Starting phenix.real_space_refine on Wed Mar 20 20:10:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of2_12867/03_2024/7of2_12867_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of2_12867/03_2024/7of2_12867.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of2_12867/03_2024/7of2_12867_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of2_12867/03_2024/7of2_12867_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of2_12867/03_2024/7of2_12867_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of2_12867/03_2024/7of2_12867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of2_12867/03_2024/7of2_12867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of2_12867/03_2024/7of2_12867_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of2_12867/03_2024/7of2_12867_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 1475 5.49 5 Mg 85 5.21 5 S 296 5.16 5 C 58572 2.51 5 N 18404 2.21 5 O 22360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "T TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 101195 Number of models: 1 Model: "" Number of chains: 64 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: 29940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 29940 Classifications: {'RNA': 1410} Modifications used: {'rna2p_pur': 152, 'rna2p_pyr': 108, 'rna3p': 3, 'rna3p_pur': 589, 'rna3p_pyr': 558} Link IDs: {'rna2p': 259, 'rna3p': 1150} Chain breaks: 12 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 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: 3152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3152 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 2 Chain: "D" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1774 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 12, 'TRANS': 214} 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: "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: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1283 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 11, 'TRANS': 146} 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: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1654 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 14, 'TRANS': 190} 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: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} 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: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1731 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 18, 'TRANS': 189} 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: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 679 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 6, 'TRANS': 77} 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: "l" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 221 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "m" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "o" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 797 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} 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: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 18, 'TRANS': 138} Chain breaks: 1 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: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 145 Unusual residues: {' MG': 81, 'GTP': 2} Classifications: {'undetermined': 83} Link IDs: {None: 82} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 264 SG CYS 0 110 143.851 40.265 126.386 1.00 67.93 S ATOM 286 SG CYS 0 113 147.136 41.543 124.881 1.00 71.28 S ATOM 366 SG CYS 0 123 144.095 43.439 124.292 1.00 63.96 S ATOM 389 SG CYS 0 126 144.368 39.907 122.695 1.00 67.94 S ATOM 2605 SG CYS 4 76 66.620 110.712 167.964 1.00 61.55 S ATOM 2628 SG CYS 4 79 70.301 110.047 167.866 1.00 60.57 S ATOM 2752 SG CYS 4 92 67.850 107.183 167.212 1.00 58.78 S ATOM 54244 SG CYS I 64 90.284 114.393 198.617 1.00 74.24 S ATOM 94808 SG CYS r 70 89.525 110.449 199.052 1.00 68.47 S ATOM 94829 SG CYS r 73 92.774 111.968 198.761 1.00 68.53 S ATOM 95123 SG CYS r 108 89.856 111.949 195.756 1.00 67.67 S Time building chain proxies: 39.68, per 1000 atoms: 0.39 Number of scatterers: 101195 At special positions: 0 Unit cell: (235.2, 238.35, 228.9, 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 296 16.00 P 1475 15.00 Mg 85 11.99 O 22360 8.00 N 18404 7.00 C 58572 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: 38.19 Conformation dependent library (CDL) restraints added in 10.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " 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 79 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 92 " pdb=" ZN r 301 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 70 " pdb="ZN ZN r 301 " - pdb=" SG CYS I 64 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 73 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 108 " Number of angles added : 15 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16152 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: 282 helices and 80 sheets defined 42.1% alpha, 14.2% beta 385 base pairs and 688 stacking pairs defined. Time for finding SS restraints: 63.65 Creating SS restraints... Processing helix chain '0' and resid 86 through 96 removed outlier: 3.735A 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: 3.919A 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: 3.609A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG 3 113 " --> pdb=" O ALA 3 109 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 3.630A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.437A 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: 3.918A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 4.763A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 182 removed outlier: 3.748A pdb=" N HIS 3 181 " --> pdb=" O TYR 3 177 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASP 3 182 " --> pdb=" O GLN 3 178 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 177 through 182' Processing