Starting phenix.real_space_refine on Thu Feb 22 19:23:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of3_12868/02_2024/7of3_12868_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of3_12868/02_2024/7of3_12868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of3_12868/02_2024/7of3_12868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of3_12868/02_2024/7of3_12868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of3_12868/02_2024/7of3_12868_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of3_12868/02_2024/7of3_12868_updated.pdb" } resolution = 2.7 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= 0.002 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 1448 5.49 5 Mg 58 5.21 5 S 311 5.16 5 C 58753 2.51 5 N 18352 2.21 5 O 22301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 122": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 101226 Number of models: 1 Model: "" Number of chains: 61 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: 29436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1386, 29436 Classifications: {'RNA': 1386} Modifications used: {'rna2p_pur': 149, 'rna2p_pyr': 110, 'rna3p_pur': 586, 'rna3p_pyr': 541} Link IDs: {'rna2p': 258, 'rna3p': 1127} Chain breaks: 17 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: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1832 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 13, 'TRANS': 220} Chain breaks: 1 Chain: "E" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2405 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 24, 'TRANS': 280} 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: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1153 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} 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: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1568 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 16, 'TRANS': 174} Chain breaks: 1 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: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 11, 'TRANS': 108} Chain: "a" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 686 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 10, 'TRANS': 71} 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: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1702 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 18, 'TRANS': 186} 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: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 121 Unusual residues: {' MG': 57, 'GTP': 2} Classifications: {'undetermined': 59} Link IDs: {None: 58} 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 0 110 143.774 39.315 126.335 1.00 74.47 S ATOM 286 SG CYS 0 113 147.122 40.591 124.949 1.00 78.06 S ATOM 366 SG CYS 0 123 144.023 42.538 124.422 1.00 69.43 S ATOM 389 SG CYS 0 126 144.430 39.088 122.660 1.00 73.98 S ATOM 2605 SG CYS 4 76 65.963 108.641 169.339 1.00 83.23 S ATOM 2628 SG CYS 4 79 69.676 108.150 168.525 1.00 78.27 S ATOM 2752 SG CYS 4 92 67.178 105.288 168.025 1.00 74.90 S ATOM 55129 SG CYS I 64 92.338 112.992 198.163 1.00 88.82 S ATOM 94944 SG CYS r 70 90.340 109.476 199.225 1.00 80.05 S ATOM 94965 SG CYS r 73 92.554 111.011 200.099 1.00 79.47 S ATOM 95259 SG CYS r 108 89.488 111.240 197.156 1.00 77.46 S Time building chain proxies: 40.20, per 1000 atoms: 0.40 Number of scatterers: 101226 At special positions: 0 Unit cell: (234.15, 237.3, 229.95, 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 311 16.00 P 1448 15.00 Mg 58 11.99 O 22301 8.00 N 18352 7.00 C 58753 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: 38.75 Conformation dependent library (CDL) restraints added in 10.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " 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 70 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 108 " pdb="ZN ZN r 301 " - pdb=" SG CYS I 64 " Number of angles added : 15 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16298 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 304 helices and 80 sheets defined 43.6% alpha, 13.4% beta 378 base pairs and 691 stacking pairs defined. Time for finding SS restraints: 57.21 Creating SS restraints... Processing helix chain '0' and resid 86 through 96 removed outlier: 3.871A pdb=" N ASN 0 96 " --> pdb=" O CYS 0 92 " (cutoff:3.500A) Processing helix chain '0' and resid 123 through 146 Processing helix chain '2' and resid 56 through 64 Processing helix chain '2' and resid 65 through 73 removed outlier: 3.902A pdb=" N THR 2 72 " --> pdb=" O ARG 2 68 " (cutoff:3.500A) Proline residue: 2 73 - end of helix Processing helix chain '2' and resid 74 through 86 Processing helix chain '3' and resid 107 through 114 removed outlier: 3.600A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG 3 113 " --> pdb=" O ALA 3 109 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 3.881A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N THR 3 137 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 132 through 137' Processing helix chain '3' and resid 138 through 146 removed outlier: 3.773A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 4.798A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 182 removed outlier: 4.557A pdb=" N ASP 3 182 " --> pdb=" O GLN 3 178 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 40 removed outlier: 5.032A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 52 removed outlier: 4.258A pdb=" N GLU 5 51 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE 5 52 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 47 through 52' Processing helix chain '5' and resid 116 through 125 Processing helix chain '5' and resid 133 through 142 removed outlier: 4.100A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP 5 141 " --> pdb=" O LEU 5 137 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP 5 142 " --> pdb=" O SER 5 138 " (cutoff:3.500A) Processing helix chain '5' and resid 149 through 163 Processing helix chain '5' and resid 172 through 196 Proline residue: 5 178 - end of helix removed outlier: 4.185A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LYS 5 194 " --> pdb=" O SER 5 190 " (cutoff:3.500A) Proline residue: 5 196 - end of helix Processing helix chain '5' and resid 241 through 252 removed outlier: 4.084A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 304 removed outlier: 5.037A pdb=" N LEU 5 304 " --> pdb=" O ARG 5 300 " (cutoff:3.500A) Processing helix chain '5' and resid 305 through 329 Processing helix chain '5' and resid 407 through 420 removed outlier: 4.126A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 49 removed outlier: 5.264A pdb=" N GLU 6 49 " --> pdb=" O LEU 6 45 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 68 removed outlier: 3.814A pdb=" N TYR 6 57 " --> pdb=" O SER 6 53 " (cutoff:3.500A) Proline residue: 6 68 - end of helix Processing helix chain '6' and resid 73 through 79 removed outlier: 3.789A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 99 through 117 removed outlier: 5.401A pdb=" N VAL 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) Processing helix chain '6' and resid 118 through 126 Processing helix chain '6' and resid 131 through 143 Processing helix chain '6' and resid 144 through 156 Processing helix chain '6' and resid 194 through 199 Processing helix chain '6' and resid 292 through 297 Processing helix chain '6' and resid 299 through 308 removed outlier: 3.619A pdb=" N HIS 6 307 " --> pdb=" O PHE 6 303 " (cutoff:3.500A) Processing helix chain '6' and resid 324 through 333 Processing helix chain '6' and resid 363 through 371 removed outlier: 4.350A pdb=" N ASP 6 367 " --> pdb=" O LEU 6 363 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ASP 6 371 " --> pdb=" O ASP 6 367 " (cutoff:3.500A) Processing helix chain '6' and resid 157 through 163 removed outlier: 4.009A pdb=" N PHE 6 162 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 60 Proline residue: 7 60 - end of helix Processing helix chain '7' and resid 87 through 96 Processing helix chain '7' and resid 97 through 103 Processing helix chain '7' and resid 135 through 158 removed outlier: 3.990A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 186 through 191 removed outlier: 3.755A pdb=" N ASP 7 190 " --> pdb=" O ASP 7 186 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU 7 191 " --> pdb=" O SER 7 187 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 186 through 191' Processing helix chain '7' and resid 195 through 213 Processing helix chain '7' and resid 222 through 231 Processing helix chain '7' and resid 233 through 248 Proline residue: 7 248 - end of helix Processing helix chain '7' and resid 309 through 322 removed outlier: 4.239A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 4.849A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) Processing helix chain '8' and resid 107 through 154 removed outlier: 3.567A pdb=" N THR 8 111 " --> pdb=" O THR 8 107 " (cutoff:3.500A) Processing helix chain '8' and resid 155 through 164 removed outlier: 5.209A pdb=" N ALA 8 159 " --> pdb=" O PRO 8 155 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU 8 160 " --> pdb=" O LYS 8 156 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS 8 163 " --> pdb=" O ALA 8 159 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '8' and resid 165 through 170 removed outlier: 3.891A pdb=" N LEU 8 168 " --> pdb=" O ASP 8 165 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE 8 169 " --> pdb=" O PRO 8 166 " (cutoff:3.500A) Proline residue: 8 170 - end of helix No H-bonds generated for 'chain '8' and resid 165 through 170' Processing helix chain '9' and resid 27 through 34 Processing helix chain '9' and resid 53 through 58 removed outlier: 3.582A pdb=" N VAL 9 57 " --> pdb=" O ILE 9 53 " (cutoff:3.500A) Proline residue: 9 58 - end of helix No H-bonds generated for 'chain '9' and resid 53 through 58' Processing helix chain '9' and resid 87 through 96 Processing helix chain '9' and resid 97 through 106 Processing helix chain 'C' and resid 39 through 57 removed outlier: 4.589A pdb=" N VAL C 54 " --> pdb=" O MET C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 removed outlier: 4.774A pdb=" N GLU C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 97 through 106 removed outlier: 3.631A pdb=" N HIS C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.728A pdb=" N LEU C 163 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Proline residue: C 165 - end of helix Processing helix chain 'C' and resid 185A through 195 removed outlier: 5.502A pdb=" N LEU C 189 " --> pdb=" O GLY C 185A" (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 222 through 228 removed outlier: 4.705A pdb=" N GLY C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 245 removed outlier: 3.611A pdb=" N TRP C 241 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 4.903A 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 279 removed outlier: 3.698A pdb=" N LYS C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 274 through 279' Processing helix chain 'C' and resid 280 through 300 Proline residue: C 285 - end of helix removed outlier: 5.593A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 331 removed outlier: 4.015A pdb=" N TYR C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL C 320 " --> pdb=" O GLN C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 349 Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.744A pdb=" N LEU D 187 " --> pdb=" O PRO D 183 " (cutoff:3.500A) Proline residue: D 188 - end of helix No H-bonds generated for 'chain 'D' and resid 183 through 188' Processing helix chain 'D' and resid 259 through 267 removed outlier: 3.713A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 297 removed outlier: 4.633A pdb=" N SER D 294 " --> pdb=" O PRO D 290 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LYS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 removed outlier: 4.249A pdb=" N ASN D 253 " --> pdb=" O VAL D 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 3.676A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 3.720A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.199A pdb=" N LYS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 158' Processing helix chain 'E' and resid 159 through 169 Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.656A pdb=" N PHE E 198 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ARG E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 through 199' Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 108 removed outlier: 4.605A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 6.155A pdb=" N ARG F 121 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 185 Processing helix chain 'F' and resid 199 through 211 removed outlier: 3.577A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 3.837A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 5.028A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 3.704A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG F 279 " --> pdb=" O TRP F 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 103 removed outlier: 3.655A pdb=" N MET G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 116 Processing helix chain 'G' and resid 120 through 135 Processing helix chain 'G' and resid 137 through 149 Proline residue: G 149 - end of helix Processing helix chain 'G' and resid 155 through 170 Processing helix chain 'G' and resid 173 through 183 removed outlier: 3.589A pdb=" N ARG G 178 " --> pdb=" O GLY G 174 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL G 179 " --> pdb=" O LYS G 175 " (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 226 removed outlier: 4.038A pdb=" N ARG G 224 " --> pdb=" O PRO G 220 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASP G 226 " --> pdb=" O VAL G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 239 removed outlier: 6.061A pdb=" N GLU G 231 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 252 removed outlier: 4.601A pdb=" N GLU G 252 " --> pdb=" O ILE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 272 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 79 removed outlier: 3.595A pdb=" N ARG H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 74 through 79' Processing helix chain 'H' and resid 85 through 90 removed outlier: 3.895A pdb=" N ARG H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Proline residue: H 90 - end of helix No H-bonds generated for 'chain 'H' and resid 85 through 90' Processing helix chain 'H' and resid 115 through 121 Processing helix chain 'H' and resid 122 through 127 Processing helix chain 'H' and resid 133 through 147 Processing helix chain 'I' and resid 41 through 52 Processing helix chain 'I' and resid 61 through 66 Proline residue: I 66 - end of helix Processing helix chain 'I' and resid 77 through 93 removed outlier: 3.714A pdb=" N GLN I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 120 removed outlier: 3.911A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 139 Proline residue: I 133 - end of helix removed outlier: 3.862A pdb=" N GLU I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 172 removed outlier: 3.651A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) Proline residue: I 172 - end of helix Processing helix chain 'I' and resid 187 through 197 Processing helix chain 'J' and resid 36 through 41 removed outlier: 3.821A pdb=" N GLN J 41 " --> pdb=" O PRO J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 4.314A pdb=" N LYS J 61 " --> pdb=" O THR J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 96 removed outlier: 3.704A pdb=" N PHE J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 125 removed outlier: 4.086A pdb=" N ILE J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA J 125 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 152 removed outlier: 4.128A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER J 143 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY J 152 " --> pdb=" O ALA J 148 " (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 70 through 75 Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 101 through 113 Proline residue: K 113 - end of helix Processing helix chain 'K' and resid 115 through 126 removed outlier: 5.011A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU K 125 " --> pdb=" O MET K 121 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N HIS K 126 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 Processing helix chain 'K' and resid 154 through 159 removed outlier: 5.508A pdb=" N THR K 159 " --> pdb=" O LEU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 167 Proline residue: K 167 - end of helix Processing helix chain 'L' and resid 44 through 49 Processing helix chain 'L' and resid 125 through 131 removed outlier: 4.714A pdb=" N LYS L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 125 through 131' Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'M' and resid 10 through 20 removed outlier: 3.542A pdb=" N ASP M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 55 through 60 Processing helix chain 'M' and resid 73 through 79 Proline residue: M 79 - end of helix Processing helix chain 'M' and resid 97 through 108 Processing helix chain 'M' and resid 117 through 125 Processing helix chain 'M' and resid 160 through 171 removed outlier: 3.583A pdb=" N GLY M 171 " --> pdb=" O ILE M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 190 Proline residue: M 190 - end of helix Processing helix chain 'M' and resid 191 through 197 removed outlier: 3.664A pdb=" N GLY M 197 " --> pdb=" O PHE M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 216 Proline residue: M 212 - end of helix Processing helix chain 'M' and resid 225 through 241 removed outlier: 3.859A pdb=" N PHE M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Proline residue: M 230 - end of helix Processing helix chain 'M' and resid 246 through 251 removed outlier: 3.985A pdb=" N ASP M 250 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLU M 251 " --> pdb=" O ILE M 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 246 through 251' Processing helix chain 'M' and resid 252 through 258 Processing helix chain 'M' and resid 287 through 296 Processing helix chain 'N' and resid 98 through 113 Processing helix chain 'N' and resid 168 through 184 removed outlier: 4.601A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) Proline residue: N 184 - end of helix Processing helix chain 'N' and resid 191 through 209 Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 225 through 231 removed outlier: 4.494A pdb=" N VAL N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 4.447A 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: 4.315A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 81 removed outlier: 5.004A pdb=" N THR O 81 " --> pdb=" O ASP O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 98 removed outlier: 4.292A pdb=" N ILE O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 87 - end of helix removed outlier: 3.978A pdb=" N LEU O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ALA O 94 " --> pdb=" O PHE O 90 " (cutoff:3.500A) Proline residue: O 95 - end of helix Processing helix chain 'O' and resid 143 through 160 Processing helix chain 'P' and resid 54 through 60 Processing helix chain 'P' and resid 109 through 117 removed outlier: 5.249A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU P 116 " --> pdb=" O ILE P 112 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR P 117 " --> pdb=" O LYS P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 140 Processing helix chain 'P' and resid 149 through 155 Processing helix chain 'P' and resid 156 through 169 Processing helix chain 'Q' and resid 77 through 82 removed outlier: 4.141A pdb=" N ILE Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Proline residue: Q 82 - end of helix No H-bonds generated for 'chain 'Q' and resid 77 through 82' Processing helix chain 'Q' and resid 88 through 107 removed outlier: 3.891A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 193 removed outlier: 4.676A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP