210 GLN Q 239 ASN T 101 GLN T 132 HIS T 133 ASN U 23 ASN X 53 ASN ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 99 HIS b 107 GLN e 67 GLN ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 96 ASN p 152 GLN ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 315 ASN ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 104649 Z= 0.402 Angle : 0.628 21.832 148291 Z= 0.319 Chirality : 0.042 0.353 17392 Planarity : 0.005 0.073 13721 Dihedral : 19.851 179.644 29474 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.37 % Allowed : 13.35 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.09), residues: 8285 helix: 1.63 (0.10), residues: 3028 sheet: -0.00 (0.16), residues: 1035 loop : 0.43 (0.10), residues: 4222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 7 192 HIS 0.013 0.001 HIS 6 307 PHE 0.023 0.002 PHE u 140 TYR 0.027 0.002 TYR C 376 ARG 0.010 0.001 ARG j 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1486 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1309 time to evaluate : 7.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 177 outliers final: 88 residues processed: 1388 average time/residue: 1.9645 time to fit residues: 3719.5987 Evaluate side-chains 1344 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1256 time to evaluate : 6.892 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 39 residues processed: 52 average time/residue: 0.9053 time to fit residues: 92.7493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 861 optimal weight: 0.7980 chunk 655 optimal weight: 5.9990 chunk 452 optimal weight: 30.0000 chunk 96 optimal weight: 8.9990 chunk 416 optimal weight: 6.9990 chunk 585 optimal weight: 1.9990 chunk 875 optimal weight: 9.9990 chunk 926 optimal weight: 4.9990 chunk 457 optimal weight: 50.0000 chunk 829 optimal weight: 0.9990 chunk 249 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 37 ASN ** 6 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN C 229 ASN C 304 HIS D 158 GLN F 201 GLN F 228 GLN G 137 ASN H 93 ASN H 121 ASN H 126 GLN L 113 ASN L 142 GLN N 202 GLN N 210 GLN Q 239 ASN T 101 GLN T 133 ASN T 195 HIS ** T 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 53 ASN ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 76 GLN ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN h 119 GLN p 96 ASN ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 315 ASN ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 408 ASN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 63 ASN w 103 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 104649 Z= 0.283 Angle : 0.592 12.162 148291 Z= 0.300 Chirality : 0.040 0.314 17392 Planarity : 0.005 0.066 13721 Dihedral : 19.845 179.956 29474 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.27 % Allowed : 14.64 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.09), residues: 8285 helix: 1.58 (0.10), residues: 3044 sheet: -0.12 (0.15), residues: 1069 loop : 0.47 (0.10), residues: 4172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 7 192 HIS 0.013 0.001 HIS 6 307 PHE 0.023 0.001 PHE u 140 TYR 0.027 0.001 TYR u 146 ARG 0.012 0.001 ARG u 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1474 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1304 time to evaluate : 6.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 170 outliers final: 86 residues processed: 1390 average time/residue: 1.9413 time to fit residues: 3683.4380 Evaluate side-chains 1334 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1248 time to evaluate : 6.845 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 50 residues processed: 40 average time/residue: 0.9589 time to fit residues: 75.1014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 772 optimal weight: 0.0010 chunk 526 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 690 optimal weight: 1.9990 chunk 382 optimal weight: 0.5980 chunk 791 optimal weight: 50.0000 chunk 640 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 473 optimal weight: 4.9990 chunk 832 optimal weight: 0.8980 chunk 233 optimal weight: 8.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 150 GLN 5 165 GLN ** 5 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 37 ASN ** 6 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS D 158 GLN E 63 GLN F 74 GLN F 201 GLN G 137 ASN H 93 ASN H 126 GLN L 113 ASN L 142 GLN N 202 GLN N 208 ASN P 147 GLN Q 239 ASN S 76 HIS T 101 GLN T 133 ASN X 53 ASN ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 76 GLN c 193 GLN c 260 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN ** h 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 96 ASN q 142 ASN s 152 GLN s 315 ASN s 408 ASN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 63 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 104649 Z= 0.179 Angle : 0.565 14.956 148291 Z= 0.285 Chirality : 0.038 0.336 17392 Planarity : 0.004 0.054 13721 Dihedral : 19.789 179.750 29474 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.95 % Favored : 97.04 % Rotamer: Outliers : 2.18 % Allowed : 15.65 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.09), residues: 8285 helix: 1.57 (0.10), residues: 3067 sheet: -0.09 (0.16), residues: 1054 loop : 0.51 (0.10), residues: 4164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 6 214 HIS 0.011 0.001 HIS 6 307 PHE 0.024 0.001 PHE G 301 TYR 0.024 0.001 TYR N 246 ARG 0.011 0.000 ARG 7 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1315 time to evaluate : 6.