helix chain '5' and resid 35 through 40 removed outlier: 5.166A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 53 removed outlier: 3.730A pdb=" N GLU 5 51 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) Proline residue: 5 53 - end of helix Processing helix chain '5' and resid 116 through 125 Processing helix chain '5' and resid 133 through 142 removed outlier: 4.105A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP 5 141 " --> pdb=" O LEU 5 137 " (cutoff:3.500A) removed outlier: 4.012A 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: 4.158A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.634A 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: 3.988A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 304 removed outlier: 5.038A 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: 4.027A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 49 removed outlier: 5.372A pdb=" N GLU 6 49 " --> pdb=" O LEU 6 45 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 68 Proline residue: 6 68 - end of helix Processing helix chain '6' and resid 73 through 78 removed outlier: 3.774A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 99 through 117 removed outlier: 5.341A 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 Processing helix chain '6' and resid 324 through 333 removed outlier: 3.781A pdb=" N THR 6 328 " --> pdb=" O ASP 6 324 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR 6 329 " --> pdb=" O ASP 6 325 " (cutoff:3.500A) Processing helix chain '6' and resid 363 through 370 removed outlier: 4.350A pdb=" N ASP 6 367 " --> pdb=" O LEU 6 363 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) Processing helix chain '6' and resid 157 through 163 removed outlier: 3.881A pdb=" N PHE 6 162 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 60 removed outlier: 3.950A pdb=" N THR 7 59 " --> pdb=" O GLN 7 55 " (cutoff:3.500A) 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: 3.920A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 186 through 191 removed outlier: 3.865A pdb=" N ASP 7 190 " --> pdb=" O ASP 7 186 " (cutoff:3.500A) removed outlier: 5.516A 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: 4.170A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 4.807A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) Processing helix chain '8' and resid 107 through 154 Processing helix chain '8' and resid 155 through 164 removed outlier: 5.012A pdb=" N ALA 8 159 " --> pdb=" O PRO 8 155 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU 8 160 " --> pdb=" O LYS 8 156 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE 8 162 " --> pdb=" O HIS 8 158 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS 8 163 " --> pdb=" O ALA 8 159 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '8' and resid 165 through 170 removed outlier: 3.876A pdb=" N LEU 8 168 " --> pdb=" O ASP 8 165 " (cutoff:3.500A) removed outlier: 4.099A 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: 3.539A 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 95 Processing helix chain '9' and resid 96 through 106 Processing helix chain '9' and resid 113 through 118 removed outlier: 4.424A pdb=" N TYR 9 117 " --> pdb=" O ASN 9 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 removed outlier: 3.929A pdb=" N LEU C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP C 132 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 169 removed outlier: 3.732A pdb=" N HIS C 160 " --> pdb=" O GLY C 156 " (cutoff:3.500A) Proline residue: C 169 - end of helix Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 214 through 233 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 255 through 290 removed outlier: 4.394A pdb=" N GLN C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 316 Processing helix chain 'C' and resid 358 through 370 removed outlier: 4.098A pdb=" N ILE C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE C 365 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER C 366 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR C 368 " --> pdb=" O SER C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 404 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 443 through 459 Processing helix chain 'C' and resid 473 through 482 Processing helix chain 'C' and resid 503 through 515 Proline residue: C 515 - end of helix Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.694A 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: 3.644A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 3.639A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 3.784A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.388A pdb=" N LYS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 6.205A 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: 4.609A pdb=" N PHE E 198 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 5.196A 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 92 through 108 removed outlier: 4.600A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 6.170A 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: 3.606A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 3.776A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 5.021A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 3.867A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 89 removed outlier: 3.634A pdb=" N THR F 89 " --> pdb=" O PRO F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 84 through 89' Processing helix chain 'H' and resid 74 through 79 removed outlier: 3.608A pdb=" N ARG H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.191A 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: 4.026A 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 122 Processing helix chain 'H' and resid 133 through 147 Processing helix chain 'I' and resid 41 through 52 removed outlier: 3.552A pdb=" N GLU I 52 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 66 removed outlier: 4.024A pdb=" N LEU I 65 " --> pdb=" O HIS