Q 192 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 200 removed outlier: 4.086A pdb=" N SER Q 198 " --> pdb=" O LEU Q 194 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N PHE Q 200 " --> pdb=" O GLU Q 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 removed outlier: 3.660A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 262 removed outlier: 3.701A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 268 removed outlier: 4.263A pdb=" N PHE Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 290 Processing helix chain 'R' and resid 16 through 29 removed outlier: 4.000A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 38 removed outlier: 4.482A pdb=" N ARG R 37 " --> pdb=" O GLY R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 44 removed outlier: 4.120A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 64 removed outlier: 3.815A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS R 61 " --> pdb=" O ARG R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 79 removed outlier: 3.601A pdb=" N HIS R 79 " --> pdb=" O ALA R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 Processing helix chain 'R' and resid 98 through 109 Processing helix chain 'R' and resid 110 through 134 Processing helix chain 'S' and resid 68 through 90 Processing helix chain 'S' and resid 150 through 155 removed outlier: 3.513A pdb=" N VAL S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ARG S 155 " --> pdb=" O LYS S 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 150 through 155' Processing helix chain 'T' and resid 49 through 57 removed outlier: 3.680A pdb=" N LYS T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN T 55 " --> pdb=" O TRP T 51 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE T 57 " --> pdb=" O LYS T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 95 removed outlier: 3.925A pdb=" N TYR T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 110 removed outlier: 3.714A pdb=" N PHE T 108 " --> pdb=" O ALA T 104 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN T 109 " --> pdb=" O GLN T 105 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASP T 110 " --> pdb=" O LEU T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 131 removed outlier: 4.120A pdb=" N LYS T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 206 removed outlier: 3.628A pdb=" N ARG T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 60 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'V' and resid 28 through 36 Proline residue: V 36 - end of helix Processing helix chain 'V' and resid 116 through 121 removed outlier: 4.762A pdb=" N LYS V 121 " --> pdb=" O HIS V 117 " (cutoff:3.500A) 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 121 removed outlier: 3.739A pdb=" N LEU W 120 " --> pdb=" O LEU W 116 " (cutoff:3.500A) Proline residue: W 121 - end of helix Processing helix chain 'X' and resid 7 through 19 removed outlier: 3.787A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY X 19 " --> pdb=" O GLN X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 25 Proline residue: X 25 - end of helix Processing helix chain 'X' and resid 26 through 35 removed outlier: 5.431A pdb=" N GLU X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 79 removed outlier: 3.955A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG X 77 " --> pdb=" O PRO X 73 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU X 79 " --> pdb=" O SER X 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 72 through 79' Processing helix chain 'X' and resid 128 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 192 Processing helix chain 'X' and resid 197 through 204 removed outlier: 4.572A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL X 204 " --> pdb=" O GLU X 200 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 220 Processing helix chain 'X' and resid 225 through 244 removed outlier: 3.619A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 69 removed outlier: 4.669A pdb=" N PHE Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASP Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 63 through 69' Processing helix chain 'Y' and resid 70 through 75 removed outlier: 3.589A pdb=" N TRP Y 74 " --> pdb=" O ASP Y 70 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLY Y 75 " --> pdb=" O PRO Y 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 70 through 75' Processing helix chain 'Y' and resid 86 through 94 removed outlier: 3.866A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS Y 93 " --> pdb=" O GLN Y 89 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 removed outlier: 3.561A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 158 removed outlier: 4.747A pdb=" N LEU Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 192 removed outlier: 5.464A pdb=" N LYS Y 192 " --> pdb=" O TRP Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 198 removed outlier: 5.050A pdb=" N ARG Y 198 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 238 removed outlier: 4.436A pdb=" N ASP Y 206 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 48 removed outlier: 4.320A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ALA Z 48 " --> pdb=" O LYS Z 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 48' 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 114 Processing helix chain 'a' and resid 68 through 73 removed outlier: 4.115A pdb=" N THR a 72 " --> pdb=" O PRO a 68 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS a 73 " --> pdb=" O TYR a 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 68 through 73' Processing helix chain 'a' and resid 104 through 117 Processing helix chain 'a' and resid 119 through 124 removed outlier: 4.690A pdb=" N TRP a 123 " --> pdb=" O THR a 119 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR a 124 " --> pdb=" O LYS a 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 119 through 124' Processing helix chain 'a' and resid 127 through 135 removed outlier: 6.123A pdb=" N ASN a 135 " --> pdb=" O ARG a 131 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.557A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG b 21 " --> pdb=" O ASN b 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 16 through 21' Processing helix chain 'b' and resid 37 through 50 removed outlier: 3.640A pdb=" N ARG b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA b 43 " --> pdb=" O SER b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 59 Proline residue: b 59 - end of helix Processing helix chain 'b' and resid 93 through 107 Processing helix chain 'c' and resid 34 through 54 removed outlier: 5.401A pdb=" N ALA c 38 " --> pdb=" O GLY c 34 " (cutoff:3.500A) Proline residue: c 54 - end of helix Processing helix chain 'c' and resid 59 through 64 removed outlier: 3.929A pdb=" N LYS c 63 " --> pdb=" O ARG c 59 " (cutoff:3.500A) Proline residue: c 64 - end of helix No H-bonds generated for 'chain 'c' and resid 59 through 64' Processing helix chain 'c' and resid 67 through 80 Processing helix chain 'c' and resid 84 through 94 removed outlier: 5.330A pdb=" N ASN c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 107 removed outlier: 3.774A pdb=" N GLN c 107 " --> pdb=" O ALA c 103 " (cutoff:3.500A) Processing helix chain 'c' and resid 122 through 146 Proline residue: c 146 - end of helix Processing helix chain 'c' and resid 149 through 162 Processing helix chain 'c' and resid 163 through 174 Processing helix chain 'c' and resid 187 through 206 Processing helix chain 'c' and resid 207 through 224 removed outlier: 3.684A pdb=" N ILE c 220 " --> pdb=" O ARG c 216 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET c 223 " --> pdb=" O LEU c 219 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR c 224 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 4.000A pdb=" N LYS c 233 " --> pdb=" O PHE c 229 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 249 Processing helix chain 'c' and resid 288 through 306 Processing helix chain 'd' and resid 48 through 54 removed outlier: 4.593A pdb=" N THR d 52 " --> pdb=" O PRO d 48 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU d 53 " --> pdb=" O LYS d 49 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS d 54 " --> pdb=" O PHE d 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 48 through 54' Processing helix chain 'd' and resid 118 through 130 removed outlier: 4.153A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 155 Proline residue: d 138 - end of helix Processing helix chain 'd' and resid 156 through 164 removed outlier: 3.957A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 174 Proline residue: d 170 - end of helix Processing helix chain 'e' and resid 64 through 82 Processing helix chain 'e' and resid 116 through 132 removed outlier: 3.605A pdb=" N LEU e 120 " --> pdb=" O LEU e 116 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE e 131 " --> pdb=" O LYS e 127 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 143 removed outlier: 4.685A pdb=" N GLU e 142 " --> pdb=" O THR e 138 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS e 143 " --> pdb=" O GLU e 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 138 through 143' Processing helix chain 'e' and resid 183 through 194 removed outlier: 4.064A pdb=" N ALA e 193 " --> pdb=" O GLU e 189 " (cutoff:3.500A) Processing helix chain 'e' and resid 256 through 264 removed outlier: 6.501A pdb=" N LEU e 260 " --> pdb=" O THR e 256 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY e 261 " --> pdb=" O LYS e 257 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 277 removed outlier: 3.545A pdb=" N GLN e 271 " --> pdb=" O LYS e 267 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL e 272 " --> pdb=" O TYR e 268 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ARG e 273 " --> pdb=" O LEU e 269 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N SER e 277 " --> pdb=" O ARG e 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 64 removed outlier: 4.634A pdb=" N LYS f 64 " --> pdb=" O LYS f 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 99 through 118 Processing helix chain 'f' and resid 163 through 178 removed outlier: 3.645A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 53 removed outlier: 4.388A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) Proline residue: g 53 - end of helix Processing helix chain 'g' and resid 116 through 132 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 93 through 109 Processing helix chain 'h' and resid 113 through 121 removed outlier: 4.308A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET h 120 " --> pdb=" O ARG h 116 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N CYS h 121 " --> pdb=" O LEU h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 132 removed outlier: 3.768A pdb=" N VAL h 132 " --> pdb=" O ASP h 128 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 147 removed outlier: 4.162A pdb=" N SER h 146 " --> pdb=" O GLU h 142 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ASN h 147 " --> pdb=" O LEU h 143 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 54 Processing helix chain 'i' and resid 59 through 64 Processing helix chain 'i' and resid 69 through 75 removed outlier: 4.005A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE i 74 " --> pdb=" O PRO i 70 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ARG i 75 " --> pdb=" O LYS i 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 69 through 75' Processing helix chain 'i' and resid 86 through 98 Processing helix chain 'i' and resid 103 through 123 Processing helix chain 'j' and resid 24 through 32 Processing helix chain 'j' and resid 60 through 105 Processing helix chain 'j' and resid 41 through 46 removed outlier: 4.269A pdb=" N LEU j 46 " --> pdb=" O GLY j 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 41 through 46' Processing helix chain 'k' and resid 27 through 37 removed outlier: 3.715A pdb=" N ARG k 31 " --> pdb=" O VAL k 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 47 removed outlier: 5.061A pdb=" N THR k 45 " --> pdb=" O LYS k 41 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 96 Processing helix chain 'o' and resid 28 through 52 removed outlier: 4.075A pdb=" N MET o 51 " --> pdb=" O TYR o 47 " (cutoff:3.500A) Proline residue: o 52 - end of helix Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 63 through 81 removed outlier: 4.016A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 removed outlier: 4.113A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS o 99 " --> pdb=" O LEU o 95 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LYS o 100 " --> pdb=" O ASN o 96 " (cutoff:3.500A) Processing helix chain 'p' and resid 44 through 50 Proline residue: p 50 - end of helix Processing helix chain 'p' and resid 54 through 60 removed outlier: 4.329A pdb=" N ALA p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TRP p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 72 through 77 removed outlier: 4.865A pdb=" N THR p 77 " --> pdb=" O LEU p 73 " (cutoff:3.500A) Processing helix chain 'p' and resid 112 through 123 Processing helix chain 'p' and resid 142 through 163 Processing helix chain 'p' and resid 174 through 190 removed outlier: 3.870A pdb=" N ILE p 178 " --> pdb=" O LYS p 174 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLN p 190 " --> pdb=" O GLU p 186 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 53 removed outlier: 3.950A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 48 through 53' Processing helix chain 'q' and resid 54 through 65 Processing helix chain 'q' and resid 71 through 76 removed outlier: 4.253A pdb=" N LEU q 75 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TRP q 76 " --> pdb=" O PRO q 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 71 through 76' 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 76 Processing helix chain 'r' and resid 85 through 94 removed outlier: 4.166A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ARG r 94 " --> pdb=" O SER r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 106 Processing helix chain 'r' and resid 108 through 126 Processing helix chain 'r' and resid 178 through 183 removed outlier: 4.029A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP r 183 " --> pdb=" O PRO r 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 178 through 183' 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 140 through 155 Processing helix chain 's' and resid 164 through 193 removed outlier: 4.886A pdb=" N SER s 169 " --> pdb=" O ARG s 165 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU s 170 " --> pdb=" O TYR s 166 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU s 174 " --> pdb=" O GLU s 170 " (cutoff:3.500A) Proline residue: s 175 - end of helix Proline residue: s 190 - end of helix Proline residue: s 193 - end of helix Processing helix chain 's' and resid 267 through 272 removed outlier: 4.227A pdb=" N LEU s 271 " --> pdb=" O LYS s 267 " (cutoff:3.500A) Proline residue: s 272 - end of helix No H-bonds generated for 'chain 's' and resid 267 through 272' Processing helix chain 's' and resid 307 through 315 Processing helix chain 's' and resid 318 through 344 removed outlier: 4.204A pdb=" N VAL s 322 " --> pdb=" O ASP s 318 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 387 removed outlier: 5.336A pdb=" N ASN s 386 " --> pdb=" O GLN s 382 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN s 387 " --> pdb=" O ALA s 383 " (cutoff:3.500A) Processing helix chain 's' and resid 414 through 427 removed outlier: 3.813A pdb=" N LEU s 418 " --> pdb=" O ASN s 414 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 105 Processing helix chain 'u' and resid 131 through 150 Processing helix chain 'u' and resid 181 through 189 Processing helix chain 'u' and resid 190 through 196 Processing helix chain 'v' and resid 5 through 24 removed outlier: 3.944A pdb=" N VAL v 9 " --> pdb=" O SER v 5 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU v 10 " --> pdb=" O ARG v 6 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU v 23 " --> pdb=" O GLN v 19 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ARG v 24 " --> pdb=" O GLY v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 41 Processing helix chain 'v' and resid 47 through 64 removed outlier: 3.617A pdb=" N ARG v 51 " --> pdb=" O ASP v 47 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU v 52 " --> pdb=" O ALA v 48 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG v 53 " --> pdb=" O GLU v 49 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 90 removed outlier: 3.573A pdb=" N TYR w 90 " --> pdb=" O VAL w 86 " (cutoff:3.500A) Processing helix chain 'w' and resid 111 through 126 removed outlier: 4.954A pdb=" N GLU w 125 " --> pdb=" O ALA w 121 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 139 removed outlier: 4.175A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N MET w 139 " --> pdb=" O ALA w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 140 through 152 Processing helix chain 'w' and resid 104 through 109 Processing sheet with id= 1, first strand: chain '0' and resid 107 through 111 removed outlier: 4.043A pdb=" N HIS 0 115 " --> pdb=" O CYS 0 110 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '0' and resid 155 through 159 Processing sheet with id= 3, first strand: chain '1' and resid 17 through 22 removed outlier: 5.971A pdb=" N PHE 1 28 " --> pdb=" O SER 1 22 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '1' and resid 41 through 46 removed outlier: 5.954A pdb=" N LEU 1 41 " --> pdb=" O GLU 1 58 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '3' and resid 122 through 125 removed outlier: 5.560A pdb=" N TRP 3 122 " --> pdb=" O CYS 3 150 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '4' and resid 66 through 69 removed outlier: 6.843A pdb=" N TRP 4 88 " --> pdb=" O GLN 4 102 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '5' and resid 126 through 130 removed outlier: 5.312A pdb=" N VAL 5 351 " --> pdb=" O ASP 5 348 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '5' and resid 200 through 205 removed outlier: 8.695A pdb=" N ARG 5 200 " --> pdb=" O LYS 5 233 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '5' and resid 206 through 214 removed outlier: 6.219A pdb=" N SER 5 207 " --> pdb=" O GLY 5 226 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLY 5 226 " --> pdb=" O SER 5 207 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU 5 219 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '5' and resid 350 through 353 removed outlier: 8.599A pdb=" N ARG 5 350 " --> pdb=" O LEU 5 382 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '6' and resid 183 through 187 removed outlier: 3.708A pdb=" N ASP 6 183 " --> pdb=" O VAL 6 179 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '6' and resid 190 through 193 removed outlier: 4.604A pdb=" N ARG 6 322 " --> pdb=" O VAL 6 193 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ARG 6 267 " --> pdb=" O LEU 6 221 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR 6 232 " --> pdb=" O SER 6 220 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '6' and resid 215 through 218 removed outlier: 4.031A pdb=" N TRP 6 235 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '6' and resid 272 through 276 removed outlier: 6.589A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR 6 310 " --> pdb=" O ASP 6 276 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '7' and resid 77 through 82 removed outlier: 4.549A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE 7 127 " --> pdb=" O VAL 7 70 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '7' and resid 164 through 167 removed outlier: 6.964A pdb=" N ASP 7 182 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '7' and resid 217 through 221 Processing sheet with id= 18, first strand: chain '7' and resid 281 through 286 removed outlier: 5.509A pdb=" N ILE 7 294 " --> pdb=" O LEU 7 286 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '9' and resid 42 through 45 removed outlier: 3.756A pdb=" N ARG 9 49 " --> pdb=" O THR 9 45 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'C' and