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 80 residues processed: 1395 average time/residue: 1.9064 time to fit residues: 3644.9043 Evaluate side-chains 1325 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1245 time to evaluate : 6.806 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 47 residues processed: 37 average time/residue: 0.8802 time to fit residues: 66.7082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 311 optimal weight: 0.6980 chunk 834 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 544 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 927 optimal weight: 2.9990 chunk 770 optimal weight: 9.9990 chunk 429 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 306 optimal weight: 40.0000 chunk 487 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 GLN ** 5 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 37 ASN ** 6 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS D 158 GLN D 271 ASN E 63 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 GLN F 228 GLN G 137 ASN H 93 ASN H 121 ASN I 150 HIS L 113 ASN L 142 GLN N 202 GLN N 210 GLN P 147 GLN Q 239 ASN T 101 GLN T 133 ASN ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 76 GLN ** Z 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 193 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN ** o 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 96 ASN q 142 ASN s 315 ASN s 408 ASN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 104649 Z= 0.268 Angle : 0.591 21.083 148291 Z= 0.298 Chirality : 0.039 0.309 17392 Planarity : 0.005 0.060 13721 Dihedral : 19.726 179.938 29474 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.91 % Favored : 97.08 % Rotamer: Outliers : 2.18 % Allowed : 16.70 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.09), residues: 8285 helix: 1.57 (0.10), residues: 3068 sheet: -0.05 (0.16), residues: 1054 loop : 0.49 (0.10), residues: 4163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP 6 235 HIS 0.009 0.001 HIS 6 307 PHE 0.035 0.001 PHE 6 318 TYR 0.028 0.001 TYR N 246 ARG 0.015 0.000 ARG u 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1433 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1270 time to evaluate : 6.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 94 residues processed: 1358 average time/residue: 1.9014 time to fit residues: 3547.2081 Evaluate side-chains 1328 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1234 time to evaluate : 6.889 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 55 residues processed: 44 average time/residue: 0.9590 time to fit residues: 81.7654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 894 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 528 optimal weight: 6.9990 chunk 677 optimal weight: 0.9990 chunk 524 optimal weight: 6.9990 chunk 781 optimal weight: 50.0000 chunk 518 optimal weight: 0.3980 chunk 924 optimal weight: 0.8980 chunk 578 optimal weight: 20.0000 chunk 563 optimal weight: 3.9990 chunk 426 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 45 HIS ** 5 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 37 ASN ** 6 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS D 158 GLN D 271 ASN E 63 GLN F 201 GLN G 137 ASN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN H 121 ASN L 113 ASN L 142 GLN N 202 GLN N 210 GLN P 147 GLN Q 239 ASN T 101 GLN T 133 ASN ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 76 GLN c 168 HIS ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN o 33 GLN p 96 ASN s 315 ASN s 397 GLN s 408 ASN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 63 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 104649 Z= 0.175 Angle : 0.571 16.129 148291 Z= 0.287 Chirality : 0.038 0.322 17392 Planarity : 0.004 0.056 13721 Dihedral : 19.711 179.633 29474 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.97 % Favored : 97.02 % Rotamer: Outliers : 2.07 % Allowed : 17.32 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 8285 helix: 1.62 (0.10), residues: 3060 sheet: -0.06 (0.16), residues: 1055 loop : 0.50 (0.10), residues: 4170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP 6 235 HIS 0.011 0.001 HIS 6 307 PHE 0.023 0.001 PHE 6 318 TYR 0.021 0.001 TYR 5 176 ARG 0.012 0.000 ARG h 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1433 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1278 time to evaluate : 7.