I 61 " (cutoff:3.500A) Proline residue: I 66 - end of helix No H-bonds generated for 'chain 'I' and resid 61 through 66' Processing helix chain 'I' and resid 77 through 93 Processing helix chain 'I' and resid 105 through 120 removed outlier: 3.882A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.343A 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: 4.066A pdb=" N GLU I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 172 removed outlier: 3.686A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 3.861A 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 43 removed outlier: 3.733A pdb=" N GLN J 41 " --> pdb=" O PRO J 37 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ARG J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 4.299A pdb=" N LYS J 61 " --> pdb=" O THR J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 96 removed outlier: 3.846A pdb=" N PHE J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 125 removed outlier: 4.076A pdb=" N ILE J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA J 125 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 152 removed outlier: 4.163A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER J 143 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 4.073A 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: 4.943A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 5.009A 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: 5.480A 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: 4.585A pdb=" N LYS L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 5.736A 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 Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 55 through 60 removed outlier: 3.630A pdb=" N ARG M 59 " --> pdb=" O GLY M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.527A pdb=" N ILE M 78 " --> pdb=" O PHE M 74 " (cutoff:3.500A) 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: 3.591A 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: 3.531A 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: 3.825A 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: 3.990A pdb=" N ASP M 250 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 5.493A 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 68 through 74 removed outlier: 4.684A pdb=" N ILE N 72 " --> pdb=" O ASN N 68 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 113 Processing helix chain 'N' and resid 168 through 183 removed outlier: 3.842A pdb=" N VAL N 172 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) 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: 4.521A pdb=" N VAL N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 4.412A 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: 4.328A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 80 Processing helix chain 'O' and resid 82 through 98 removed outlier: 4.318A pdb=" N ILE O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 87 - end of helix removed outlier: 3.969A pdb=" N LEU O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 5.307A 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: 4.604A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU P 116 " --> pdb=" O ILE P 112 " (cutoff:3.500A) removed outlier: 5.987A 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: 4.067A 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: 3.898A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 194 removed outlier: 4.645A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP Q 192 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 removed outlier: 3.557A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 268 removed outlier: 3.647A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Proline residue: Q 263 - end of helix removed outlier: 4.582A pdb=" N GLU Q 266 " --> pdb=" O GLN Q 262 " (cutoff:3.500A) removed outlier: 4.271A 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: 3.870A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA R 28 " --> pdb=" O VAL R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 38 removed outlier: 4.398A pdb=" N ARG R 37 " --> pdb=" O GLY R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 80 removed outlier: 4.204A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 Processing helix chain 'R' and resid 98 through 108 Processing helix chain 'R' and resid 109 through 134 Processing helix chain 'S' and resid 68 through 90 Processing helix chain 'T' and resid 49 through 57 removed outlier: 3.618A pdb=" N LYS T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN T 55 " --> pdb=" O TRP T 51 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE T 57 " --> pdb=" O LYS T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 95 removed outlier: 3.845A pdb=" N TYR T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 110 removed outlier: 3.689A pdb=" N PHE T 108 " --> pdb=" O ALA T 104 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN T 109 " --> pdb=" O GLN T 105 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ASP T 110 " --> pdb=" O LEU T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 131 removed outlier: 4.156A pdb=" N LYS T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 206 removed outlier: 3.641A 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: 4.697A 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 120 Processing helix chain 'X' and resid 7 through 19 removed outlier: 3.822A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 4.606A 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: 5.714A pdb=" N GLU X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 79 removed outlier: 3.967A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG X 77 " --> pdb=" O PRO X 73 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 4.406A 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: 3.717A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 220 Processing helix chain 'X' and resid 225 through 244 removed outlier: 