resid 130 through 133 removed outlier: 5.331A pdb=" N ARG C 130 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C' and resid 230 through 236 removed outlier: 6.887A pdb=" N GLN C 230 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN C 199 " --> pdb=" O ASP C 175 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASP C 255 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ASP C 250 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY C 303 " --> pdb=" O ARG C 382 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LYS C 379 " --> pdb=" O GLU C 339 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLN C 335 " --> pdb=" O LEU C 383 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 361 through 365 Processing sheet with id= 23, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.674A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 217 through 220 removed outlier: 3.763A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'D' and resid 138 through 144 removed outlier: 5.278A pdb=" N ASP D 138 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'E' and resid 98 through 101 Processing sheet with id= 27, first strand: chain 'E' and resid 105 through 111 removed outlier: 3.816A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASN E 281 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLU E 330 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'E' and resid 131 through 134 removed outlier: 3.541A pdb=" N LYS E 131 " --> pdb=" O SER E 146 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR E 191 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'E' and resid 265 through 269 removed outlier: 4.367A pdb=" N GLN E 202 " --> pdb=" O VAL E 273 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'E' and resid 142 through 148 No H-bonds generated for sheet with id= 30 Processing sheet with id= 31, first strand: chain 'F' and resid 46 through 50 Processing sheet with id= 32, first strand: chain 'F' and resid 186 through 189 Processing sheet with id= 33, first strand: chain 'H' and resid 55 through 58 removed outlier: 7.032A pdb=" N ILE H 55 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'H' and resid 94 through 98 removed outlier: 3.757A pdb=" N LEU H 98 " --> pdb=" O ASP H 110 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP H 110 " --> pdb=" O LEU H 98 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'I' and resid 94 through 100 removed outlier: 4.216A pdb=" N ALA I 97 " --> pdb=" O LEU I 154 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'J' and resid 18 through 25 removed outlier: 3.501A pdb=" N ILE J 70 " --> pdb=" O ILE J 20 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA J 22 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL J 24 " --> pdb=" O LEU J 66 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS J 81 " --> pdb=" O LYS J 69 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU J 71 " --> pdb=" O GLU J 79 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU J 79 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'K' and resid 55 through 60 removed outlier: 5.297A pdb=" N ASP K 22 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'K' and resid 77 through 81 removed outlier: 7.322A pdb=" N GLY K 86 " --> pdb=" O THR K 81 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'L' and resid 38 through 41 Processing sheet with id= 40, first strand: chain 'L' and resid 72 through 76 Processing sheet with id= 41, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 42, first strand: chain 'M' and resid 273 through 277 Processing sheet with id= 43, first strand: chain 'N' and resid 93 through 96 removed outlier: 5.294A pdb=" N HIS N 149 " --> pdb=" O ILE N 131 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'N' and resid 118 through 123 removed outlier: 3.990A pdb=" N PHE N 119 " --> pdb=" O GLY N 164 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ALA N 186 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.138A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N TYR O 104 " --> pdb=" O LYS O 126 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'P' and resid 80 through 85 removed outlier: 6.720A pdb=" N VAL P 90 " --> pdb=" O THR P 107 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Q' and resid 130 through 135 removed outlier: 6.666A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'Q' and resid 139 through 142 removed outlier: 7.849A pdb=" N ALA Q 147 " --> pdb=" O LEU Q 166 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'S' and resid 105 through 109 Processing sheet with id= 50, first strand: chain 'S' and resid 112 through 117 removed outlier: 3.816A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU S 126 " --> pdb=" O VAL S 160 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'S' and resid 162 through 165 Processing sheet with id= 52, first strand: chain 'S' and resid 168 through 175 removed outlier: 4.063A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'T' and resid 71 through 78 removed outlier: 4.968A pdb=" N ALA T 71 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS T 177 " --> pdb=" O ALA T 143 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASN T 139 " --> pdb=" O GLY T 181 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'T' and resid 152 through 159 No H-bonds generated for sheet with id= 54 Processing sheet with id= 55, first strand: chain 'U' and resid 26 through 29 removed outlier: 4.359A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'V' and resid 92 through 97 removed outlier: 5.903A pdb=" N ASN V 92 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'V' and resid 132 through 135 removed outlier: 7.315A pdb=" N GLU V 132 " --> pdb=" O THR V 148 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG V 145 " --> pdb=" O ILE V 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE V 154 " --> pdb=" O ARG V 145 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG V 152 " --> pdb=" O SER V 147 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'W' and resid 81 through 84 removed outlier: 4.370A pdb=" N CYS W 88 " --> pdb=" O GLY W 84 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'W' and resid 97 through 103 Processing sheet with id= 60, first strand: chain 'X' and resid 49 through 53 removed outlier: 5.373A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN X 58 " --> pdb=" O ASN X 53 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'X' and resid 85 through 92 removed outlier: 4.988A pdb=" N LYS X 99 " --> pdb=" O ALA X 92 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 63, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.260A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'a' and resid 44 through 52 removed outlier: 5.218A pdb=" N ASN a 44 " --> pdb=" O VAL a 65 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL a 65 " --> pdb=" O ASN a 44 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'b' and resid 61 through 68 removed outlier: 4.124A pdb=" N ALA b 83 " --> pdb=" O TYR b 79 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'c' and resid 254 through 257 Processing sheet with id= 67, first strand: chain 'c' and resid 269 through 275 removed outlier: 3.792A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'd' and resid 212 through 218 removed outlier: 3.971A pdb=" N TYR d 245 " --> pdb=" O ILE d 265 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'e' and resid 53 through 57 removed outlier: 5.604A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU e 159 " --> pdb=" O LEU e 53 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG e 162 " --> pdb=" O HIS e 251 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N HIS e 251 " --> pdb=" O ARG e 162 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'e' and resid 201 through 204 removed outlier: 7.036A pdb=" N GLU e 201 " --> pdb=" O LEU e 239 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'f' and resid 123 through 127 removed outlier: 4.720A pdb=" N GLU f 123 " --> pdb=" O GLN f 158 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR f 125 " --> pdb=" O VAL f 156 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET f 127 " --> pdb=" O GLU f 154 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLU f 154 " --> pdb=" O MET f 127 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'g' and resid 95 through 101 removed outlier: 5.469A pdb=" N VAL g 137 " --> pdb=" O LYS g 150 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'k' and resid 49 through 56 removed outlier: 4.151A pdb=" N PHE k 20 " --> pdb=" O ASP k 54 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS k 72 " --> pdb=" O PHE k 68 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'm' and resid 63 through 67 removed outlier: 5.461A pdb=" N ARG m 73 " --> pdb=" O PRO m 53 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU m 55 " --> pdb=" O ARG m 73 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'p' and resid 78 through 82 Processing sheet with id= 76, first strand: chain 'r' and resid 35 through 41 removed outlier: 4.030A pdb=" N PHE r 35 " --> pdb=" O THR r 54 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 's' and resid 90 through 93 removed outlier: 4.113A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N HIS s 281 " --> pdb=" O TYR s 209 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 's' and resid 112 through 116 removed outlier: 6.376A pdb=" N ASN s 391 " --> pdb=" O ASN s 375 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN s 375 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS s 393 " --> pdb=" O GLN s 373 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLN s 373 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY s 395 " --> pdb=" O CYS s 371 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N CYS s 371 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLN s 397 " --> pdb=" O PHE s 369 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N PHE s 369 " --> pdb=" O GLN s 397 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N LYS s 365 " --> pdb=" O LEU s 401 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR s 297 " --> pdb=" O ILE s 241 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 's' and resid 241 through 244 removed outlier: 6.693A pdb=" N ILE s 241 " --> pdb=" O HIS s 296 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'u' and resid 107 through 114 removed outlier: 3.927A pdb=" N ASP u 108 " --> pdb=" O SER u 128 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP u 122 " --> pdb=" O VAL u 114 " (cutoff:3.500A) 2805 hydrogen bonds defined for protein. 8319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 923 hydrogen bonds 1574 hydrogen bond angles 0 basepair planarities 378 basepair parallelities 691 stacking parallelities Total time for adding SS restraints: 65.72 Time building geometry restraints manager: 42.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 23362 1.33 - 1.45: 29467 1.45 - 1.57: 50286 1.57 - 1.69: 2871 1.69 - 1.82: 489 Bond restraints: 106475 Sorted by residual: bond pdb=" C2 GTP A3358 " pdb=" N3 GTP A3358 " ideal model delta sigma weight residual 1.380 1.331 0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" C2 GTP A3359 " pdb=" N3 GTP A3359 " ideal model delta sigma weight residual 1.380 1.332 0.048 2.00e-02 2.50e+03 5.80e+00 bond pdb=" C4' GTP A3359 " pdb=" O4' GTP A3359 " ideal model delta sigma weight residual 1.410 1.452 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C4' GTP A3358 " pdb=" O4' GTP A3358 " ideal model delta sigma weight residual 1.410 1.451 -0.041 2.00e-02 2.50e+03 4.24e+00 bond pdb=" N GLU R 126 " pdb=" CA GLU R 126 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.21e-02 6.83e+03 4.19e+00 ... (remaining 106470 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.35: 8307 105.35 - 112.70: 59109 112.70 - 120.06: 39802 120.06 - 127.41: 39927 127.41 - 134.77: 3692 Bond angle restraints: 150837 Sorted by residual: angle pdb=" C LEU u 149 " pdb=" N LYS u 150 " pdb=" CA LYS u 150 " ideal model delta sigma weight residual 122.84 114.50 8.34 1.81e+00 3.05e-01 2.12e+01 angle pdb=" PA GTP A3358 " pdb=" O3A GTP A3358 " pdb=" PB GTP A3358 " ideal model delta sigma weight residual 120.50 133.03 -12.53 3.00e+00 1.11e-01 1.74e+01 angle pdb=" C1' GTP A3359 " pdb=" C2' GTP A3359 " pdb=" C3' GTP A3359 " ideal model delta sigma weight residual 111.00 98.69 12.31 3.00e+00 1.11e-01 1.68e+01 angle pdb=" PB GTP A3359 " pdb=" O3B GTP A3359 " pdb=" PG GTP A3359 " ideal model delta sigma weight residual 120.50 132.64 -12.14 3.00e+00 1.11e-01 1.64e+01 angle pdb=" PA GTP A3359 " pdb=" O3A GTP A3359 " pdb=" PB GTP A3359 " ideal model delta sigma weight residual 120.50 132.09 -11.59 3.00e+00 1.11e-01 1.49e+01 ... (remaining 150832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 61845 36.00 - 72.00: 3297 72.00 - 108.00: 460 108.00 - 144.00: 25 144.00 - 180.00: 34 Dihedral angle restraints: 65661 sinusoidal: 40505 harmonic: 25156 Sorted by residual: dihedral pdb=" O4' C A2079 " pdb=" C1' C A2079 " pdb=" N1 C A2079 " pdb=" C2 C A2079 " ideal model delta sinusoidal sigma weight residual -160.00 19.55 -179.55 1 1.50e+01 4.44e-03 8.53e+01 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 21.89 178.11 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 18.06 -178.06 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 65658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 14957 0.045 - 0.090: 1967 0.090 - 0.135: 696 0.135 - 0.180: 40 0.180 - 0.225: 5 Chirality restraints: 17665 Sorted by residual: chirality pdb=" C1' U A1759 " pdb=" O4' U A1759 " pdb=" C2' U A1759 " pdb=" N1 U A1759 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C3' GTP A3358 " pdb=" C2' GTP A3358 " pdb=" C4' GTP A3358 " pdb=" O3' GTP A3358 " both_signs ideal model delta sigma weight residual False -2.47 -2.68 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C2' GTP A3359 " pdb=" C1' GTP A3359 " pdb=" C3' GTP A3359 " pdb=" O2' GTP A3359 " both_signs ideal model delta sigma weight residual False -2.47 -2.68 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 17662 not shown) Planarity restraints: 14003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 124 " 0.026 2.00e-02 2.50e+03 5.33e-02 2.84e+01 pdb=" C ARG R 124 " -0.092 2.00e-02 2.50e+03 pdb=" O ARG R 124 " 0.035 2.00e-02 2.50e+03 pdb=" N HIS R 125 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A1759 " -0.032 2.00e-02 2.50e+03 1.68e-02 6.33e+00 pdb=" N1 U A1759 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U A1759 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U A1759 " 0.006 2.00e-02 2.50e+03 pdb=" N3 U A1759 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U A1759 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U A1759 " -0.014 2.00e-02 2.50e+03 pdb=" C5 U A1759 " 0.004 2.00e-02 2.50e+03 pdb=" C6 U A1759 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2892 " 0.032 2.00e-02 2.50e+03 1.48e-02 6.02e+00 pdb=" N9 A A2892 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A A2892 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A A2892 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A2892 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A A2892 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A A2892 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A A2892 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A A2892 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A A2892 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A A2892 " -0.004 2.00e-02 2.50e+03 ... (remaining 14000 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 352 2.39 - 3.02: 58670 3.02 - 3.64: 170068 3.64 - 4.27: 270714 4.27 - 4.90: 408309 Nonbonded interactions: 908113 Sorted by model distance: nonbonded pdb=" O2' G A2403 " pdb=" OP1 U A2404 " model vdw 1.761 2.440 nonbonded pdb=" OP1 A A2430 " pdb="MG MG A3313 " model vdw 1.818 2.170 nonbonded pdb=" OP1 A A1961 " pdb="MG MG A3313 " model vdw 1.835 2.170 nonbonded pdb=" O2' G A2643 " pdb=" OP2 G A2645 " model vdw 1.846 2.440 nonbonded pdb=" O2' G A3123 " pdb=" O6 G A3132 " model vdw 1.876 2.440 ... (remaining 908108 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 12.960 Check model and map are aligned: 1.140 Set scattering table: 0.720 Process input model: 297.440 Find NCS groups from input model: 3.070 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:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 330.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 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 : 0.003 0.049 106475 Z= 0.197 Angle : 0.504 12.530 150837 Z= 0.259 Chirality : 0.037 0.225 17665 Planarity : 0.004 0.053 14003 Dihedral : 19.054 179.998 49363 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.18 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 1.34 (0.09), residues: 8462 helix: 2.00 (0.10), residues: 3084 sheet: -0.27 (0.16), residues: 1056 loop : 0.51 (0.10), residues: 4322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP s 335 HIS 0.010 0.001 HIS S 76 PHE 0.016 0.001 PHE F 106 TYR 0.036 0.001 TYR 5 176 ARG 0.008 0.000 ARG R 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1915 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1915 time to evaluate : 7.351 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: 0 132 LYS cc_start: 0.8793 (mtpp) cc_final: 0.8446 (mtmm) REVERT: 2 52 GLU cc_start: 0.8361 (mp0) cc_final: 0.8025 (mp0) REVERT: 4 69 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8675 (mmtm) REVERT: 4 74 LYS cc_start: 0.9256 (mtpt) cc_final: 0.8986 (mtmm) REVERT: 6 43 SER cc_start: 0.9072 (p) cc_final: 0.8836 (p) REVERT: 7 235 TYR cc_start: 0.8763 (m-80) cc_final: 0.8502 (m-80) REVERT: 8 116 LEU cc_start: 0.9387 (mm) cc_final: 0.9168 (pp) REVERT: 9 59 GLU cc_start: 0.8216 (tt0) cc_final: 0.8005 (tt0) REVERT: 9 84 THR cc_start: 0.9132 (p) cc_final: 0.8823 (t) REVERT: 9 90 GLN cc_start: 0.8539 (tt0) cc_final: 0.7689 (tt0) REVERT: C 52 TYR cc_start: 0.9043 (m-10) cc_final: 0.8651 (m-80) REVERT: C 153 MET cc_start: 0.8339 (mmm) cc_final: 0.8137 (mmm) REVERT: C 206 SER cc_start: 0.8614 (m) cc_final: 0.8370 (p) REVERT: C 212 ARG cc_start: 0.7686 (ttm170) cc_final: 0.6935 (ttp80) REVERT: C 349 MET cc_start: 0.8985 (ttm) cc_final: 0.8710 (tpp) REVERT: C 353 CYS cc_start: 0.8479 (m) cc_final: 0.8192 (p) REVERT: C 376 TYR cc_start: 0.7802 (t80) cc_final: 0.7569 (t80) REVERT: D 161 ASP cc_start: 0.8202 (m-30) cc_final: 0.7789 (m-30) REVERT: D 277 ARG cc_start: 0.7016 (ttm110) cc_final: 0.6681 (ttt90) REVERT: F 201 GLN cc_start: 0.8436 (tp40) cc_final: 0.8211 (tp-100) REVERT: G 274 TYR cc_start: 0.9176 (t80) cc_final: 0.8233 (t80) REVERT: H 113 SER cc_start: 0.8958 (m) cc_final: 0.8400 (m) REVERT: I 95 MET cc_start: 0.7526 (ppp) cc_final: 0.6991 (ppp) REVERT: I 99 CYS cc_start: 0.8256 (m) cc_final: 0.7527 (t) REVERT: I 107 GLU cc_start: 0.8914 (pm20) cc_final: 0.8528 (pp20) REVERT: I 119 HIS cc_start: 0.7424 (t70) cc_final: 0.6983 (t-90) REVERT: I 123 MET cc_start: 0.8367 (tmm) cc_final: 0.8129 (tmm) REVERT: J 54 ASN cc_start: 0.9138 (m-40) cc_final: 0.8658 (m-40) REVERT: J 115 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7604 (tptt) REVERT: J 118 TYR cc_start: 0.5909 (m-80) cc_final: 0.5464 (m-80) REVERT: K 52 ASP cc_start: 0.8365 (t0) cc_final: 0.8031 (t0) REVERT: K 139 LYS cc_start: 0.9031 (mttp) cc_final: 0.8677 (mmmm) REVERT: K 153 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8927 (mtmm) REVERT: O 40 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7852 (mt-10) REVERT: O 74 ARG cc_start: 0.8418 (mtp-110) cc_final: 0.8112 (mtm110) REVERT: P 106 SER cc_start: 0.8584 (p) cc_final: 0.8372 (p) REVERT: P 132 LEU cc_start: 0.9321 (tp) cc_final: 0.8964 (tm) REVERT: Q 184 ASP cc_start: 0.8418 (m-30) cc_final: 0.8098 (m-30) REVERT: T 119 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7760 (mt-10) REVERT: V 49 ILE cc_start: 0.9122 (mm) cc_final: 0.8615 (mm) REVERT: V 60 ASP cc_start: 0.8431 (m-30) cc_final: 0.8139 (m-30) REVERT: V 75 LYS cc_start: 0.8308 (tttt) cc_final: 0.8035 (tttm) REVERT: V 82 GLN cc_start: 0.8845 (mp10) cc_final: 0.8304 (mp10) REVERT: V 92 ASN cc_start: 0.9105 (t0) cc_final: 0.8190 (t0) REVERT: V 119 GLN cc_start: 0.9071 (mt0) cc_final: 0.8825 (mt0) REVERT: V 124 ASP cc_start: 0.5487 (t70) cc_final: 0.4896 (t0) REVERT: W 93 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7983 (mm-30) REVERT: W 111 THR cc_start: 0.8941 (p) cc_final: 0.8419 (p) REVERT: Y 70 ASP cc_start: 0.8492 (t70) cc_final: 0.8172 (t0) REVERT: Z 47 GLN cc_start: 0.8780 (mt0) cc_final: 0.7991 (mt0) REVERT: c 238 MET cc_start: 0.9122 (tpp) cc_final: 0.8875 (mmm) REVERT: c 305 TYR cc_start: 0.9235 (m-10) cc_final: 0.8826 (m-10) REVERT: d 151 CYS cc_start: 0.7673 (m) cc_final: 0.7442 (m) REVERT: d 274 GLN cc_start: 0.8594 (tt0) cc_final: 0.8238 (tt0) REVERT: e 154 ASP cc_start: 0.8170 (p0) cc_final: 0.7885 (m-30) REVERT: g 42 VAL cc_start: 0.8599 (p) cc_final: 0.8395 (p) REVERT: h 88 ASP cc_start: 0.8734 (m-30) cc_final: 0.8428 (m-30) REVERT: h 135 GLN cc_start: 0.8008 (pt0) cc_final: 0.7687 (pt0) REVERT: j 81 SER cc_start: 0.9095 (m) cc_final: 0.8889 (p) REVERT: k 28 GLU cc_start: 0.8285 (tp30) cc_final: 0.7714 (tp30) REVERT: k 32 THR cc_start: 0.9187 (p) cc_final: 0.8671 (p) REVERT: k 66 VAL cc_start: 0.8860 (t) cc_final: 0.8448 (p) REVERT: k 68 PHE cc_start: 0.8011 (m-80) cc_final: 0.7440 (m-10) REVERT: k 84 LEU cc_start: 0.9376 (mm) cc_final: 0.9172 (tm) REVERT: p 117 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8381 (mm110) REVERT: p 152 GLN cc_start: 0.8968 (tp40) cc_final: 0.8054 (tp40) REVERT: p 153 LYS cc_start: 0.9206 (mtmt) cc_final: 0.8969 (mtmm) REVERT: p 156 ASP cc_start: 0.8281 (m-30) cc_final: 0.7742 (m-30) REVERT: p 157 MET cc_start: 0.8177 (mtm) cc_final: 0.7870 (mtp) REVERT: q 44 ASP cc_start: 0.8556 (t0) cc_final: 0.8184 (t0) REVERT: r 54 THR cc_start: 0.8813 (p) cc_final: 0.8471 (p) REVERT: r 174 MET cc_start: 0.9162 (mtm) cc_final: 0.8960 (mtp) REVERT: u 95 ASP cc_start: 0.8928 (m-30) cc_final: 0.8456 (m-30) REVERT: u 96 MET cc_start: 0.8557 (tpt) cc_final: 0.8330 (tpt) REVERT: u 99 SER cc_start: 0.9239 (p) cc_final: 0.8699 (p) REVERT: u 105 ASN cc_start: 0.8902 (m-40) cc_final: 0.8514 (t0) REVERT: u 136 HIS cc_start: 0.8971 (m90) cc_final: 0.8768 (m90) REVERT: u 159 ILE cc_start: 0.9374 (mt) cc_final: 0.9171 (mt) REVERT: u 160 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7999 (mt-10) REVERT: u 165 ASP cc_start: 0.8265 (p0) cc_final: 0.8050 (p0) REVERT: u 166 ASP cc_start: 0.8330 (p0) cc_final: 0.7836 (p0) REVERT: v 16 LEU cc_start: 0.9084 (mm) cc_final: 0.8609 (mm) REVERT: v 19 GLN cc_start: 0.8696 (tt0) cc_final: 0.8259 (pt0) REVERT: v 56 GLU cc_start: 0.9132 (tp30) cc_final: 0.8898 (tp30) REVERT: w 116 VAL cc_start: 0.9138 (t) cc_final: 0.8912 (m) REVERT: w 119 ILE cc_start: 0.9557 (mm) cc_final: 0.9287 (mp) outliers start: 0 outliers final: 5 residues processed: 1915 average time/residue: 1.8875 time to fit residues: 4891.8484 Evaluate side-chains 1351 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1346 time to evaluate : 6.