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 155 outliers final: 84 residues processed: 1369 average time/residue: 1.9068 time to fit residues: 3583.8757 Evaluate side-chains 1311 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1227 time to evaluate : 7.523 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 59 residues processed: 30 average time/residue: 1.1264 time to fit residues: 64.4993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 571 optimal weight: 6.9990 chunk 369 optimal weight: 0.9990 chunk 552 optimal weight: 9.9990 chunk 278 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 587 optimal weight: 4.9990 chunk 629 optimal weight: 0.9980 chunk 456 optimal weight: 30.0000 chunk 86 optimal weight: 20.0000 chunk 726 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 96 ASN 1 45 HIS 5 165 GLN ** 5 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 37 ASN ** 6 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS D 158 GLN D 271 ASN E 63 GLN F 74 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 ASN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN H 121 ASN H 126 GLN L 33 GLN L 113 ASN L 142 GLN N 178 GLN N 202 GLN Q 239 ASN T 101 GLN ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 76 GLN Z 62 ASN a 46 ASN c 260 GLN ** e 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 96 ASN s 315 ASN s 408 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 104649 Z= 0.373 Angle : 0.636 15.492 148291 Z= 0.321 Chirality : 0.042 0.343 17392 Planarity : 0.005 0.077 13721 Dihedral : 19.699 179.534 29474 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.97 % Favored : 97.02 % Rotamer: Outliers : 1.82 % Allowed : 18.11 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.09), residues: 8285 helix: 1.56 (0.10), residues: 3037 sheet: -0.10 (0.15), residues: 1070 loop : 0.49 (0.10), residues: 4178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP 6 235 HIS 0.020 0.001 HIS 0 115 PHE 0.020 0.002 PHE G 301 TYR 0.022 0.002 TYR 5 176 ARG 0.017 0.001 ARG C 345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1378 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1242 time to evaluate : 7.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 89 residues processed: 1323 average time/residue: 1.8857 time to fit residues: 3427.5704 Evaluate side-chains 1298 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1209 time to evaluate : 6.039 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 64 residues processed: 29 average time/residue: 0.7454 time to fit residues: 48.4722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 840 optimal weight: 10.0000 chunk 885 optimal weight: 30.0000 chunk 807 optimal weight: 4.9990 chunk 861 optimal weight: 10.0000 chunk 518 optimal weight: 0.6980 chunk 375 optimal weight: 0.0980 chunk 676 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 778 optimal weight: 9.9990 chunk 814 optimal weight: 0.9990 chunk 858 optimal weight: 0.1980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 45 HIS ** 3 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 37 ASN ** 6 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS D 158 GLN D 271 ASN E 63 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 GLN F 228 GLN G 137 ASN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN H 121 ASN H 126 GLN L 33 GLN L 113 ASN L 142 GLN N 202 GLN P 134 GLN Q 139 GLN Q 239 ASN T 101 GLN T 133 ASN T 195 HIS ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 260 GLN ** e 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN h 119 GLN o 33 GLN p 96 ASN s 315 ASN s 319 GLN s 408 ASN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 104649 Z= 0.189 Angle : 0.594 16.806 148291 Z= 0.298 Chirality : 0.038 0.285 17392 Planarity : 0.004 0.063 13721 Dihedral : 19.706 179.815 29474 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.92 % Favored : 97.07 % Rotamer: Outliers : 1.54 % Allowed : 18.60 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.09), residues: 8285 helix: 1.57 (0.10), residues: 3047 sheet: -0.09 (0.16), residues: 1055 loop : 0.49 (0.10), residues: 4183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP 6 235 HIS 0.013 0.001 HIS W 107 PHE 0.029 0.001 PHE u 92 TYR 0.027 0.001 TYR N 246 ARG 0.017 0.000 ARG I 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16570 Ramachandran restraints generated. 8285 Oldfield, 0 Emsley, 8285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1376 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1261 time to evaluate : 6.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 83 residues processed: 1334 average time/residue: 1.8692 time to fit residues: 3411.1080 Evaluate side-chains 1298 residues out of total 7477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1215 time to evaluate : 5.992 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 65 residues processed: 21 average time/residue: 0.9427 time to fit residues: 44.0057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 959 random chunks: chunk 565 optimal weight: 7.9990 chunk 910 optimal weight: 2.9990 chunk 555 optimal weight: 4.9990 chunk 432 optimal weight: 6.9990 chunk 633 optimal weight: 0.6980 chunk 955 optimal weight: 7.9990 chunk 879 optimal weight: 10.0000 chunk 760 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 587 optimal weight: 0.9990 chunk 466 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 298, in __init__ self.caller(self.nqh_flips) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 681, in nqh_flips phenix.refinement.nqh_flips.ncs_aware(model = self.model, log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/nqh_flips.py", line 12, in __init__ self.model.flip_nqh() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/model/model.py", line 691, in flip_nqh mon_lib_srv = self.get_mon_lib_srv()) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/rotamer/nqh.py", line 218, in flip pdb_hierarchy = tmp_pdb_hierarchy) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/