3.632A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 69 removed outlier: 4.641A pdb=" N PHE Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 5.085A 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: 5.650A pdb=" N GLY Y 75 " --> pdb=" O PRO Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 94 removed outlier: 3.789A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS Y 93 " --> pdb=" O GLN Y 89 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 removed outlier: 3.632A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 129 through 158 removed outlier: 4.006A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 192 removed outlier: 5.550A pdb=" N LYS Y 192 " --> pdb=" O TRP Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 198 removed outlier: 4.950A pdb=" N ARG Y 198 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 203 through 238 removed outlier: 4.659A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 48 removed outlier: 4.401A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) removed outlier: 5.695A 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: 4.107A pdb=" N THR a 72 " --> pdb=" O PRO a 68 " (cutoff:3.500A) removed outlier: 5.679A 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 127 through 135 removed outlier: 5.848A pdb=" N ASN a 135 " --> pdb=" O ARG a 131 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.644A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 4.539A 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: 3.733A pdb=" N ARG b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.245A 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: 5.421A 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: 3.808A 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: 5.275A pdb=" N ASN c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 107 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: 3.820A pdb=" N ILE c 220 " --> pdb=" O ARG c 216 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 5.068A 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: 4.223A pdb=" N THR c 224 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 3.923A 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: 4.417A pdb=" N THR d 52 " --> pdb=" O PRO d 48 " (cutoff:3.500A) Processing helix chain 'd' and resid 118 through 130 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: 3.632A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 177 Proline residue: d 170 - end of helix removed outlier: 5.053A pdb=" N ASP d 175 " --> pdb=" O ASP d 171 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE d 176 " --> pdb=" O MET d 172 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 82 Processing helix chain 'e' and resid 116 through 132 removed outlier: 3.586A pdb=" N LEU e 120 " --> pdb=" O LEU e 116 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE e 131 " --> pdb=" O LYS e 127 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 143 removed outlier: 4.755A pdb=" N GLU e 142 " --> pdb=" O THR e 138 " (cutoff:3.500A) removed outlier: 3.716A 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: 3.965A pdb=" N ALA e 193 " --> pdb=" O GLU e 189 " (cutoff:3.500A) Processing helix chain 'e' and resid 256 through 264 removed outlier: 6.442A pdb=" N LEU e 260 " --> pdb=" O THR e 256 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY e 261 " --> pdb=" O LYS e 257 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 277 removed outlier: 3.636A pdb=" N GLN e 271 " --> pdb=" O LYS e 267 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL e 272 " --> pdb=" O TYR e 268 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ARG e 273 " --> pdb=" O LEU e 269 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N SER e 277 " --> pdb=" O ARG e 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 64 removed outlier: 3.631A pdb=" N ILE f 63 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS f 64 " --> pdb=" O LYS f 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 59 through 64' Processing helix chain 'f' and resid 99 through 118 Processing helix chain 'f' and resid 163 through 178 removed outlier: 3.572A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU f 178 " --> pdb=" O ILE f 174 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 53 removed outlier: 4.471A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 3.652A 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: 4.195A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N CYS h 121 " --> pdb=" O LEU h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 133 Proline residue: h 133 - end of helix Processing helix chain 'h' and resid 138 through 147 removed outlier: 4.754A 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 74 removed outlier: 4.115A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE i 74 " --> pdb=" O PRO i 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 69 through 74' 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 removed outlier: 3.636A pdb=" N ARG j 28 " --> pdb=" O GLY j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 60 through 107 Processing helix chain 'j' and resid 41 through 46 removed outlier: 4.293A 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 39 removed outlier: 3.780A pdb=" N SER k 39 " --> pdb=" O GLN k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 40 through 47 removed outlier: 3.547A pdb=" N ASN k 46 " --> pdb=" O VAL k 42 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 96 Processing helix chain 'l' and resid 114 through 135 removed outlier: 3.528A pdb=" N TRP l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN l 135 " --> pdb=" O ARG l 131 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 52 removed outlier: 4.099A 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: 4.004A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 removed outlier: 3.513A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS o 99 " --> pdb=" O LEU o 95 " (cutoff:3.500A) removed