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain d residue 128 TYR Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain s residue 228 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 827 optimal weight: 0.0770 chunk 742 optimal weight: 9.9990 chunk 412 optimal weight: 9.9990 chunk 253 optimal weight: 10.0000 chunk 501 optimal weight: 0.9980 chunk 396 optimal weight: 0.8980 chunk 768 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 chunk 467 optimal weight: 9.9990 chunk 571 optimal weight: 8.9990 chunk 889 optimal weight: 8.9990 overall best weight: 3.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 102 GLN 5 94 HIS 5 160 HIS ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN C 71 GLN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN D 221 ASN D 227 GLN D 235 GLN F 63 GLN F 74 GLN F 184 GLN F 228 GLN F 257 GLN ** G 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 GLN G 287 ASN H 126 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN I 151 ASN ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN L 72 GLN L 113 ASN L 142 GLN M 53 HIS M 219 ASN N 98 HIS N 178 GLN N 209 ASN P 147 GLN P 162 GLN P 176 GLN Q 139 GLN R 147 GLN S 91 GLN S 118 ASN T 202 GLN T 210 HIS U 23 ASN V 117 HIS X 15 GLN X 241 GLN Y 89 GLN Y 99 HIS Y 147 GLN Y 183 GLN Z 62 ASN ** Z 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 44 ASN a 46 ASN a 137 ASN c 249 ASN d 77 HIS d 154 ASN d 220 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 118 HIS k 93 HIS o 94 HIS ** q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 142 ASN s 152 GLN s 179 GLN ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 397 GLN v 42 ASN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 106475 Z= 0.332 Angle : 0.601 14.727 150837 Z= 0.305 Chirality : 0.040 0.310 17665 Planarity : 0.005 0.057 14003 Dihedral : 20.716 179.853 31131 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.41 % Allowed : 11.50 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 1.25 (0.09), residues: 8462 helix: 1.82 (0.09), residues: 3084 sheet: -0.24 (0.15), residues: 1080 loop : 0.53 (0.10), residues: 4298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Z 81 HIS 0.010 0.001 HIS E 280 PHE 0.025 0.002 PHE d 145 TYR 0.034 0.002 TYR 5 176 ARG 0.011 0.001 ARG 6 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1550 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1366 time to evaluate : 7.021 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: 2 52 GLU cc_start: 0.8381 (mp0) cc_final: 0.8071 (mp0) REVERT: 4 69 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8689 (mmtm) REVERT: 6 50 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8681 (mmtp) REVERT: 6 116 ASN cc_start: 0.8843 (t0) cc_final: 0.8601 (t0) REVERT: 6 329 TYR cc_start: 0.7183 (m-80) cc_final: 0.6981 (m-80) REVERT: 7 143 TRP cc_start: 0.9295 (OUTLIER) cc_final: 0.6686 (m-90) REVERT: 8 121 TRP cc_start: 0.8459 (t-100) cc_final: 0.8106 (t-100) REVERT: 9 59 GLU cc_start: 0.8166 (tt0) cc_final: 0.7956 (tt0) REVERT: C 52 TYR cc_start: 0.9095 (m-10) cc_final: 0.8882 (m-80) REVERT: C 206 SER cc_start: 0.8650 (m) cc_final: 0.8332 (p) REVERT: C 212 ARG cc_start: 0.7672 (ttm170) cc_final: 0.6937 (ttp80) REVERT: C 349 MET cc_start: 0.8959 (ttm) cc_final: 0.8688 (tpp) REVERT: C 353 CYS cc_start: 0.8496 (m) cc_final: 0.8201 (p) REVERT: D 135 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7018 (mtm-85) REVERT: D 161 ASP cc_start: 0.8243 (m-30) cc_final: 0.7861 (m-30) REVERT: D 249 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8529 (m-40) REVERT: D 277 ARG cc_start: 0.6896 (ttm110) cc_final: 0.6598 (ttt90) REVERT: F 201 GLN cc_start: 0.8455 (tp40) cc_final: 0.8214 (tp-100) REVERT: G 189 MET cc_start: 0.8426 (mtp) cc_final: 0.8112 (mtp) REVERT: G 274 TYR cc_start: 0.9146 (t80) cc_final: 0.8238 (t80) REVERT: H 138 LYS cc_start: 0.8713 (ttpp) cc_final: 0.7449 (ttpp) REVERT: I 105 SER cc_start: 0.8625 (p) cc_final: 0.7655 (p) REVERT: I 108 ASP cc_start: 0.8773 (m-30) cc_final: 0.7849 (m-30) REVERT: I 109 LYS cc_start: 0.9118 (mmtp) cc_final: 0.8792 (mmtp) REVERT: I 119 HIS cc_start: 0.7669 (t70) cc_final: 0.7317 (t-90) REVERT: I 132 LYS cc_start: 0.9226 (mmtp) cc_final: 0.8886 (mptt) REVERT: I 140 TYR cc_start: 0.8632 (m-80) cc_final: 0.8401 (m-80) REVERT: I 144 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8429 (mm) REVERT: I 185 ILE cc_start: 0.7901 (pp) cc_final: 0.7116 (mp) REVERT: J 92 LYS cc_start: 0.9066 (ptmt) cc_final: 0.8788 (pttp) REVERT: J 115 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7367 (tptt) REVERT: J 118 TYR cc_start: 0.5674 (m-80) cc_final: 0.5322 (m-80) REVERT: J 142 ARG cc_start: 0.8922 (ptp-110) cc_final: 0.8574 (ptp-110) REVERT: J 154 ARG cc_start: 0.8943 (mtp-110) cc_final: 0.8713 (ttm110) REVERT: K 52 ASP cc_start: 0.8346 (t0) cc_final: 0.8017 (t0) REVERT: K 143 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: K 164 ASP cc_start: 0.8571 (m-30) cc_final: 0.8336 (m-30) REVERT: O 40 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7996 (mt-10) REVERT: O 82 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7525 (mt-10) REVERT: Q 99 MET cc_start: 0.8946 (mtp) cc_final: 0.8668 (mtm) REVERT: Q 184 ASP cc_start: 0.8422 (m-30) cc_final: 0.8171 (m-30) REVERT: Q 186 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8928 (p) REVERT: S 153 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9160 (mm) REVERT: S 165 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6926 (pp20) REVERT: U 46 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8538 (mmt) REVERT: U 131 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7146 (tp30) REVERT: U 133 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8719 (mm-30) REVERT: U 134 ARG cc_start: 0.8181 (tmm-80) cc_final: 0.7894 (tmm-80) REVERT: V 75 LYS cc_start: 0.8345 (tttt) cc_final: 0.8141 (ttmm) REVERT: V 92 ASN cc_start: 0.9084 (t0) cc_final: 0.8139 (t0) REVERT: V 119 GLN cc_start: 0.9036 (mt0) cc_final: 0.8797 (mt0) REVERT: W 93 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8028 (mm-30) REVERT: W 111 THR cc_start: 0.8895 (p) cc_final: 0.8534 (p) REVERT: Y 147 GLN cc_start: 0.8395 (tp40) cc_final: 0.7733 (tp40) REVERT: Y 151 ASP cc_start: 0.7664 (m-30) cc_final: 0.7387 (m-30) REVERT: Z 43 GLU cc_start: 0.7305 (tm-30) cc_final: 0.7057 (tm-30) REVERT: Z 84 ASP cc_start: 0.8269 (m-30) cc_final: 0.7988 (m-30) REVERT: b 45 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: c 238 MET cc_start: 0.9100 (tpp) cc_final: 0.8844 (tpp) REVERT: c 305 TYR cc_start: 0.9255 (m-10) cc_final: 0.8931 (m-10) REVERT: d 124 ARG cc_start: 0.8777 (mmm160) cc_final: 0.8448 (mmm160) REVERT: d 159 ARG cc_start: 0.7803 (mtp-110) cc_final: 0.7544 (mtp-110) REVERT: e 258 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8159 (p0) REVERT: i 49 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: j 97 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8321 (ttmm) REVERT: k 28 GLU cc_start: 0.8276 (tp30) cc_final: 0.7690 (tp30) REVERT: k 32 THR cc_start: 0.9169 (p) cc_final: 0.8785 (p) REVERT: k 73 ARG cc_start: 0.6884 (pmt-80) cc_final: 0.6505 (pmt-80) REVERT: k 84 LEU cc_start: 0.9329 (mm) cc_final: 0.9120 (tm) REVERT: o 91 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: p 117 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8536 (mm110) REVERT: p 152 GLN cc_start: 0.8965 (tp40) cc_final: 0.8078 (tp40) REVERT: p 153 LYS cc_start: 0.9208 (mtmt) cc_final: 0.8914 (mtmm) REVERT: p 156 ASP cc_start: 0.8307 (m-30) cc_final: 0.7713 (m-30) REVERT: p 157 MET cc_start: 0.8344 (mtm) cc_final: 0.8019 (mtp) REVERT: p 183 MET cc_start: 0.8306 (tmm) cc_final: 0.8035 (tmm) REVERT: q 44 ASP cc_start: 0.8657 (t0) cc_final: 0.8312 (t0) REVERT: r 50 GLU cc_start: 0.6308 (pm20) cc_final: 0.6035 (pm20) REVERT: r 174 MET cc_start: 0.9140 (mtm) cc_final: 0.8834 (mtp) REVERT: s 385 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: u 93 ASP cc_start: 0.8703 (p0) cc_final: 0.8408 (p0) REVERT: u 95 ASP cc_start: 0.8765 (m-30) cc_final: 0.8538 (m-30) REVERT: u 96 MET cc_start: 0.8602 (tpt) cc_final: 0.8268 (tpt) REVERT: u 99 SER cc_start: 0.9159 (p) cc_final: 0.8411 (p) REVERT: u 105 ASN cc_start: 0.8904 (m-40) cc_final: 0.8598 (t0) REVERT: u 141 TYR cc_start: 0.8882 (t80) cc_final: 0.8310 (t80) REVERT: u 145 MET cc_start: 0.8237 (mmp) cc_final: 0.7927 (mmp) REVERT: u 160 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7992 (mt-10) REVERT: u 165 ASP cc_start: 0.8384 (p0) cc_final: 0.8081 (p0) REVERT: u 166 ASP cc_start: 0.8213 (p0) cc_final: 0.7989 (p0) REVERT: u 175 MET cc_start: 0.8550 (ptp) cc_final: 0.8183 (ptp) REVERT: v 19 GLN cc_start: 0.8707 (tt0) cc_final: 0.8280 (mm110) REVERT: v 54 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8693 (tm-30) REVERT: v 56 GLU cc_start: 0.9113 (tp30) cc_final: 0.8787 (tp30) REVERT: v 59 LEU cc_start: 0.9514 (mt) cc_final: 0.9303 (mp) REVERT: w 116 VAL cc_start: 0.9113 (t) cc_final: 0.8892 (m) outliers start: 184 outliers final: 65 residues processed: 1428 average time/residue: 1.8138 time to fit residues: 3547.3655 Evaluate side-chains 1344 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1265 time to evaluate : 7.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 164 THR Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 6 residue 44 ASN Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 257 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 249 ASN Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 149 HIS Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 165 GLU Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain U residue 46 MET Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 127 TYR Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 111 SER Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 45 GLU Chi-restraints excluded: chain c residue 249 ASN Chi-restraints excluded: chain d residue 216 MET Chi-restraints excluded: chain e residue 258 ASP Chi-restraints excluded: chain e residue 278 ASP Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain g residue 122 LYS Chi-restraints excluded: chain h residue 141 ASP Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 49 GLU Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 111 GLU Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 132 ARG Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 254 ASP Chi-restraints excluded: chain s residue 385 GLN Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 187 ILE Chi-restraints excluded: chain u residue 201 ASP Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 34 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 494 optimal weight: 10.0000 chunk 276 optimal weight: 10.0000 chunk 740 optimal weight: 3.9990 chunk 606 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 891 optimal weight: 20.0000 chunk 963 optimal weight: 0.3980 chunk 794 optimal weight: 8.9990 chunk 884 optimal weight: 3.9990 chunk 303 optimal weight: 0.8980 chunk 715 optimal weight: 4.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 384 GLN ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 234 HIS ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 55 GLN 9 90 GLN D 182 HIS F 63 GLN F 228 GLN F 257 GLN ** G 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN L 72 GLN L 142 GLN N 98 HIS N 178 GLN O 154 GLN P 162 GLN P 176 GLN R 89 ASN R 147 GLN S 118 ASN T 133 ASN T 202 GLN V 35 ASN Y 88 GLN Y 89 GLN Z 47 GLN Z 62 ASN ** Z 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 46 ASN a 137 ASN b 27 GLN d 154 ASN d 220 GLN d 274 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 85 ASN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 125 ASN p 182 ASN ** q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 142 ASN ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 106475 Z= 0.256 Angle : 0.569 11.483 150837 Z= 0.290 Chirality : 0.039 0.309 17665 Planarity : 0.004 0.044 14003 Dihedral : 20.675 179.221 31125 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.51 % Allowed : 13.39 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 8462 helix: 1.74 (0.09), residues: 3091 sheet: -0.27 (0.15), residues: 1082 loop : 0.51 (0.10), residues: 4289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 110 HIS 0.007 0.001 HIS k 93 PHE 0.022 0.001 PHE d 145 TYR 0.037 0.001 TYR v 13 ARG 0.009 0.000 ARG U 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1512 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1320 time to evaluate : 7.206 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: 0 102 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8573 (mttm) REVERT: 1 38 ARG cc_start: 0.8423 (mmm160) cc_final: 0.8007 (mtp-110) REVERT: 2 52 GLU cc_start: 0.8343 (mp0) cc_final: 0.8063 (mp0) REVERT: 6 50 LYS cc_start: 0.8981 (mmmm) cc_final: 0.8749 (mmtp) REVERT: 6 116 ASN cc_start: 0.8945 (t0) cc_final: 0.8694 (t0) REVERT: 6 124 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7429 (ptt90) REVERT: 6 329 TYR cc_start: 0.7083 (m-80) cc_final: 0.6854 (m-80) REVERT: 7 143 TRP cc_start: 0.9288 (OUTLIER) cc_final: 0.6670 (m-90) REVERT: 7 247 ASN cc_start: 0.8883 (t0) cc_final: 0.8612 (p0) REVERT: 8 121 TRP cc_start: 0.8673 (t-100) cc_final: 0.8399 (t-100) REVERT: 9 90 GLN cc_start: 0.8491 (tt0) cc_final: 0.7336 (tt0) REVERT: 9 124 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7923 (tm-30) REVERT: C 206 SER cc_start: 0.8626 (m) cc_final: 0.8272 (p) REVERT: C 212 ARG cc_start: 0.7685 (ttm170) cc_final: 0.6914 (ttp80) REVERT: C 349 MET cc_start: 0.8979 (ttm) cc_final: 0.8717 (tpp) REVERT: C 353 CYS cc_start: 0.8498 (m) cc_final: 0.8168 (p) REVERT: C 380 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8088 (mtm) REVERT: D 135 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.6769 (mtm-85) REVERT: D 161 ASP cc_start: 0.8228 (m-30) cc_final: 0.7843 (m-30) REVERT: D 249 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8460 (m-40) REVERT: D 277 ARG cc_start: 0.6765 (ttm110) cc_final: 0.6498 (ttt90) REVERT: F 201 GLN cc_start: 0.8442 (tp40) cc_final: 0.8209 (tp-100) REVERT: G 159 MET cc_start: 0.9220 (tpt) cc_final: 0.8572 (tpt) REVERT: G 217 HIS cc_start: 0.8118 (t-90) cc_final: 0.7912 (t-90) REVERT: G 274 TYR cc_start: 0.9110 (t80) cc_final: 0.8216 (t80) REVERT: H 110 ASP cc_start: 0.8664 (p0) cc_final: 0.8356 (p0) REVERT: H 138 LYS cc_start: 0.8480 (ttpp) cc_final: 0.7914 (ttpp) REVERT: I 108 ASP cc_start: 0.8714 (m-30) cc_final: 0.8255 (m-30) REVERT: I 117 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6269 (ptt180) REVERT: I 119 HIS cc_start: 0.7722 (t70) cc_final: 0.7329 (t70) REVERT: I 123 MET cc_start: 0.8345 (tmm) cc_final: 0.8129 (tmm) REVERT: I 132 LYS cc_start: 0.9222 (mmtp) cc_final: 0.8933 (mptt) REVERT: I 175 PRO cc_start: 0.8324 (Cg_endo) cc_final: 0.8064 (Cg_exo) REVERT: I 185 ILE cc_start: 0.7944 (pp) cc_final: 0.7178 (mp) REVERT: J 55 GLU cc_start: 0.8841 (tp30) cc_final: 0.8571 (tm-30) REVERT: J 92 LYS cc_start: 0.9055 (ptmt) cc_final: 0.8788 (pttp) REVERT: J 115 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7159 (tptt) REVERT: J 118 TYR cc_start: 0.5478 (m-80) cc_final: 0.5212 (m-80) REVERT: J 142 ARG cc_start: 0.8935 (ptp-110) cc_final: 0.8642 (ptp-110) REVERT: K 52 ASP cc_start: 0.8358 (t0) cc_final: 0.8022 (t0) REVERT: K 164 ASP cc_start: 0.8555 (m-30) cc_final: 0.8335 (m-30) REVERT: L 43 ASN cc_start: 0.8190 (t0) cc_final: 0.7925 (t0) REVERT: O 40 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7996 (mt-10) REVERT: P 162 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8170 (mt0) REVERT: Q 99 MET cc_start: 0.8924 (mtp) cc_final: 0.8677 (mtm) REVERT: Q 184 ASP cc_start: 0.8467 (m-30) cc_final: 0.8234 (m-30) REVERT: S 165 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6964 (pp20) REVERT: U 46 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8562 (mmt) REVERT: U 135 GLN cc_start: 0.9019 (tp40) cc_final: 0.8807 (tp40) REVERT: V 75 LYS cc_start: 0.8379 (tttt) cc_final: 0.8145 (ttmm) REVERT: V 82 GLN cc_start: 0.8874 (mp10) cc_final: 0.8414 (mp10) REVERT: V 92 ASN cc_start: 0.9090 (t0) cc_final: 0.8168 (t0) REVERT: V 119 GLN cc_start: 0.9012 (mt0) cc_final: 0.8683 (mt0) REVERT: W 93 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7942 (mm-30) REVERT: W 112 GLU cc_start: 0.8257 (pp20) cc_final: 0.7820 (pp20) REVERT: Y 147 GLN cc_start: 0.8385 (tp40) cc_final: 0.7751 (tp-100) REVERT: Y 151 ASP cc_start: 0.7641 (m-30) cc_final: 0.7368 (m-30) REVERT: Z 131 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: a 56 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8288 (mtp180) REVERT: c 238 MET cc_start: 0.9063 (tpp) cc_final: 0.8822 (tpp) REVERT: d 128 TYR cc_start: 0.8533 (m-80) cc_final: 0.8137 (m-80) REVERT: d 154 ASN cc_start: 0.8394 (t0) cc_final: 0.8148 (t0) REVERT: d 159 ARG cc_start: 0.7961 (mtp-110) cc_final: 0.7505 (ttm-80) REVERT: e 123 MET cc_start: 0.8298 (ppp) cc_final: 0.7872 (ppp) REVERT: e 149 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6493 (tp) REVERT: f 178 LEU cc_start: 0.8791 (tp) cc_final: 0.8295 (mp) REVERT: h 93 ASP cc_start: 0.8453 (t70) cc_final: 0.8235 (t70) REVERT: h 135 GLN cc_start: 0.7609 (pt0) cc_final: 0.7142 (pt0) REVERT: h 142 GLU cc_start: 0.7798 (tp30) cc_final: 0.7593 (tp30) REVERT: i 49 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: i 84 LYS cc_start: 0.9176 (ttpp) cc_final: 0.8887 (ttpp) REVERT: k 28 GLU cc_start: 0.8231 (tp30) cc_final: 0.7666 (tp30) REVERT: k 32 THR cc_start: 0.9176 (p) cc_final: 0.8815 (p) REVERT: o 91 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: p 117 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8561 (mm110) REVERT: p 149 ASP cc_start: 0.8689 (t0) cc_final: 0.8284 (t0) REVERT: p 152 GLN cc_start: 0.8968 (tp40) cc_final: 0.8005 (tp40) REVERT: p 153 LYS cc_start: 0.9199 (mtmt) cc_final: 0.8825 (mtmm) REVERT: p 156 ASP cc_start: 0.8280 (m-30) cc_final: 0.7645 (m-30) REVERT: p 157 MET cc_start: 0.8361 (mtm) cc_final: 0.8065 (mtp) REVERT: p 182 ASN cc_start: 0.8592 (m-40) cc_final: 0.8289 (m110) REVERT: p 183 MET cc_start: 0.8349 (tmm) cc_final: 0.7732 (tmm) REVERT: q 44 ASP cc_start: 0.8681 (t0) cc_final: 0.8301 (t0) REVERT: q 111 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: r 132 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7096 (mmp-170) REVERT: s 385 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: u 93 ASP cc_start: 0.8722 (p0) cc_final: 0.8437 (p0) REVERT: u 95 ASP cc_start: 0.8682 (m-30) cc_final: 0.8472 (m-30) REVERT: u 96 MET cc_start: 0.8613 (tpt) cc_final: 0.8235 (tpt) REVERT: u 99 SER cc_start: 0.9171 (p) cc_final: 0.8416 (p) REVERT: u 141 TYR cc_start: 0.8835 (t80) cc_final: 0.8500 (t80) REVERT: u 144 LYS cc_start: 0.8765 (tppt) cc_final: 0.8518 (tppt) REVERT: u 145 MET cc_start: 0.8336 (mmp) cc_final: 0.7942 (mmp) REVERT: u 160 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8220 (mt-10) REVERT: u 165 ASP cc_start: 0.8321 (p0) cc_final: 0.8021 (p0) REVERT: u 166 ASP cc_start: 0.8222 (p0) cc_final: 0.7984 (p0) REVERT: v 19 GLN cc_start: 0.8743 (tt0) cc_final: 0.8411 (mm110) REVERT: v 27 ASP cc_start: 0.8578 (t0) cc_final: 0.8342 (t0) REVERT: v 54 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8746 (tm-30) REVERT: v 55 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9241 (pp) outliers start: 192 outliers final: 82 residues processed: 1402 average time/residue: 1.8264 time to fit residues: 3504.4945 Evaluate side-chains 1350 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1249 time to evaluate : 6.