outlier: 5.898A 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 72 through 77 removed outlier: 4.946A pdb=" N THR p 77 " --> pdb=" O LEU p 73 " (cutoff:3.500A) Processing helix chain 'p' and resid 112 through 124 Processing helix chain 'p' and resid 142 through 163 Processing helix chain 'p' and resid 174 through 190 removed outlier: 4.177A pdb=" N ILE p 178 " --> pdb=" O LYS p 174 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLN p 190 " --> pdb=" O GLU p 186 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 53 removed outlier: 3.959A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 3.605A 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 64 Processing helix chain 'q' and resid 71 through 76 removed outlier: 4.402A pdb=" N LEU q 75 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 4.408A 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: 4.507A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 5.674A 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: 4.025A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 5.083A 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 removed outlier: 3.688A pdb=" N TRP s 105 " --> pdb=" O ASN s 101 " (cutoff:3.500A) Processing helix chain 's' and resid 140 through 155 Processing helix chain 's' and resid 167 through 193 removed outlier: 4.123A 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: 4.371A 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: 4.185A pdb=" N VAL s 322 " --> pdb=" O ASP s 318 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 387 removed outlier: 5.218A pdb=" N ASN s 386 " --> pdb=" O GLN s 382 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN s 387 " --> pdb=" O ALA s 383 " (cutoff:3.500A) Processing helix chain 's' and resid 414 through 427 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: 4.006A pdb=" N VAL v 9 " --> pdb=" O SER v 5 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU v 10 " --> pdb=" O ARG v 6 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU v 23 " --> pdb=" O GLN v 19 " (cutoff:3.500A) removed outlier: 5.898A 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: 3.654A pdb=" N ARG v 51 " --> pdb=" O ASP v 47 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU v 52 " --> pdb=" O ALA v 48 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG v 53 " --> pdb=" O GLU v 49 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 90 removed outlier: 3.674A pdb=" N TYR w 90 " --> pdb=" O VAL w 86 " (cutoff:3.500A) Processing helix chain 'w' and resid 111 through 126 removed outlier: 4.950A pdb=" N GLU w 125 " --> pdb=" O ALA w 121 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 139 removed outlier: 4.239A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) removed outlier: 4.712A 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 155 through 159 Processing sheet with id= 2, first strand: chain '1' and resid 17 through 22 removed outlier: 5.923A pdb=" N PHE 1 28 " --> pdb=" O SER 1 22 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '1' and resid 41 through 46 removed outlier: 5.978A pdb=" N LEU 1 41 " --> pdb=" O GLU 1 58 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '3' and resid 122 through 125 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain '4' and resid 79 through 84 removed outlier: 6.865A pdb=" N TRP 4 88 " --> pdb=" O GLN 4 102 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '5' and resid 126 through 130 removed outlier: 5.188A pdb=" N VAL 5 351 " --> pdb=" O ASP 5 348 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ARG 5 200 " --> pdb=" O LYS 5 233 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '5' and resid 208 through 214 removed outlier: 4.790A pdb=" N LEU 5 219 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '5' and resid 230 through 233 removed outlier: 6.552A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '5' and resid 350 through 353 removed outlier: 8.551A pdb=" N ARG 5 350 " --> pdb=" O LEU 5 382 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '6' and resid 183 through 187 removed outlier: 4.569A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS 6 174 " --> pdb=" O THR 6 205 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '6' and resid 231 through 234 removed outlier: 6.616A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TRP 6 235 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '6' and resid 310 through 314 removed outlier: 8.233A pdb=" N THR 6 310 " --> pdb=" O ASP 6 276 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '6' and resid 213 through 221 removed outlier: 5.267A pdb=" N LEU 6 213 " --> pdb=" O GLN 6 275 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARG 6 267 " --> pdb=" O LEU 6 221 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '7' and resid 77 through 82 removed outlier: 4.779A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N PHE 7 127 " --> pdb=" O VAL 7 70 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '7' and resid 164 through 167 removed outlier: 6.966A pdb=" N ASP 7 182 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '7' and resid 217 through 221 removed outlier: 4.796A pdb=" N LYS 7 253 " --> pdb=" O SER 7 264 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '7' and resid 281 through 286 removed outlier: 5.376A pdb=" N ILE 7 294 " --> pdb=" O LEU 7 286 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '9' and resid 42 through 45 removed outlier: 3.709A pdb=" N ARG 9 49 " --> pdb=" O THR 9 45 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'C' and resid 133 through 137 removed outlier: 7.211A pdb=" N LEU C 100 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN C 138 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'C' and resid 332 through 338 removed outlier: 3.810A pdb=" N THR C 350 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLY C 301 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C' and resid 463 through 468 Processing sheet with id= 22, first strand: chain 'C' and resid 97 through 101 Processing sheet with id= 23, first strand: chain 'D' and resid 128 through 131 removed outlier: 3.847A pdb=" N GLN D 128 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY D 179 " --> pdb=" O THR D 162 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU D 164 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 189 through 193 removed outlier: 6.564A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU D 237 " --> pdb=" O TYR D 295 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'D' and resid 139 through 144 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: 3.775A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ASN E 281 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU E 330 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'E' and resid 175 through 182 removed outlier: 3.528A pdb=" N THR E 175 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.010A 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: 4.505A pdb=" N GLN E 202 " --> pdb=" O VAL E 273 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'F' and resid 46 through 50 Processing sheet with id= 31, first strand: chain 'F' and resid 186 through 189 Processing sheet with id= 32, first strand: chain 'H' and resid 55 through 58 removed outlier: 7.109A pdb=" N ILE H 55 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'H' and resid 94 through 98 removed outlier: 3.593A pdb=" N LEU H 98 " --> pdb=" O ASP H 110 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP H 110 " --> pdb=" O LEU H 98 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'I' and resid 94 through 100 removed outlier: 4.194A pdb=" N ALA I 97 " --> pdb=" O LEU I 154 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'J' and resid 18 through 25 removed outlier: 3.535A pdb=" N ILE J 70 " --> pdb=" O ILE J 20 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA J 22 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL J 24 " --> pdb=" O LEU J 66 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY J 83 " --> pdb=" O PRO J 67 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS J 81 " --> pdb=" O LYS J 69 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'K' and resid 55 through 60 removed outlier: 5.225A pdb=" N ASP K 22 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'K' and resid 77 through 81 removed outlier: 7.435A pdb=" N GLY K 86 " --> pdb=" O THR K 81 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'L' and resid 38 through 41 Processing sheet with id= 39, first strand: chain 'L' and resid 72 through 76 Processing sheet with id= 40, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 41, first strand: chain 'M' and resid 273 through 277 Processing sheet with id= 42, first strand: chain 'N' and resid 93 through 96 Processing sheet with id= 43, first strand: chain 'N' and resid 118 through 123 removed outlier: 5.469A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ALA N 186 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.225A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TYR O 104 " --> pdb=" O LYS O 126 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'P' and resid 80 through 85 removed outlier: 6.332A pdb=" N VAL P 90 " --> pdb=" O THR P 107 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Q' and resid 130 through 135 removed outlier: 6.621A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Q' and resid 139 through 142 removed outlier: 3.878A pdb=" N GLN Q 139 " --> pdb=" O ILE Q 150 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'S' and resid 105 through 109 Processing sheet with id= 49, first strand: chain 'S' and resid 112 through 117 removed outlier: 3.805A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU S 126 " --> pdb=" O VAL S 160 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'S' and resid 154 through 157 removed outlier: 3.562A pdb=" N SER S 197 " --> pdb=" O GLU S 157 " (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: 4.078A 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: 4.908A pdb=" N ALA T 71 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS T 177 " --> pdb=" O ALA T 143 " (cutoff:3.500A) removed outlier: 5.867A 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: 4.321A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP U 38 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY U 75 " --> pdb=" O PRO U 90 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'V' and resid 92 through 97 removed outlier: 5.953A 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: 7.321A pdb=" N GLU V 132 " --> pdb=" O THR V 148 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG V 145 " --> pdb=" O ILE V 154 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE V 154 " --> pdb=" O ARG V 145 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG V 152 " --> pdb=" O SER V 147 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'W' and resid 97 through 101 Processing sheet with id= 59, first strand: chain 'X' and resid 49 through 53 removed outlier: 5.231A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN X 58 " --> pdb=" O ASN X 53 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'X' and resid 85 through 92 removed outlier: 5.081A pdb=" N LYS X 99 " --> pdb=" O ALA X 92 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 62, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.242A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'a' and resid 44 through 52 removed outlier: 5.569A pdb=" N ASN a 44 " --> pdb=" O VAL a 65 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL a 65 " --> pdb=" O ASN a 44 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'b' and resid 61 through 68 removed outlier: 3.943A pdb=" N ALA b 83 " --> pdb=" O TYR b 79 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'c' and resid 254 through 257 Processing sheet with id= 66, first strand: chain 'c' and resid 269 through 275 removed outlier: 