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 102 LYS Chi-restraints excluded: chain 0 residue 164 THR Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 62 ILE Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 6 residue 43 SER Chi-restraints excluded: chain 6 residue 44 ASN Chi-restraints excluded: chain 6 residue 124 ARG Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 257 ILE Chi-restraints excluded: chain 8 residue 126 GLN Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 249 ASN Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 117 ARG Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 162 GLN Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 165 GLU Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 151 GLN Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 46 MET Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 127 TYR Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 111 SER Chi-restraints excluded: chain V residue 150 SER Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 42 ASP Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 50 LEU Chi-restraints excluded: chain e residue 149 LEU Chi-restraints excluded: chain e residue 278 ASP Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain g residue 144 THR Chi-restraints excluded: chain h residue 141 ASP Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 49 GLU Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 111 GLU Chi-restraints excluded: chain q residue 113 LYS Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 110 GLU Chi-restraints excluded: chain r residue 132 ARG Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 254 ASP Chi-restraints excluded: chain s residue 385 GLN Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 196 LEU Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 34 SER Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain w residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 880 optimal weight: 6.9990 chunk 670 optimal weight: 5.9990 chunk 462 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 425 optimal weight: 0.6980 chunk 598 optimal weight: 40.0000 chunk 894 optimal weight: 0.0470 chunk 947 optimal weight: 3.9990 chunk 467 optimal weight: 1.9990 chunk 848 optimal weight: 8.9990 chunk 255 optimal weight: 10.0000 overall best weight: 2.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 170 GLN 4 102 GLN ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN F 257 GLN G 167 GLN ** G 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN I 100 GLN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN N 98 HIS N 173 GLN N 178 GLN O 69 ASN P 176 GLN R 147 GLN T 133 ASN T 202 GLN V 35 ASN Y 89 GLN Z 62 ASN ** Z 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN d 220 GLN d 274 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 142 ASN ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 106475 Z= 0.237 Angle : 0.565 11.860 150837 Z= 0.288 Chirality : 0.038 0.309 17665 Planarity : 0.004 0.051 14003 Dihedral : 20.625 179.257 31125 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.64 % Allowed : 14.71 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 1.18 (0.09), residues: 8462 helix: 1.72 (0.09), residues: 3093 sheet: -0.24 (0.15), residues: 1067 loop : 0.49 (0.10), residues: 4302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Z 81 HIS 0.010 0.001 HIS k 93 PHE 0.028 0.001 PHE d 145 TYR 0.037 0.001 TYR v 13 ARG 0.013 0.000 ARG h 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1511 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1309 time to evaluate : 7.201 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: 0 102 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8591 (mttm) REVERT: 1 39 GLU cc_start: 0.8369 (pm20) cc_final: 0.8068 (pm20) REVERT: 2 52 GLU cc_start: 0.8345 (mp0) cc_final: 0.8069 (mp0) REVERT: 6 50 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8747 (mmtp) REVERT: 6 116 ASN cc_start: 0.8985 (t0) cc_final: 0.8728 (t0) REVERT: 6 124 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7359 (ptt90) REVERT: 6 235 TRP cc_start: 0.7132 (p-90) cc_final: 0.6854 (p90) REVERT: 6 330 ILE cc_start: 0.9496 (mt) cc_final: 0.9276 (mt) REVERT: 7 143 TRP cc_start: 0.9296 (OUTLIER) cc_final: 0.6684 (m-90) REVERT: 8 121 TRP cc_start: 0.8675 (t-100) cc_final: 0.8315 (t-100) REVERT: 9 94 GLU cc_start: 0.7324 (mp0) cc_final: 0.6837 (mp0) REVERT: 9 133 ARG cc_start: 0.8980 (ttp80) cc_final: 0.8584 (ttp-170) REVERT: C 206 SER cc_start: 0.8611 (m) cc_final: 0.8291 (p) REVERT: C 212 ARG cc_start: 0.7656 (ttm170) cc_final: 0.6864 (ttp80) REVERT: C 349 MET cc_start: 0.8979 (ttm) cc_final: 0.8698 (tpp) REVERT: C 353 CYS cc_start: 0.8500 (m) cc_final: 0.8167 (p) REVERT: C 380 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8079 (mtm) REVERT: D 135 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.6751 (mtm-85) REVERT: D 161 ASP cc_start: 0.8235 (m-30) cc_final: 0.7846 (m-30) REVERT: D 249 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8455 (m-40) REVERT: D 277 ARG cc_start: 0.6762 (ttm110) cc_final: 0.6496 (ttt90) REVERT: F 201 GLN cc_start: 0.8441 (tp40) cc_final: 0.8201 (tp-100) REVERT: G 181 TYR cc_start: 0.8689 (m-80) cc_final: 0.7918 (t80) REVERT: G 274 TYR cc_start: 0.9093 (t80) cc_final: 0.8135 (t80) REVERT: H 70 LYS cc_start: 0.8419 (pttp) cc_final: 0.8208 (pttm) REVERT: I 107 GLU cc_start: 0.8476 (pm20) cc_final: 0.8161 (pm20) REVERT: I 108 ASP cc_start: 0.8498 (m-30) cc_final: 0.7996 (m-30) REVERT: I 117 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6303 (ptt180) REVERT: I 119 HIS cc_start: 0.7733 (t70) cc_final: 0.7348 (t70) REVERT: I 124 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8888 (mmmm) REVERT: I 132 LYS cc_start: 0.9194 (mmtp) cc_final: 0.8915 (mptt) REVERT: I 175 PRO cc_start: 0.8503 (Cg_endo) cc_final: 0.8295 (Cg_exo) REVERT: J 52 GLU cc_start: 0.9130 (tp30) cc_final: 0.8384 (tp30) REVERT: J 84 GLN cc_start: 0.6512 (pt0) cc_final: 0.6166 (pm20) REVERT: J 118 TYR cc_start: 0.5520 (m-80) cc_final: 0.5263 (m-80) REVERT: J 142 ARG cc_start: 0.8956 (ptp-110) cc_final: 0.8659 (ptp-110) REVERT: K 52 ASP cc_start: 0.8330 (t0) cc_final: 0.7996 (t0) REVERT: K 143 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: K 164 ASP cc_start: 0.8491 (m-30) cc_final: 0.8219 (m-30) REVERT: L 43 ASN cc_start: 0.8173 (t0) cc_final: 0.7885 (t0) REVERT: L 135 SER cc_start: 0.9123 (m) cc_final: 0.8804 (m) REVERT: N 202 GLN cc_start: 0.8334 (tp40) cc_final: 0.8016 (tp40) REVERT: O 40 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8009 (mt-10) REVERT: Q 99 MET cc_start: 0.8917 (mtp) cc_final: 0.8694 (mtm) REVERT: S 165 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7040 (pp20) REVERT: T 167 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7716 (ttm) REVERT: U 46 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8511 (mmt) REVERT: V 82 GLN cc_start: 0.8879 (mp10) cc_final: 0.8512 (mp10) REVERT: V 92 ASN cc_start: 0.9094 (t0) cc_final: 0.8200 (t0) REVERT: W 93 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7934 (mm-30) REVERT: W 112 GLU cc_start: 0.8107 (pp20) cc_final: 0.7902 (pp20) REVERT: W 120 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8953 (mp) REVERT: Y 97 ASP cc_start: 0.8254 (m-30) cc_final: 0.7965 (m-30) REVERT: Y 147 GLN cc_start: 0.8416 (tp40) cc_final: 0.7739 (tp-100) REVERT: Y 151 ASP cc_start: 0.7638 (m-30) cc_final: 0.7369 (m-30) REVERT: Z 131 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7978 (tm-30) REVERT: a 56 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8272 (mtp180) REVERT: b 45 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: c 238 MET cc_start: 0.9032 (tpp) cc_final: 0.8808 (mmm) REVERT: d 128 TYR cc_start: 0.8476 (m-80) cc_final: 0.8155 (m-80) REVERT: d 154 ASN cc_start: 0.8470 (t0) cc_final: 0.8104 (t0) REVERT: e 149 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6503 (tp) REVERT: e 200 MET cc_start: 0.6508 (mpp) cc_final: 0.6023 (mpp) REVERT: e 258 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8139 (p0) REVERT: f 178 LEU cc_start: 0.8923 (tp) cc_final: 0.8412 (mp) REVERT: g 40 GLU cc_start: 0.6843 (tp30) cc_final: 0.6559 (tp30) REVERT: h 135 GLN cc_start: 0.7646 (pt0) cc_final: 0.7219 (pt0) REVERT: i 49 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: j 97 LYS cc_start: 0.8678 (ttmm) cc_final: 0.8297 (ttmm) REVERT: k 28 GLU cc_start: 0.8210 (tp30) cc_final: 0.7699 (tp30) REVERT: k 32 THR cc_start: 0.9169 (p) cc_final: 0.8750 (p) REVERT: k 84 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9176 (tm) REVERT: o 91 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: p 117 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8553 (mm110) REVERT: p 149 ASP cc_start: 0.8688 (t0) cc_final: 0.8318 (t0) REVERT: p 152 GLN cc_start: 0.8955 (tp40) cc_final: 0.7995 (tp40) REVERT: p 153 LYS cc_start: 0.9201 (mtmt) cc_final: 0.8922 (mtmm) REVERT: p 156 ASP cc_start: 0.8267 (m-30) cc_final: 0.7644 (m-30) REVERT: p 157 MET cc_start: 0.8405 (mtm) cc_final: 0.8114 (mtp) REVERT: p 182 ASN cc_start: 0.8549 (m-40) cc_final: 0.8231 (m110) REVERT: p 183 MET cc_start: 0.8370 (tmm) cc_final: 0.7721 (tmm) REVERT: q 44 ASP cc_start: 0.8686 (t0) cc_final: 0.8301 (t0) REVERT: q 111 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: r 132 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7264 (mmp-170) REVERT: u 97 MET cc_start: 0.8459 (ttp) cc_final: 0.7879 (ttm) REVERT: u 104 GLU cc_start: 0.8263 (tp30) cc_final: 0.7964 (tp30) REVERT: u 144 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8462 (ttmm) REVERT: u 160 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8170 (mt-10) REVERT: u 165 ASP cc_start: 0.8326 (p0) cc_final: 0.8022 (p0) REVERT: u 166 ASP cc_start: 0.8220 (p0) cc_final: 0.8015 (p0) REVERT: u 175 MET cc_start: 0.8454 (ptm) cc_final: 0.8226 (ptp) REVERT: v 19 GLN cc_start: 0.8728 (tt0) cc_final: 0.8384 (mm110) REVERT: v 27 ASP cc_start: 0.8685 (t0) cc_final: 0.8377 (t0) REVERT: v 54 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8447 (tm-30) outliers start: 202 outliers final: 81 residues processed: 1402 average time/residue: 1.9522 time to fit residues: 3847.1185 Evaluate side-chains 1349 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1245 time to evaluate : 7.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 102 LYS Chi-restraints excluded: chain 0 residue 164 THR Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 6 residue 124 ARG Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 257 ILE Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 147 LEU Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 249 ASN Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 117 ARG Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 18 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain S residue 165 GLU Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 151 GLN Chi-restraints excluded: chain T residue 167 MET Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 46 MET Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 127 TYR Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 111 SER Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 42 ASP Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 45 GLU Chi-restraints excluded: chain c residue 50 LEU Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain e residue 149 LEU Chi-restraints excluded: chain e residue 258 ASP Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 144 THR Chi-restraints excluded: chain h residue 141 ASP Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 49 GLU Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain p residue 181 GLU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 111 GLU Chi-restraints excluded: chain q residue 113 LYS Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 132 ARG Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 254 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 144 LYS Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 196 LEU Chi-restraints excluded: chain u residue 201 ASP Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 46 GLU Chi-restraints excluded: chain w residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 788 optimal weight: 6.9990 chunk 537 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 705 optimal weight: 10.0000 chunk 390 optimal weight: 6.9990 chunk 808 optimal weight: 0.0970 chunk 654 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 483 optimal weight: 1.9990 chunk 850 optimal weight: 7.9990 chunk 239 optimal weight: 8.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 228 GLN F 257 GLN H 126 GLN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN N 98 HIS O 69 ASN P 176 GLN R 147 GLN T 133 ASN T 202 GLN V 35 ASN Y 89 GLN Z 62 ASN ** Z 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN d 220 GLN d 274 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 ASN ** q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 142 ASN s 386 ASN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 106475 Z= 0.302 Angle : 0.583 10.433 150837 Z= 0.297 Chirality : 0.040 0.309 17665 Planarity : 0.004 0.062 14003 Dihedral : 20.586 179.837 31125 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.77 % Allowed : 15.78 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 8462 helix: 1.69 (0.09), residues: 3087 sheet: -0.27 (0.15), residues: 1067 loop : 0.45 (0.10), residues: 4308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 110 HIS 0.016 0.001 HIS k 93 PHE 0.026 0.001 PHE d 145 TYR 0.037 0.001 TYR v 13 ARG 0.015 0.001 ARG h 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1477 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1265 time to evaluate : 7.053 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: 0 128 GLU cc_start: 0.8468 (tp30) cc_final: 0.8241 (tm-30) REVERT: 1 38 ARG cc_start: 0.8426 (mmm160) cc_final: 0.8108 (mtp-110) REVERT: 6 50 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8733 (mmtp) REVERT: 6 116 ASN cc_start: 0.9008 (t0) cc_final: 0.8761 (t0) REVERT: 6 124 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7274 (ptt90) REVERT: 6 207 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7946 (pp20) REVERT: 6 235 TRP cc_start: 0.7159 (p-90) cc_final: 0.6861 (p90) REVERT: 7 143 TRP cc_start: 0.9346 (OUTLIER) cc_final: 0.6892 (m-90) REVERT: 8 125 LYS cc_start: 0.5713 (pttp) cc_final: 0.5473 (pttt) REVERT: 8 126 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: 9 90 GLN cc_start: 0.8385 (tt0) cc_final: 0.7895 (tm-30) REVERT: 9 133 ARG cc_start: 0.8967 (ttp80) cc_final: 0.8671 (ttp-170) REVERT: C 206 SER cc_start: 0.8632 (m) cc_final: 0.8349 (p) REVERT: C 212 ARG cc_start: 0.7665 (ttm170) cc_final: 0.6883 (ttp80) REVERT: C 349 MET cc_start: 0.8996 (ttm) cc_final: 0.8574 (tpp) REVERT: C 353 CYS cc_start: 0.8508 (m) cc_final: 0.8155 (p) REVERT: C 380 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8088 (mtm) REVERT: D 161 ASP cc_start: 0.8255 (m-30) cc_final: 0.7867 (m-30) REVERT: D 249 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8456 (m-40) REVERT: D 277 ARG cc_start: 0.6751 (ttm110) cc_final: 0.6488 (ttt90) REVERT: E 207 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8959 (t) REVERT: F 201 GLN cc_start: 0.8474 (tp40) cc_final: 0.8216 (tp-100) REVERT: G 96 MET cc_start: 0.8972 (tpt) cc_final: 0.8760 (mmm) REVERT: G 157 MET cc_start: 0.9065 (mmp) cc_final: 0.8788 (pmt) REVERT: G 181 TYR cc_start: 0.8702 (m-80) cc_final: 0.7916 (t80) REVERT: G 274 TYR cc_start: 0.9062 (t80) cc_final: 0.8108 (t80) REVERT: H 110 ASP cc_start: 0.8659 (p0) cc_final: 0.8375 (p0) REVERT: H 138 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8236 (ttpp) REVERT: I 107 GLU cc_start: 0.8496 (pm20) cc_final: 0.8220 (pm20) REVERT: I 108 ASP cc_start: 0.8564 (m-30) cc_final: 0.8203 (m-30) REVERT: I 117 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6322 (ptt180) REVERT: I 119 HIS cc_start: 0.7851 (t70) cc_final: 0.7569 (t-90) REVERT: I 166 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8423 (ptt90) REVERT: I 175 PRO cc_start: 0.8593 (Cg_endo) cc_final: 0.8386 (Cg_exo) REVERT: J 52 GLU cc_start: 0.9164 (tp30) cc_final: 0.8873 (tp30) REVERT: J 142 ARG cc_start: 0.8961 (ptp-110) cc_final: 0.8689 (ptp-110) REVERT: K 52 ASP cc_start: 0.8354 (t0) cc_final: 0.7997 (t0) REVERT: K 143 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: N 202 GLN cc_start: 0.8350 (tp40) cc_final: 0.7979 (tp40) REVERT: O 40 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8039 (mt-10) REVERT: P 158 MET cc_start: 0.9384 (mmp) cc_final: 0.9066 (mmp) REVERT: S 165 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7094 (pp20) REVERT: T 100 ASP cc_start: 0.8355 (m-30) cc_final: 0.8090 (m-30) REVERT: T 163 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7755 (mtp180) REVERT: T 167 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7768 (ttm) REVERT: U 46 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8573 (mmt) REVERT: V 92 ASN cc_start: 0.9088 (t0) cc_final: 0.8195 (t0) REVERT: W 57 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: W 93 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7941 (mm-30) REVERT: W 120 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8971 (mp) REVERT: Y 76 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8426 (mp10) REVERT: Y 97 ASP cc_start: 0.8277 (m-30) cc_final: 0.7939 (m-30) REVERT: Y 147 GLN cc_start: 0.8443 (tp40) cc_final: 0.7747 (tp-100) REVERT: Y 151 ASP cc_start: 0.7645 (m-30) cc_final: 0.7366 (m-30) REVERT: Z 131 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: a 56 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8221 (mtp180) REVERT: b 45 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: d 123 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8204 (tmm-80) REVERT: d 124 ARG cc_start: 0.8784 (mmm160) cc_final: 0.8385 (mmm160) REVERT: d 154 ASN cc_start: 0.8511 (t0) cc_final: 0.8086 (t0) REVERT: d 219 ARG cc_start: 0.8207 (mtp-110) cc_final: 0.7801 (mtp-110) REVERT: e 149 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6490 (tp) REVERT: e 200 MET cc_start: 0.6506 (OUTLIER) cc_final: 0.6067 (mpp) REVERT: e 258 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8144 (p0) REVERT: f 96 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7764 (m) REVERT: h 116 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7947 (mtp85) REVERT: h 135 GLN cc_start: 0.8037 (pt0) cc_final: 0.7755 (pt0) REVERT: i 49 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: k 28 GLU cc_start: 0.8170 (tp30) cc_final: 0.7766 (tp30) REVERT: k 85 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8091 (mt-10) REVERT: o 91 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8309 (tt0) REVERT: o 93 ASP cc_start: 0.8145 (t70) cc_final: 0.7901 (t0) REVERT: p 117 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8496 (mm110) REVERT: p 149 ASP cc_start: 0.8699 (t0) cc_final: 0.8326 (t0) REVERT: p 152 GLN cc_start: 0.8959 (tp40) cc_final: 0.8001 (tp40) REVERT: p 153 LYS cc_start: 0.9207 (mtmt) cc_final: 0.8914 (mtmm) REVERT: p 156 ASP cc_start: 0.8265 (m-30) cc_final: 0.7628 (m-30) REVERT: p 157 MET cc_start: 0.8438 (mtm) cc_final: 0.8217 (mtp) REVERT: p 179 ARG cc_start: 0.9015 (tmm-80) cc_final: 0.8805 (tmm-80) REVERT: p 181 GLU cc_start: 0.8693 (pp20) cc_final: 0.8340 (OUTLIER) REVERT: p 182 ASN cc_start: 0.8435 (m-40) cc_final: 0.7971 (m-40) REVERT: p 183 MET cc_start: 0.8368 (tmm) cc_final: 0.7811 (tmm) REVERT: q 44 ASP cc_start: 0.8690 (t0) cc_final: 0.8293 (t0) REVERT: q 111 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: r 132 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7310 (mmp-170) REVERT: u 93 ASP cc_start: 0.8660 (p0) cc_final: 0.8448 (p0) REVERT: u 96 MET cc_start: 0.8760 (tpp) cc_final: 0.8488 (tpt) REVERT: u 97 MET cc_start: 0.8512 (ttp) cc_final: 0.7719 (ttm) REVERT: u 104 GLU cc_start: 0.8452 (tp30) cc_final: 0.8095 (tp30) REVERT: u 144 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8491 (ttmm) REVERT: u 145 MET cc_start: 0.8310 (mmm) cc_final: 0.8093 (mmp) REVERT: u 149 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8398 (mp) REVERT: u 165 ASP cc_start: 0.8494 (p0) cc_final: 0.8202 (p0) REVERT: u 166 ASP cc_start: 0.8293 (p0) cc_final: 0.7977 (p0) REVERT: v 19 GLN cc_start: 0.8774 (tt0) cc_final: 0.8462 (mm110) REVERT: v 27 ASP cc_start: 0.8703 (t0) cc_final: 0.8396 (t0) REVERT: v 54 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8357 (tm-30) REVERT: v 55 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9107 (pp) REVERT: w 123 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.8018 (mm-30) outliers start: 212 outliers final: 115 residues processed: 1363 average time/residue: 1.8015 time to fit residues: 3367.7067 Evaluate side-chains 1362 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1216 time to evaluate : 7.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 164 THR Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 42 THR Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 1 residue 62 ILE Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 6 residue 43 SER Chi-restraints excluded: chain 6 residue 124 ARG Chi-restraints excluded: chain 6 residue 207 GLU Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 154 ILE Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 257 ILE Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 126 GLN Chi-restraints excluded: chain 8 residue 147 LEU Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 94 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 249 ASN Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 117 ARG Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 200 LYS Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 18 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 165 GLU Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 151 GLN Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 167 MET Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 46 MET Chi-restraints excluded: chain U residue 103 GLN Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 127 TYR Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 111 SER Chi-restraints excluded: chain V residue 150 SER Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 76 GLN Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 45 GLU Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain c residue 50 LEU Chi-restraints excluded: chain c residue 53 CYS Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain e residue 126 GLN Chi-restraints excluded: chain e residue 149 LEU Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain e residue 258 ASP Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 96 THR Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 122 LYS Chi-restraints excluded: chain g residue 144 THR Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 141 ASP Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 49 GLU Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 66 VAL Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 111 GLU Chi-restraints excluded: chain q residue 113 LYS Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 110 GLU Chi-restraints excluded: chain r residue 132 ARG Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 254 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 144 LYS Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 149 LEU Chi-restraints excluded: chain u residue 164 THR Chi-restraints excluded: chain u residue 196 LEU Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 46 GLU Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain v residue 62 LEU Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain w residue 123 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 318 optimal weight: 30.0000 chunk 853 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 556 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 948 optimal weight: 7.9990 chunk 787 optimal weight: 20.0000 chunk 439 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 313 optimal weight: 8.9990 chunk 497 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 266 HIS ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 243 ASN ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 228 GLN H 126 GLN I 61 HIS ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN L 72 GLN L 142 GLN O 69 ASN R 147 GLN T 133 ASN T 202 GLN U 4 ASN V 35 ASN Y 89 GLN Z 62 ASN Z 126 GLN a 46 ASN a 137 ASN b 58 ASN c 249 ASN d 220 GLN d 274 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 176 HIS ** q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 142 ASN ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 156 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 106475 Z= 0.433 Angle : 0.636 10.097 150837 Z= 0.324 Chirality : 0.042 0.304 17665 Planarity : 0.005 0.070 14003 Dihedral : 20.598 179.356 31123 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.84 % Allowed : 16.83 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 1.01 (0.09), residues: 8462 helix: 1.58 (0.09), residues: 3093 sheet: -0.35 (0.15), residues: 1091 loop : 0.41 (0.10), residues: 4278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Z 81 HIS 0.006 0.001 HIS Z 67 PHE 0.027 0.002 PHE I 134 TYR 0.040 0.002 TYR v 13 ARG 0.016 0.001 ARG h 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1241 time to evaluate : 6.992 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: 1 38 ARG cc_start: 0.8437 (mmm160) cc_final: 0.8027 (mtp-110) REVERT: 6 50 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8765 (mmtp) REVERT: 6 116 ASN cc_start: 0.9062 (t0) cc_final: 0.8824 (t0) REVERT: 6 124 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7352 (ptt90) REVERT: 6 207 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8064 (pp20) REVERT: 7 143 TRP cc_start: 0.9406 (OUTLIER) cc_final: 0.7015 (m-90) REVERT: 8 121 TRP cc_start: 0.8705 (t-100) cc_final: 0.8470 (t-100) REVERT: 8 125 LYS cc_start: 0.5825 (pttp) cc_final: 0.5519 (pttp) REVERT: 9 90 GLN cc_start: 0.8375 (tt0) cc_final: 0.8153 (tt0) REVERT: 9 94 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: C 153 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.6624 (mmm) REVERT: C 206 SER cc_start: 0.8644 (m) cc_final: 0.8334 (p) REVERT: C 212 ARG cc_start: 0.7698 (ttm170) cc_final: 0.6919 (ttp80) REVERT: C 349 MET cc_start: 0.8986 (ttm) cc_final: 0.8446 (tpt) REVERT: C 353 CYS cc_start: 0.8516 (m) cc_final: 0.8231 (p) REVERT: D 161 ASP cc_start: 0.8325 (m-30) cc_final: 0.7948 (m-30) REVERT: D 249 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8495 (m-40) REVERT: D 277 ARG cc_start: 0.6749 (ttm110) cc_final: 0.6494 (ttt90) REVERT: E 207 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9002 (t) REVERT: F 201 GLN cc_start: 0.8505 (tp40) cc_final: 0.8237 (tp-100) REVERT: G 96 MET cc_start: 0.8996 (tpt) cc_final: 0.8793 (mmm) REVERT: G 157 MET cc_start: 0.9081 (mmp) cc_final: 0.8765 (pmt) REVERT: G 181 TYR cc_start: 0.8706 (m-80) cc_final: 0.7899 (t80) REVERT: G 274 TYR cc_start: 0.9052 (t80) cc_final: 0.8127 (t80) REVERT: H 70 LYS cc_start: 0.8456 (pttp) cc_final: 0.8245 (pttm) REVERT: I 107 GLU cc_start: 0.8539 (pm20) cc_final: 0.8244 (pm20) REVERT: I 108 ASP cc_start: 0.8522 (m-30) cc_final: 0.7934 (m-30) REVERT: I 117 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6473 (ptt180) REVERT: I 119 HIS cc_start: 0.7826 (t70) cc_final: 0.7565 (t-90) REVERT: I 167 ILE cc_start: 0.7530 (pt) cc_final: 0.7210 (pt) REVERT: J 52 GLU cc_start: 0.9214 (tp30) cc_final: 0.8903 (tp30) REVERT: J 142 ARG cc_start: 0.8953 (ptp-110) cc_final: 0.8436 (ptp-110) REVERT: K 52 ASP cc_start: 0.8381 (t0) cc_final: 0.8019 (t0) REVERT: N 202 GLN cc_start: 0.8375 (tp40) cc_final: 0.8005 (tp40) REVERT: O 40 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8068 (mt-10) REVERT: P 158 MET cc_start: 0.9409 (mmp) cc_final: 0.9135 (mmp) REVERT: T 163 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7690 (mtp180) REVERT: T 167 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7806 (ttm) REVERT: V 78 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: V 92 ASN cc_start: 0.9110 (t0) cc_final: 0.8205 (t0) REVERT: W 57 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: W 93 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7973 (mm-30) REVERT: W 112 GLU cc_start: 0.8196 (pp20) cc_final: 0.7979 (pp20) REVERT: W 120 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9041 (mp) REVERT: Y 76 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8435 (mp10) REVERT: Y 97 ASP cc_start: 0.8344 (m-30) cc_final: 0.7965 (m-30) REVERT: Y 115 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9398 (tp) REVERT: Y 147 GLN cc_start: 0.8487 (tp40) cc_final: 0.7813 (tp-100) REVERT: Y 151 ASP cc_start: 0.7686 (m-30) cc_final: 0.7432 (m-30) REVERT: Z 84 ASP cc_start: 0.8273 (m-30) cc_final: 0.8036 (m-30) REVERT: Z 131 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: a 56 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8236 (mtp180) REVERT: b 45 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: d 124 ARG cc_start: 0.8770 (mmm160) cc_final: 0.8418 (mmm160) REVERT: d 154 ASN cc_start: 0.8561 (t0) cc_final: 0.8141 (t160) REVERT: e 149 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6424 (tp) REVERT: e 200 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.6014 (mpp) REVERT: e 258 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8184 (p0) REVERT: f 96 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7829 (m) REVERT: h 116 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8037 (mtp85) REVERT: h 135 GLN cc_start: 0.8244 (pt0) cc_final: 0.7679 (pt0) REVERT: h 137 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7938 (ptt180) REVERT: h 142 GLU cc_start: 0.8009 (tp30) cc_final: 0.7705 (tp30) REVERT: i 49 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: k 28 GLU cc_start: 0.8100 (tp30) cc_final: 0.7674 (tp30) REVERT: k 73 ARG cc_start: 0.6953 (pmt-80) cc_final: 0.6562 (pmt-80) REVERT: k 76 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8096 (mtt) REVERT: k 85 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8131 (mt-10) REVERT: o 91 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: o 93 ASP cc_start: 0.8105 (t70) cc_final: 0.7871 (t0) REVERT: p 117 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8552 (mm110) REVERT: p 152 GLN cc_start: 0.8973 (tp40) cc_final: 0.8046 (tp40) REVERT: p 153 LYS cc_start: 0.9239 (mtmt) cc_final: 0.8985 (mtmm) REVERT: p 156 ASP cc_start: 0.8283 (m-30) cc_final: 0.7719 (m-30) REVERT: p 157 MET cc_start: 0.8453 (mtm) cc_final: 0.8249 (mtp) REVERT: p 183 MET cc_start: 0.8423 (tmm) cc_final: 0.7757 (tmm) REVERT: q 44 ASP cc_start: 0.8696 (t0) cc_final: 0.8271 (t0) REVERT: q 111 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: r 48 ILE cc_start: 0.8304 (mp) cc_final: 0.8098 (mp) REVERT: r 132 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7342 (mmp-170) REVERT: u 96 MET cc_start: 0.8882 (tpp) cc_final: 0.8593 (tpt) REVERT: u 104 GLU cc_start: 0.8504 (tp30) cc_final: 0.8107 (tp30) REVERT: u 117 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8448 (mp0) REVERT: u 141 TYR cc_start: 0.8942 (t80) cc_final: 0.8170 (t80) REVERT: u 145 MET cc_start: 0.8367 (mmm) cc_final: 0.8108 (mmp) REVERT: u 149 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8348 (mp) REVERT: u 160 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8000 (mt-10) REVERT: u 165 ASP cc_start: 0.8587 (p0) cc_final: 0.8318 (p0) REVERT: u 166 ASP cc_start: 0.8274 (p0) cc_final: 0.7912 (p0) REVERT: u 171 ASP cc_start: 0.8580 (t70) cc_final: 0.8329 (t0) REVERT: v 19 GLN cc_start: 0.8785 (tt0) cc_final: 0.8534 (mm110) REVERT: v 27 ASP cc_start: 0.8772 (t0) cc_final: 0.8484 (t0) REVERT: v 52 GLU cc_start: 0.9149 (pm20) cc_final: 0.8875 (pm20) REVERT: v 54 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8381 (tm-30) REVERT: v 55 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9119 (pp) outliers start: 217 outliers final: 119 residues processed: 1350 average time/residue: 1.8050 time to fit residues: 3350.8900 Evaluate side-chains 1340 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1190 time to evaluate : 7.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 164 THR Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 42 THR Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 1 residue 62 ILE Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 6 residue 124 ARG Chi-restraints excluded: chain 6 residue 207 GLU Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 257 ILE Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 126 GLN Chi-restraints excluded: chain 8 residue 147 LEU Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 94 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 249 ASN Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 117 ARG Chi-restraints excluded: chain I residue 132 LYS Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 18 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 167 MET Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 103 GLN Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 127 TYR Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 111 SER Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 76 GLN Chi-restraints excluded: chain Y residue 115 LEU Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 45 GLU Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain c residue 50 LEU Chi-restraints excluded: chain c residue 53 CYS Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain e residue 126 GLN Chi-restraints excluded: chain e residue 149 LEU Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain e residue 258 ASP Chi-restraints excluded: chain f residue 96 THR Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 122 LYS Chi-restraints excluded: chain g residue 144 THR Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 137 ARG Chi-restraints excluded: chain h residue 141 ASP Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 49 GLU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain j residue 100 GLU Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 66 VAL Chi-restraints excluded: chain k residue 76 MET Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 111 GLU Chi-restraints excluded: chain q residue 113 LYS Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 110 GLU Chi-restraints excluded: chain r residue 132 ARG Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 266 CYS Chi-restraints excluded: chain s residue 336 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain u residue 121 THR Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 149 LEU Chi-restraints excluded: chain u residue 164 THR Chi-restraints excluded: chain u residue 196 LEU Chi-restraints excluded: chain u residue 201 ASP Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain v residue 62 LEU Chi-restraints excluded: chain w residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 914 optimal weight: 0.0570 chunk 106 optimal weight: 30.0000 chunk 540 optimal weight: 0.8980 chunk 692 optimal weight: 7.9990 chunk 536 optimal weight: 3.9990 chunk 798 optimal weight: 9.9990 chunk 529 optimal weight: 0.9980 chunk 944 optimal weight: 6.9990 chunk 591 optimal weight: 3.9990 chunk 575 optimal weight: 5.9990 chunk 436 optimal weight: 9.9990 overall best weight: 1.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 384 GLN ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN H 126 GLN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN L 48 ASN L 72 GLN N 98 HIS P 142 ASN P 176 GLN Q 139 GLN R 147 GLN T 202 GLN V 35 ASN Z 62 ASN a 137 ASN c 42 GLN c 249 ASN ** d 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 220 GLN d 274 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 176 HIS p 182 ASN p 184 ASN ** q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 142 ASN ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 106475 Z= 0.205 Angle : 0.581 10.397 150837 Z= 0.295 Chirality : 0.038 0.307 17665 Planarity : 0.004 0.080 14003 Dihedral : 20.631 179.991 31123 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.36 % Allowed : 18.00 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 1.05 (0.09), residues: 8462 helix: 1.61 (0.09), residues: 3098 sheet: -0.31 (0.15), residues: 1056 loop : 0.42 (0.10), residues: 4308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Z 81 HIS 0.013 0.001 HIS k 93 PHE 0.039 0.001 PHE I 173 TYR 0.049 0.001 TYR v 13 ARG 0.019 0.000 ARG s 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1257 time to evaluate : 8.659 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: 0 157 VAL cc_start: 0.9556 (t) cc_final: 0.9354 (p) REVERT: 1 38 ARG cc_start: 0.8383 (mmm160) cc_final: 0.8136 (mtp-110) REVERT: 6 50 LYS cc_start: 0.9012 (mmmm) cc_final: 0.8777 (mmtp) REVERT: 6 116 ASN cc_start: 0.9062 (t0) cc_final: 0.8816 (t0) REVERT: 6 124 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7354 (ptt90) REVERT: 6 218 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8212 (tp) REVERT: 7 143 TRP cc_start: 0.9321 (OUTLIER) cc_final: 0.6861 (m-90) REVERT: 8 126 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: 9 90 GLN cc_start: 0.8381 (tt0) cc_final: 0.7759 (tt0) REVERT: 9 94 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: C 153 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.6590 (mmm) REVERT: C 206 SER cc_start: 0.8637 (m) cc_final: 0.8312 (p) REVERT: C 212 ARG cc_start: 0.7717 (ttm170) cc_final: 0.7186 (ptm-80) REVERT: C 349 MET cc_start: 0.9019 (ttm) cc_final: 0.8486 (tpt) REVERT: C 353 CYS cc_start: 0.8503 (m) cc_final: 0.8213 (p) REVERT: D 161 ASP cc_start: 0.8228 (m-30) cc_final: 0.7843 (m-30) REVERT: D 277 ARG cc_start: 0.6733 (ttm110) cc_final: 0.6487 (ttt90) REVERT: F 201 GLN cc_start: 0.8444 (tp40) cc_final: 0.8174 (tp-100) REVERT: G 96 MET cc_start: 0.9027 (tpt) cc_final: 0.8816 (mmm) REVERT: G 181 TYR cc_start: 0.8703 (m-80) cc_final: 0.7891 (t80) REVERT: G 274 TYR cc_start: 0.9016 (t80) cc_final: 0.8072 (t80) REVERT: H 70 LYS cc_start: 0.8453 (pttp) cc_final: 0.8236 (pttm) REVERT: I 107 GLU cc_start: 0.8555 (pm20) cc_final: 0.8280 (pm20) REVERT: I 108 ASP cc_start: 0.8587 (m-30) cc_final: 0.8007 (m-30) REVERT: I 117 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6588 (ptt180) REVERT: I 119 HIS cc_start: 0.7788 (t70) cc_final: 0.7583 (t-90) REVERT: I 166 ARG cc_start: 0.8663 (mtm180) cc_final: 0.8300 (ptt90) REVERT: J 142 ARG cc_start: 0.8963 (ptp-110) cc_final: 0.8438 (ptp-110) REVERT: K 52 ASP cc_start: 0.8308 (t0) cc_final: 0.7997 (t0) REVERT: L 135 SER cc_start: 0.9186 (m) cc_final: 0.8915 (m) REVERT: N 202 GLN cc_start: 0.8342 (tp40) cc_final: 0.8082 (tp40) REVERT: O 40 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8002 (mt-10) REVERT: P 158 MET cc_start: 0.9395 (mmp) cc_final: 0.9125 (mmp) REVERT: T 163 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7810 (mtp180) REVERT: T 167 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7732 (ttm) REVERT: U 46 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8537 (mmt) REVERT: V 82 GLN cc_start: 0.8822 (mp10) cc_final: 0.8491 (mp10) REVERT: V 92 ASN cc_start: 0.9072 (t0) cc_final: 0.8173 (t0) REVERT: V 128 ARG cc_start: 0.8733 (tpp-160) cc_final: 0.8295 (mmp80) REVERT: W 57 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: W 120 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9006 (mp) REVERT: Y 76 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8383 (mp10) REVERT: Y 97 ASP cc_start: 0.8299 (m-30) cc_final: 0.7941 (m-30) REVERT: Y 115 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9399 (tp) REVERT: Y 147 GLN cc_start: 0.8440 (tp40) cc_final: 0.7767 (tp-100) REVERT: Y 151 ASP cc_start: 0.7605 (m-30) cc_final: 0.7332 (m-30) REVERT: Z 84 ASP cc_start: 0.8227 (m-30) cc_final: 0.7987 (m-30) REVERT: Z 131 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: a 56 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8179 (mtp180) REVERT: c 305 TYR cc_start: 0.9167 (m-10) cc_final: 0.8934 (m-10) REVERT: d 123 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8234 (tmm-80) REVERT: d 124 ARG cc_start: 0.8726 (mmm160) cc_final: 0.8374 (mmm160) REVERT: d 154 ASN cc_start: 0.8553 (t0) cc_final: 0.8096 (t0) REVERT: e 70 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.9042 (ttm) REVERT: e 149 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6442 (tp) REVERT: e 200 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.6035 (mpp) REVERT: e 258 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8139 (p0) REVERT: f 96 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7689 (m) REVERT: g 40 GLU cc_start: 0.7098 (tp30) cc_final: 0.6783 (tp30) REVERT: h 116 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7973 (mtp85) REVERT: h 135 GLN cc_start: 0.8221 (pt0) cc_final: 0.7927 (pt0) REVERT: j 103 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7156 (ptp90) REVERT: k 28 GLU cc_start: 0.8066 (tp30) cc_final: 0.7682 (tp30) REVERT: k 73 ARG cc_start: 0.6884 (pmt-80) cc_final: 0.6577 (pmt-80) REVERT: k 85 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8003 (mt-10) REVERT: o 91 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: o 93 ASP cc_start: 0.8106 (t70) cc_final: 0.7861 (t0) REVERT: p 46 ASP cc_start: 0.8232 (p0) cc_final: 0.8026 (p0) REVERT: p 117 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8483 (mm110) REVERT: p 149 ASP cc_start: 0.8695 (t0) cc_final: 0.8360 (t0) REVERT: p 152 GLN cc_start: 0.8964 (tp40) cc_final: 0.8026 (tp40) REVERT: p 153 LYS cc_start: 0.9242 (mtmt) cc_final: 0.8955 (mtmm) REVERT: p 156 ASP cc_start: 0.8274 (m-30) cc_final: 0.7668 (m-30) REVERT: p 182 ASN cc_start: 0.8593 (m-40) cc_final: 0.8257 (m110) REVERT: p 183 MET cc_start: 0.8376 (tmm) cc_final: 0.7726 (tmm) REVERT: q 44 ASP cc_start: 0.8676 (t0) cc_final: 0.8257 (t0) REVERT: q 127 LYS cc_start: 0.9475 (mtpp) cc_final: 0.9210 (mttp) REVERT: r 132 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7283 (mmp-170) REVERT: u 96 MET cc_start: 0.8870 (tpp) cc_final: 0.8632 (tpt) REVERT: u 103 GLN cc_start: 0.8946 (tt0) cc_final: 0.8637 (tm-30) REVERT: u 141 TYR cc_start: 0.8676 (t80) cc_final: 0.8310 (t80) REVERT: u 145 MET cc_start: 0.8400 (mmm) cc_final: 0.8133 (mmp) REVERT: u 160 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7833 (mt-10) REVERT: u 165 ASP cc_start: 0.8493 (p0) cc_final: 0.8215 (p0) REVERT: u 166 ASP cc_start: 0.8175 (p0) cc_final: 0.7802 (p0) REVERT: v 19 GLN cc_start: 0.8739 (tt0) cc_final: 0.8445 (mm110) REVERT: v 27 ASP cc_start: 0.8760 (t0) cc_final: 0.8442 (t0) REVERT: v 39 PHE cc_start: 0.8954 (m-10) cc_final: 0.8516 (m-10) REVERT: v 54 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8602 (tm-30) REVERT: v 55 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9104 (pp) REVERT: w 120 MET cc_start: 0.8110 (mmm) cc_final: 0.7669 (mmm) outliers start: 180 outliers final: 100 residues processed: 1342 average time/residue: 1.8092 time to fit residues: 3363.1666 Evaluate side-chains 1338 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1213 time to evaluate : 7.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 164 THR Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 42 THR Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 6 residue 124 ARG Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 257 ILE Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 126 GLN Chi-restraints excluded: chain 8 residue 147 LEU Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 94 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 117 ARG Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain O residue 18 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 167 MET Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 46 MET Chi-restraints excluded: chain U residue 103 GLN Chi-restraints excluded: chain U residue 127 TYR Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 111 SER Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 76 GLN Chi-restraints excluded: chain Y residue 115 LEU Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain c residue 50 LEU Chi-restraints excluded: chain c residue 249 ASN Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 126 GLN Chi-restraints excluded: chain e residue 149 LEU Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain e residue 258 ASP Chi-restraints excluded: chain f residue 96 THR Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 122 LYS Chi-restraints excluded: chain g residue 144 THR Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 141 ASP Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 181 GLU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 111 GLU Chi-restraints excluded: chain q residue 113 LYS Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 132 ARG Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 266 CYS Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 164 THR Chi-restraints excluded: chain u residue 196 LEU Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain w residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 584 optimal weight: 0.5980 chunk 377 optimal weight: 3.9990 chunk 564 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 600 optimal weight: 2.9990 chunk 643 optimal weight: 0.3980 chunk 467 optimal weight: 9.9990 chunk 88 optimal weight: 30.0000 chunk 742 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 191 ASN 6 243 ASN ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN H 126 GLN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN N 98 HIS T 202 GLN V 35 ASN Z 62 ASN a 46 ASN a 137 ASN c 249 ASN ** d 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 220 GLN d 274 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 152 GLN ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 106475 Z= 0.254 Angle : 0.596 13.390 150837 Z= 0.302 Chirality : 0.039 0.344 17665 Planarity : 0.004 0.074 14003 Dihedral : 20.564 179.996 31123 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.28 % Allowed : 18.66 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 1.05 (0.09), residues: 8462 helix: 1.61 (0.09), residues: 3094 sheet: -0.29 (0.15), residues: 1069 loop : 0.42 (0.10), residues: 4299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP 6 235 HIS 0.010 0.001 HIS k 93 PHE 0.041 0.001 PHE I 173 TYR 0.049 0.001 TYR v 13 ARG 0.018 0.000 ARG h 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1401 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1227 time to evaluate : 7.033 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: 1 38 ARG cc_start: 0.8371 (mmm160) cc_final: 0.8117 (mtp-110) REVERT: 6 50 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8734 (mmtp) REVERT: 6 116 ASN cc_start: 0.9052 (t0) cc_final: 0.8825 (t0) REVERT: 6 124 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7357 (ptt90) REVERT: 6 207 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8085 (pp20) REVERT: 6 218 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8226 (tp) REVERT: 7 74 ASP cc_start: 0.8688 (t0) cc_final: 0.8405 (t0) REVERT: 7 143 TRP cc_start: 0.9338 (OUTLIER) cc_final: 0.6847 (m-90) REVERT: 8 126 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7247 (mp10) REVERT: 9 90 GLN cc_start: 0.8410 (tt0) cc_final: 0.7785 (tt0) REVERT: 9 94 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: C 153 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.6638 (mmm) REVERT: C 206 SER cc_start: 0.8629 (m) cc_final: 0.8309 (p) REVERT: C 212 ARG cc_start: 0.7725 (ttm170) cc_final: 0.7199 (ptm-80) REVERT: C 220 TYR cc_start: 0.7919 (m-80) cc_final: 0.7674 (m-80) REVERT: C 349 MET cc_start: 0.8992 (ttm) cc_final: 0.8305 (tpt) REVERT: C 353 CYS cc_start: 0.8477 (m) cc_final: 0.8242 (p) REVERT: D 161 ASP cc_start: 0.8216 (m-30) cc_final: 0.7930 (m-30) REVERT: D 277 ARG cc_start: 0.6799 (ttm110) cc_final: 0.6562 (ttt90) REVERT: E 207 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.8947 (t) REVERT: F 201 GLN cc_start: 0.8466 (tp40) cc_final: 0.8195 (tp-100) REVERT: G 96 MET cc_start: 0.9026 (tpt) cc_final: 0.8804 (mmm) REVERT: G 181 TYR cc_start: 0.8713 (m-80) cc_final: 0.7893 (t80) REVERT: G 274 TYR cc_start: 0.9044 (t80) cc_final: 0.8040 (t80) REVERT: H 70 LYS cc_start: 0.8455 (pttp) cc_final: 0.8243 (pttm) REVERT: H 137 LYS cc_start: 0.9254 (mtmp) cc_final: 0.8828 (mtmm) REVERT: H 142 GLU cc_start: 0.8232 (pp20) cc_final: 0.7994 (pp20) REVERT: I 107 GLU cc_start: 0.8556 (pm20) cc_final: 0.8260 (pm20) REVERT: I 108 ASP cc_start: 0.8580 (m-30) cc_final: 0.7940 (m-30) REVERT: I 109 LYS cc_start: 0.9118 (mmmm) cc_final: 0.8905 (mmmt) REVERT: I 117 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6802 (ptt180) REVERT: I 119 HIS cc_start: 0.7938 (t70) cc_final: 0.7664 (t-90) REVERT: I 166 ARG cc_start: 0.8714 (mtm180) cc_final: 0.8330 (ptt90) REVERT: J 142 ARG cc_start: 0.8971 (ptp-110) cc_final: 0.8434 (ptp-110) REVERT: K 52 ASP cc_start: 0.8317 (t0) cc_final: 0.7977 (t0) REVERT: L 135 SER cc_start: 0.9141 (m) cc_final: 0.8873 (m) REVERT: N 202 GLN cc_start: 0.8390 (tp40) cc_final: 0.8112 (tp40) REVERT: O 40 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8015 (mt-10) REVERT: P 158 MET cc_start: 0.9396 (mmp) cc_final: 0.9134 (mmp) REVERT: T 163 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7827 (mtp180) REVERT: T 167 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7767 (ttm) REVERT: V 82 GLN cc_start: 0.8824 (mp10) cc_final: 0.8494 (mp10) REVERT: V 92 ASN cc_start: 0.9086 (t0) cc_final: 0.8185 (t0) REVERT: V 128 ARG cc_start: 0.8737 (tpp-160) cc_final: 0.8194 (mmp80) REVERT: W 57 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: W 120 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9042 (mp) REVERT: X 55 LYS cc_start: 0.8660 (ptmt) cc_final: 0.8457 (ptmt) REVERT: Y 76 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8399 (mp10) REVERT: Y 97 ASP cc_start: 0.8304 (m-30) cc_final: 0.7934 (m-30) REVERT: Y 115 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9402 (tp) REVERT: Y 147 GLN cc_start: 0.8450 (tp40) cc_final: 0.7779 (tp-100) REVERT: Y 151 ASP cc_start: 0.7592 (m-30) cc_final: 0.7304 (m-30) REVERT: Z 131 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: a 56 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8182 (mtp180) REVERT: c 305 TYR cc_start: 0.9209 (m-10) cc_final: 0.8891 (m-10) REVERT: d 124 ARG cc_start: 0.8697 (mmm160) cc_final: 0.8429 (mmm160) REVERT: d 154 ASN cc_start: 0.8530 (t0) cc_final: 0.8152 (t160) REVERT: e 139 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: e 149 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6442 (tp) REVERT: e 200 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.5988 (mpp) REVERT: e 258 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8129 (p0) REVERT: f 96 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7706 (m) REVERT: h 116 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7972 (mtp85) REVERT: h 135 GLN cc_start: 0.8240 (pt0) cc_final: 0.7743 (pt0) REVERT: h 137 ARG cc_start: 0.8439 (ptm-80) cc_final: 0.8111 (ptt180) REVERT: h 142 GLU cc_start: 0.7971 (tp30) cc_final: 0.7580 (tp30) REVERT: k 28 GLU cc_start: 0.8069 (tp30) cc_final: 0.7668 (tp30) REVERT: k 73 ARG cc_start: 0.6836 (pmt-80) cc_final: 0.6511 (pmt-80) REVERT: k 85 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7938 (mt-10) REVERT: o 91 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: o 93 ASP cc_start: 0.8061 (t70) cc_final: 0.7831 (t0) REVERT: p 117 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8492 (mm110) REVERT: p 149 ASP cc_start: 0.8702 (t0) cc_final: 0.8360 (t0) REVERT: p 152 GLN cc_start: 0.8902 (tp-100) cc_final: 0.7992 (tp40) REVERT: p 153 LYS cc_start: 0.9253 (mtmt) cc_final: 0.8974 (mtmm) REVERT: p 156 ASP cc_start: 0.8249 (m-30) cc_final: 0.7625 (m-30) REVERT: p 181 GLU cc_start: 0.8499 (pp20) cc_final: 0.8111 (pp20) REVERT: p 182 ASN cc_start: 0.8436 (m-40) cc_final: 0.7957 (m-40) REVERT: p 183 MET cc_start: 0.8320 (tmm) cc_final: 0.7689 (tmm) REVERT: q 44 ASP cc_start: 0.8684 (t0) cc_final: 0.8257 (t0) REVERT: r 132 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7280 (mmp-170) REVERT: u 100 LEU cc_start: 0.9385 (mp) cc_final: 0.9135 (mt) REVERT: u 103 GLN cc_start: 0.8931 (tt0) cc_final: 0.8642 (tm-30) REVERT: u 141 TYR cc_start: 0.8649 (t80) cc_final: 0.8308 (t80) REVERT: u 165 ASP cc_start: 0.8516 (p0) cc_final: 0.8244 (p0) REVERT: u 166 ASP cc_start: 0.8221 (p0) cc_final: 0.7874 (p0) REVERT: v 19 GLN cc_start: 0.8663 (tt0) cc_final: 0.8402 (mm110) REVERT: v 27 ASP cc_start: 0.8778 (t0) cc_final: 0.8467 (t0) REVERT: v 39 PHE cc_start: 0.8922 (m-10) cc_final: 0.8447 (m-10) REVERT: v 52 GLU cc_start: 0.9253 (pm20) cc_final: 0.8950 (pm20) REVERT: v 54 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8607 (tm-30) REVERT: v 55 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9100 (pp) REVERT: w 120 MET cc_start: 0.8266 (mmm) cc_final: 0.7868 (mmm) outliers start: 174 outliers final: 109 residues processed: 1314 average time/residue: 1.7797 time to fit residues: 3225.9031 Evaluate side-chains 1330 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1195 time to evaluate : 7.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 164 THR Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 42 THR Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 6 residue 124 ARG Chi-restraints excluded: chain 6 residue 207 GLU Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 257 ILE Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 126 GLN Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 8 residue 147 LEU Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 94 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 117 ARG Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain O residue 18 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 167 MET Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 103 GLN Chi-restraints excluded: chain U residue 127 TYR Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 111 SER Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 76 GLN Chi-restraints excluded: chain Y residue 115 LEU Chi-restraints excluded: chain Y residue 133 ASP Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain c residue 50 LEU Chi-restraints excluded: chain c residue 53 CYS Chi-restraints excluded: chain e residue 126 GLN Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain e residue 149 LEU Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain e residue 258 ASP Chi-restraints excluded: chain f residue 96 THR Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 144 THR Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 141 ASP Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 111 GLU Chi-restraints excluded: chain q residue 113 LYS Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 132 ARG Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 266 CYS Chi-restraints excluded: chain s residue 336 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain u residue 121 THR Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 154 ASP Chi-restraints excluded: chain u residue 164 THR Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain v residue 62 LEU Chi-restraints excluded: chain w residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 859 optimal weight: 6.9990 chunk 904 optimal weight: 6.9990 chunk 825 optimal weight: 3.9990 chunk 880 optimal weight: 8.9990 chunk 529 optimal weight: 3.9990 chunk 383 optimal weight: 2.9990 chunk 691 optimal weight: 0.9990 chunk 270 optimal weight: 8.9990 chunk 795 optimal weight: 30.0000 chunk 832 optimal weight: 3.9990 chunk 877 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 191 ASN 6 243 ASN ** 7 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN L 142 GLN N 98 HIS R 147 GLN T 202 GLN V 35 ASN Z 62 ASN a 137 ASN c 249 ASN ** d 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 220 GLN ** d 274 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** ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 106475 Z= 0.280 Angle : 0.609 14.552 150837 Z= 0.308 Chirality : 0.040 0.400 17665 Planarity : 0.005 0.092 14003 Dihedral : 20.540 179.823 31123 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.29 % Allowed : 18.90 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 1.03 (0.09), residues: 8462 helix: 1.58 (0.09), residues: 3099 sheet: -0.30 (0.15), residues: 1079 loop : 0.43 (0.10), residues: 4284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP 6 235 HIS 0.011 0.001 HIS k 93 PHE 0.035 0.001 PHE I 173 TYR 0.053 0.001 TYR v 13 ARG 0.020 0.000 ARG h 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1381 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1206 time to evaluate : 7.241 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: 1 38 ARG cc_start: 0.8361 (mmm160) cc_final: 0.8085 (mtp-110) REVERT: 6 50 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8720 (mmtp) REVERT: 6 116 ASN cc_start: 0.9062 (t0) cc_final: 0.8850 (t0) REVERT: 6 124 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7383 (ptt90) REVERT: 6 207 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8003 (pp20) REVERT: 6 218 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8250 (tp) REVERT: 6 325 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.8043 (m-30) REVERT: 7 74 ASP cc_start: 0.8727 (t0) cc_final: 0.8484 (t0) REVERT: 7 143 TRP cc_start: 0.9354 (OUTLIER) cc_final: 0.6928 (m-90) REVERT: 8 126 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7235 (mp10) REVERT: 9 90 GLN cc_start: 0.8434 (tt0) cc_final: 0.7817 (tt0) REVERT: 9 94 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: C 153 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.6573 (mmm) REVERT: C 206 SER cc_start: 0.8630 (m) cc_final: 0.8301 (p) REVERT: C 212 ARG cc_start: 0.7752 (ttm170) cc_final: 0.7196 (ptm-80) REVERT: C 349 MET cc_start: 0.8999 (ttm) cc_final: 0.8308 (tpt) REVERT: C 353 CYS cc_start: 0.8479 (m) cc_final: 0.8225 (p) REVERT: D 135 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.6899 (mtm-85) REVERT: D 161 ASP cc_start: 0.8215 (m-30) cc_final: 0.7923 (m-30) REVERT: D 277 ARG cc_start: 0.6835 (ttm110) cc_final: 0.6604 (ttt90) REVERT: E 207 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8952 (t) REVERT: F 201 GLN cc_start: 0.8472 (tp40) cc_final: 0.8200 (tp-100) REVERT: G 96 MET cc_start: 0.9017 (tpt) cc_final: 0.8791 (mmm) REVERT: G 181 TYR cc_start: 0.8727 (m-80) cc_final: 0.7894 (t80) REVERT: G 274 TYR cc_start: 0.9044 (t80) cc_final: 0.8047 (t80) REVERT: I 107 GLU cc_start: 0.8568 (pm20) cc_final: 0.8300 (pm20) REVERT: I 108 ASP cc_start: 0.8619 (m-30) cc_final: 0.8004 (m-30) REVERT: I 119 HIS cc_start: 0.7851 (t70) cc_final: 0.7629 (t-90) REVERT: I 166 ARG cc_start: 0.8754 (mtm180) cc_final: 0.8313 (ptt90) REVERT: J 48 GLN cc_start: 0.8431 (pp30) cc_final: 0.8172 (pp30) REVERT: J 142 ARG cc_start: 0.8952 (ptp-110) cc_final: 0.8433 (ptp-110) REVERT: K 52 ASP cc_start: 0.8321 (t0) cc_final: 0.7984 (t0) REVERT: L 135 SER cc_start: 0.9137 (m) cc_final: 0.8912 (m) REVERT: N 202 GLN cc_start: 0.8427 (tp40) cc_final: 0.8218 (tp-100) REVERT: O 40 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8017 (mt-10) REVERT: T 163 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7815 (mtp180) REVERT: T 167 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7770 (ttm) REVERT: V 82 GLN cc_start: 0.8838 (mp10) cc_final: 0.8516 (mp10) REVERT: V 92 ASN cc_start: 0.9081 (t0) cc_final: 0.8164 (t0) REVERT: V 128 ARG cc_start: 0.8731 (tpp-160) cc_final: 0.8221 (mmp80) REVERT: W 57 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: W 120 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9047 (mp) REVERT: Y 76 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8405 (mp10) REVERT: Y 97 ASP cc_start: 0.8318 (m-30) cc_final: 0.7920 (m-30) REVERT: Y 115 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9405 (tp) REVERT: Y 139 MET cc_start: 0.9222 (mtp) cc_final: 0.8989 (mtp) REVERT: Y 147 GLN cc_start: 0.8458 (tp40) cc_final: 0.7762 (tp-100) REVERT: Y 151 ASP cc_start: 0.7612 (m-30) cc_final: 0.7333 (m-30) REVERT: Z 84 ASP cc_start: 0.8232 (m-30) cc_final: 0.7984 (m-30) REVERT: a 56 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8175 (mtp180) REVERT: c 305 TYR cc_start: 0.9264 (m-10) cc_final: 0.8934 (m-10) REVERT: d 123 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8210 (tmm-80) REVERT: d 124 ARG cc_start: 0.8772 (mmm160) cc_final: 0.8329 (mmm160) REVERT: d 154 ASN cc_start: 0.8602 (t0) cc_final: 0.8109 (t160) REVERT: e 139 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: e 149 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6296 (tp) REVERT: e 200 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.6041 (mpp) REVERT: e 237 LEU cc_start: 0.9033 (pt) cc_final: 0.8406 (tm) REVERT: e 258 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8027 (p0) REVERT: f 96 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7653 (m) REVERT: g 40 GLU cc_start: 0.7084 (tp30) cc_final: 0.6849 (tp30) REVERT: h 116 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7992 (mtp85) REVERT: h 135 GLN cc_start: 0.8247 (pt0) cc_final: 0.7731 (pt0) REVERT: h 137 ARG cc_start: 0.8396 (ptm-80) cc_final: 0.8053 (ptt180) REVERT: h 142 GLU cc_start: 0.7981 (tp30) cc_final: 0.7581 (tp30) REVERT: i 49 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: k 28 GLU cc_start: 0.8039 (tp30) cc_final: 0.7667 (tp30) REVERT: k 73 ARG cc_start: 0.6801 (pmt-80) cc_final: 0.6502 (pmt-80) REVERT: o 91 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: o 93 ASP cc_start: 0.8065 (t70) cc_final: 0.7837 (t0) REVERT: p 117 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8523 (mm110) REVERT: p 149 ASP cc_start: 0.8678 (t0) cc_final: 0.8326 (t0) REVERT: p 152 GLN cc_start: 0.8990 (tp-100) cc_final: 0.8058 (tp40) REVERT: p 153 LYS cc_start: 0.9252 (mtmt) cc_final: 0.8987 (mtmm) REVERT: p 156 ASP cc_start: 0.8212 (m-30) cc_final: 0.7612 (m-30) REVERT: p 182 ASN cc_start: 0.8549 (m-40) cc_final: 0.8167 (m110) REVERT: p 183 MET cc_start: 0.8350 (tmm) cc_final: 0.7754 (tmm) REVERT: q 44 ASP cc_start: 0.8688 (t0) cc_final: 0.8251 (t0) REVERT: q 127 LYS cc_start: 0.9484 (mtpp) cc_final: 0.9218 (mttp) REVERT: r 132 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7258 (mmp-170) REVERT: u 100 LEU cc_start: 0.9628 (mp) cc_final: 0.9299 (mt) REVERT: u 104 GLU cc_start: 0.8312 (tp30) cc_final: 0.8020 (tp30) REVERT: u 165 ASP cc_start: 0.8532 (p0) cc_final: 0.8262 (p0) REVERT: u 166 ASP cc_start: 0.8198 (p0) cc_final: 0.7855 (p0) REVERT: v 19 GLN cc_start: 0.8658 (tt0) cc_final: 0.8417 (mm110) REVERT: v 27 ASP cc_start: 0.8792 (t0) cc_final: 0.8468 (t0) REVERT: v 52 GLU cc_start: 0.9256 (pm20) cc_final: 0.9055 (pm20) REVERT: v 54 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8706 (tm-30) REVERT: v 55 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9157 (pp) REVERT: w 105 MET cc_start: 0.8186 (mpm) cc_final: 0.7940 (mmp) REVERT: w 111 ASP cc_start: 0.8939 (t70) cc_final: 0.8688 (t70) REVERT: w 118 ILE cc_start: 0.9407 (mm) cc_final: 0.9014 (mm) REVERT: w 120 MET cc_start: 0.8209 (mmm) cc_final: 0.7994 (mmm) REVERT: w 122 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8124 (mmp) outliers start: 175 outliers final: 115 residues processed: 1301 average time/residue: 1.8201 time to fit residues: 3284.3158 Evaluate side-chains 1324 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1181 time to evaluate : 6.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 164 THR Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 42 THR Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 124 ARG Chi-restraints excluded: chain 6 residue 207 GLU Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 265 ILE Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 257 ILE Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 126 GLN Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 8 residue 147 LEU Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 94 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 18 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 177 ARG Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 167 MET Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 127 TYR Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 111 SER Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 150 SER Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 76 GLN Chi-restraints excluded: chain Y residue 115 LEU Chi-restraints excluded: chain Y residue 133 ASP Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain c residue 50 LEU Chi-restraints excluded: chain c residue 53 CYS Chi-restraints excluded: chain c residue 249 ASN Chi-restraints excluded: chain e residue 126 GLN Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain e residue 149 LEU Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain e residue 258 ASP Chi-restraints excluded: chain f residue 96 THR Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 144 THR Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 141 ASP Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 49 GLU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain p residue 181 GLU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 111 GLU Chi-restraints excluded: chain q residue 113 LYS Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 110 GLU Chi-restraints excluded: chain r residue 132 ARG Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 266 CYS Chi-restraints excluded: chain s residue 336 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain u residue 121 THR Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 154 ASP Chi-restraints excluded: chain u residue 164 THR Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 46 GLU Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain w residue 122 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 578 optimal weight: 6.9990 chunk 930 optimal weight: 0.4980 chunk 568 optimal weight: 1.9990 chunk 441 optimal weight: 7.9990 chunk 647 optimal weight: 9.9990 chunk 976 optimal weight: 8.9990 chunk 898 optimal weight: 0.7980 chunk 777 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 600 optimal weight: 8.9990 chunk 476 optimal weight: 3.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 191 ASN 6 243 ASN ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN L 72 GLN L 142 GLN N 98 HIS T 202 GLN V 35 ASN Z 62 ASN a 137 ASN c 249 ASN ** d 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 HIS ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 106475 Z= 0.262 Angle : 0.613 14.824 150837 Z= 0.310 Chirality : 0.039 0.413 17665 Planarity : 0.004 0.064 14003 Dihedral : 20.537 179.853 31123 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.09 % Allowed : 19.33 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 1.01 (0.09), residues: 8462 helix: 1.55 (0.09), residues: 3097 sheet: -0.31 (0.15), residues: 1079 loop : 0.42 (0.10), residues: 4286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP 6 235 HIS 0.011 0.001 HIS k 93 PHE 0.032 0.001 PHE I 173 TYR 0.027 0.001 TYR a 43 ARG 0.020 0.000 ARG h 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16924 Ramachandran restraints generated. 8462 Oldfield, 0 Emsley, 8462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1364 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1204 time to evaluate : 8.058 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: 1 38 ARG cc_start: 0.8336 (mmm160) cc_final: 0.8068 (mtp-110) REVERT: 6 50 LYS cc_start: 0.9012 (mmmm) cc_final: 0.8725 (mmtp) REVERT: 6 116 ASN cc_start: 0.9061 (t0) cc_final: 0.8855 (t0) REVERT: 6 124 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7338 (ptt90) REVERT: 6 207 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7999 (pp20) REVERT: 6 218 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8259 (tp) REVERT: 6 325 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8065 (m-30) REVERT: 7 74 ASP cc_start: 0.8702 (t0) cc_final: 0.8480 (t0) REVERT: 7 143 TRP cc_start: 0.9351 (OUTLIER) cc_final: 0.6824 (m-90) REVERT: 8 126 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: 8 139 MET cc_start: 0.7713 (ppp) cc_final: 0.7432 (ppp) REVERT: 9 90 GLN cc_start: 0.8433 (tt0) cc_final: 0.7829 (tt0) REVERT: 9 94 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: C 153 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.6595 (mmm) REVERT: C 206 SER cc_start: 0.8624 (m) cc_final: 0.8295 (p) REVERT: C 212 ARG cc_start: 0.7720 (ttm170) cc_final: 0.7155 (ptm-80) REVERT: C 349 MET cc_start: 0.8998 (ttm) cc_final: 0.8307 (tpt) REVERT: C 353 CYS cc_start: 0.8479 (m) cc_final: 0.8224 (p) REVERT: D 135 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.6871 (mtm-85) REVERT: D 161 ASP cc_start: 0.8204 (m-30) cc_final: 0.7913 (m-30) REVERT: D 277 ARG cc_start: 0.6835 (ttm110) cc_final: 0.6608 (ttt90) REVERT: E 207 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8949 (t) REVERT: F 201 GLN cc_start: 0.8464 (tp40) cc_final: 0.8204 (tp-100) REVERT: G 96 MET cc_start: 0.9014 (tpt) cc_final: 0.8790 (mmm) REVERT: G 181 TYR cc_start: 0.8737 (m-80) cc_final: 0.7889 (t80) REVERT: G 274 TYR cc_start: 0.9037 (t80) cc_final: 0.7949 (t80) REVERT: I 107 GLU cc_start: 0.8573 (pm20) cc_final: 0.8296 (pm20) REVERT: I 108 ASP cc_start: 0.8573 (m-30) cc_final: 0.7947 (m-30) REVERT: I 166 ARG cc_start: 0.8749 (mtm180) cc_final: 0.8263 (ptt90) REVERT: J 48 GLN cc_start: 0.8433 (pp30) cc_final: 0.8222 (pp30) REVERT: J 142 ARG cc_start: 0.8970 (ptp-110) cc_final: 0.8458 (ptp-110) REVERT: K 52 ASP cc_start: 0.8316 (t0) cc_final: 0.7985 (t0) REVERT: K 135 GLU cc_start: 0.7580 (tp30) cc_final: 0.7208 (tp30) REVERT: N 202 GLN cc_start: 0.8434 (tp40) cc_final: 0.8192 (tp-100) REVERT: N 247 MET cc_start: 0.9003 (mpp) cc_final: 0.8729 (mpp) REVERT: O 40 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8017 (mt-10) REVERT: P 158 MET cc_start: 0.9384 (mmp) cc_final: 0.9037 (mmp) REVERT: T 133 ASN cc_start: 0.8727 (t0) cc_final: 0.8240 (t0) REVERT: T 163 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7809 (mtp180) REVERT: T 167 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7762 (ttm) REVERT: V 82 GLN cc_start: 0.8831 (mp10) cc_final: 0.8516 (mp10) REVERT: V 92 ASN cc_start: 0.9080 (t0) cc_final: 0.8187 (t0) REVERT: V 128 ARG cc_start: 0.8715 (tpp-160) cc_final: 0.8402 (mmp80) REVERT: W 57 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: W 120 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9031 (mp) REVERT: Y 97 ASP cc_start: 0.8330 (m-30) cc_final: 0.7937 (m-30) REVERT: Y 115 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9402 (tp) REVERT: Y 139 MET cc_start: 0.9228 (mtp) cc_final: 0.8996 (mtp) REVERT: Y 147 GLN cc_start: 0.8463 (tp40) cc_final: 0.7769 (tp-100) REVERT: Y 151 ASP cc_start: 0.7655 (m-30) cc_final: 0.7379 (m-30) REVERT: Z 84 ASP cc_start: 0.8233 (m-30) cc_final: 0.7993 (m-30) REVERT: a 56 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8169 (mtp180) REVERT: c 305 TYR cc_start: 0.9257 (m-10) cc_final: 0.8934 (m-10) REVERT: d 123 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8100 (tmm-80) REVERT: d 124 ARG cc_start: 0.8740 (mmm160) cc_final: 0.8276 (mmm160) REVERT: d 154 ASN cc_start: 0.8600 (t0) cc_final: 0.8108 (t160) REVERT: e 70 MET cc_start: 0.9178 (ttm) cc_final: 0.8674 (mtm) REVERT: e 139 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: e 149 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6293 (tp) REVERT: e 200 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.6046 (mpp) REVERT: e 237 LEU cc_start: 0.9038 (pt) cc_final: 0.8402 (tm) REVERT: e 258 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8044 (p0) REVERT: f 96 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7639 (m) REVERT: f 100 MET cc_start: 0.8345 (mmp) cc_final: 0.7803 (ppp) REVERT: f 127 MET cc_start: 0.8091 (pmm) cc_final: 0.7801 (pmm) REVERT: h 116 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7986 (mtp85) REVERT: h 135 GLN cc_start: 0.8245 (pt0) cc_final: 0.7811 (pt0) REVERT: h 137 ARG cc_start: 0.8381 (ptm-80) cc_final: 0.7843 (ptt180) REVERT: h 142 GLU cc_start: 0.7993 (tp30) cc_final: 0.7705 (tp30) REVERT: i 49 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: k 28 GLU cc_start: 0.8006 (tp30) cc_final: 0.7649 (tp30) REVERT: k 73 ARG cc_start: 0.6767 (pmt-80) cc_final: 0.6490 (pmt-80) REVERT: o 91 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: o 93 ASP cc_start: 0.8059 (t70) cc_final: 0.7829 (t0) REVERT: p 46 ASP cc_start: 0.8207 (p0) cc_final: 0.7938 (p0) REVERT: p 149 ASP cc_start: 0.8671 (t0) cc_final: 0.8349 (t0) REVERT: p 152 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8031 (tp40) REVERT: p 153 LYS cc_start: 0.9252 (mtmt) cc_final: 0.8997 (mtmm) REVERT: p 156 ASP cc_start: 0.8243 (m-30) cc_final: 0.7654 (m-30) REVERT: p 183 MET cc_start: 0.8289 (tmm) cc_final: 0.7700 (tmm) REVERT: q 44 ASP cc_start: 0.8685 (t0) cc_final: 0.8248 (t0) REVERT: q 106 LYS cc_start: 0.9230 (mtpp) cc_final: 0.8983 (ptpp) REVERT: q 127 LYS cc_start: 0.9488 (mtpp) cc_final: 0.9222 (mttp) REVERT: r 132 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7258 (mmp-170) REVERT: u 93 ASP cc_start: 0.8620 (p0) cc_final: 0.8386 (p0) REVERT: u 105 ASN cc_start: 0.9136 (p0) cc_final: 0.8925 (p0) REVERT: u 165 ASP cc_start: 0.8526 (p0) cc_final: 0.8256 (p0) REVERT: u 166 ASP cc_start: 0.8169 (p0) cc_final: 0.7823 (p0) REVERT: v 19 GLN cc_start: 0.8647 (tt0) cc_final: 0.8421 (mm110) REVERT: v 27 ASP cc_start: 0.8798 (t0) cc_final: 0.8473 (t0) REVERT: v 63 ASN cc_start: 0.9322 (t0) cc_final: 0.8948 (t0) outliers start: 160 outliers final: 113 residues processed: 1289 average time/residue: 1.7910 time to fit residues: 3202.1616 Evaluate side-chains 1318 residues out of total 7640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1180 time to evaluate : 6.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 164 THR Chi-restraints excluded: chain 0 residue 174 ILE Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 42 THR Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 124 ARG Chi-restraints excluded: chain 6 residue 207 GLU Chi-restraints excluded: chain 6 residue 218 LEU Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 257 ILE Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 126 GLN Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 8 residue 147 LEU Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 94 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 18 MET Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 177 ARG Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 167 MET Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 127 TYR Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 111 SER Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 115 LEU Chi-restraints excluded: chain Y residue 133 ASP Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain c residue 50 LEU Chi-restraints excluded: chain c residue 53 CYS Chi-restraints excluded: chain c residue 249 ASN Chi-restraints excluded: chain e residue 126 GLN Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain e residue 149 LEU Chi-restraints excluded: chain e residue 200 MET Chi-restraints excluded: chain e residue 258 ASP Chi-restraints excluded: chain f residue 96 THR Chi-restraints excluded: chain g residue 144 THR Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 141 ASP Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 49 GLU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain j residue 100 GLU Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain p residue 96 ASN Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 111 GLU Chi-restraints excluded: chain q residue 113 LYS Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 110 GLU Chi-restraints excluded: chain r residue 132 ARG Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 266 CYS Chi-restraints excluded: chain s residue 336 THR Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain u residue 121 THR Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 154 ASP Chi-restraints excluded: chain u residue 164 THR Chi-restraints excluded: chain v residue 16 LEU Chi-restraints excluded: chain v residue 26 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 617 optimal weight: 0.1980 chunk 828 optimal weight: 0.5980 chunk 238 optimal weight: 8.9990 chunk 716 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 778 optimal weight: 8.9990 chunk 325 optimal weight: 7.9990 chunk 799 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 243 ASN ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN I 61 HIS ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN L 72 GLN N 98 HIS N 149 HIS T 202 GLN V 35 ASN Z 62 ASN a 137 ASN ** d 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 274 GLN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 182 ASN ** q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.080314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.051951 restraints weight = 273991.542| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 1.80 r_work: 0.2585 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2494 r_free = 0.2494 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2494 r_free = 0.2494 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 106475 Z= 0.269 Angle : 0.625 17.773 150837 Z= 0.316 Chirality : 0.040 0.422 17665 Planarity : 0.005 0.091 14003 Dihedral : 20.520 179.876 31123 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.00 % Allowed : 19.53 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.98 (0.09), residues: 8462 helix: 1.52 (0.09), residues: 3094 sheet: -0.31 (0.15), residues: 1078 loop : 0.41 (0.10), residues: 4290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP 6 235 HIS 0.011 0.001 HIS k 93 PHE 0.031 0.001 PHE k 33 TYR 0.031 0.001 TYR u 141 ARG 0.020 0.000 ARG h 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 48063.31 seconds wall clock time: 835 minutes 7.55 seconds (50107.55 seconds total)