3.782A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'd' and resid 212 through 218 removed outlier: 3.819A pdb=" N TYR d 245 " --> pdb=" O ILE d 265 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'e' and resid 175 through 178 removed outlier: 3.824A pdb=" N TRP e 178 " --> pdb=" O LEU e 47 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU e 47 " --> pdb=" O TRP e 178 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N LEU e 51 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL e 161 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU e 159 " --> pdb=" O LEU e 53 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU e 160 " --> pdb=" O VAL e 253 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG e 162 " --> pdb=" O HIS e 251 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N HIS e 251 " --> pdb=" O ARG e 162 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'e' and resid 201 through 204 removed outlier: 7.038A pdb=" N GLU e 201 " --> pdb=" O LEU e 239 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'e' and resid 44 through 55 removed outlier: 3.730A pdb=" N LYS e 230 " --> pdb=" O ARG e 46 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU e 48 " --> pdb=" O LYS e 230 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE e 232 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA e 236 " --> pdb=" O CYS e 52 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'f' and resid 123 through 127 removed outlier: 4.892A pdb=" N GLU f 123 " --> pdb=" O GLN f 158 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR f 125 " --> pdb=" O VAL f 156 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET f 127 " --> pdb=" O GLU f 154 " (cutoff:3.500A) removed outlier: 4.934A 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: 5.462A 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: 3.852A pdb=" N PHE k 20 " --> pdb=" O ASP k 54 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS k 72 " --> pdb=" O PHE k 68 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'm' and resid 53 through 56 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 42 removed outlier: 4.142A 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: 4.103A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU s 229 " --> pdb=" O ARG s 212 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 's' and resid 112 through 116 removed outlier: 6.295A pdb=" N ASN s 391 " --> pdb=" O ASN s 375 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN s 375 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N CYS s 393 " --> pdb=" O GLN s 373 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLN s 373 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY s 395 " --> pdb=" O CYS s 371 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N CYS s 371 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLN s 397 " --> pdb=" O PHE s 369 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N PHE s 369 " --> pdb=" O GLN s 397 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N LYS s 365 " --> pdb=" O LEU s 401 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) removed outlier: 3.671A 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: 6.609A 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: 3.779A pdb=" N ASP u 108 " --> pdb=" O SER u 128 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASP u 122 " --> pdb=" O VAL u 114 " (cutoff:3.500A) 2785 hydrogen bonds defined for protein. 8271 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 939 hydrogen bonds 1608 hydrogen bond angles 0 basepair planarities 385 basepair parallelities 688 stacking parallelities Total time for adding SS restraints: 66.60 Time building geometry restraints manager: 41.34 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: 26468 1.33 - 1.46: 31109 1.46 - 1.58: 45488 1.58 - 1.70: 2928 1.70 - 1.83: 469 Bond restraints: 106462 Sorted by residual: bond pdb=" C2 OMU A3039 " pdb=" N3 OMU A3039 " ideal model delta sigma weight residual 1.499 1.331 0.168 2.00e-02 2.50e+03 7.05e+01 bond pdb=" N3 OMG A3040 " pdb=" C4 OMG A3040 " ideal model delta sigma weight residual 1.492 1.350 0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" N3 OMG A2815 " pdb=" C4 OMG A2815 " ideal model delta sigma weight residual 1.492 1.352 0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" N3 OMU A3039 " pdb=" C4 OMU A3039 " ideal model delta sigma weight residual 1.457 1.330 0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" N1 OMG A3040 " pdb=" C2 OMG A3040 " ideal model delta sigma weight residual 1.462 1.341 0.121 2.00e-02 2.50e+03 3.65e+01 ... (remaining 106457 not shown) Histogram of bond angle deviations from ideal: 98.63 - 106.11: 10441 106.11 - 113.60: 60734 113.60 - 121.08: 50773 121.08 - 128.56: 26534 128.56 - 136.04: 2459 Bond angle restraints: 150941 Sorted by residual: angle pdb=" C3' U A3041 " pdb=" C2' U A3041 " pdb=" O2' U A3041 " ideal model delta sigma weight residual 114.60 125.50 -10.90 1.50e+00 4.44e-01 5.28e+01 angle pdb=" O3' U A3041 " pdb=" C3' U A3041 " pdb=" C2' U A3041 " ideal model delta sigma weight residual 109.50 119.91 -10.41 1.50e+00 4.44e-01 4.81e+01 angle pdb=" C2' OMU A3039 " pdb=" C1' OMU A3039 " pdb=" N1 OMU A3039 " ideal model delta sigma weight residual 112.00 102.60 9.40 1.50e+00 4.44e-01 3.93e+01 angle pdb=" C1' OMG A2815 " pdb=" N9 OMG A2815 " pdb=" C4 OMG A2815 " ideal model delta sigma weight residual 108.29 125.63 -17.34 3.00e+00 1.11e-01 3.34e+01 angle pdb=" C1' OMG A2815 " pdb=" N9 OMG A2815 " pdb=" C8 OMG A2815 " ideal model delta sigma weight residual 142.82 125.97 16.85 3.00e+00 1.11e-01 3.16e+01 ... (remaining 150936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 61849 35.94 - 71.89: 3307 71.89 - 107.83: 459 107.83 - 143.78: 26 143.78 - 179.72: 43 Dihedral angle restraints: 65684 sinusoidal: 40752 harmonic: 24932 Sorted by residual: dihedral pdb=" C5' U A3041 " pdb=" C4' U A3041 " pdb=" C3' U A3041 " pdb=" O3' U A3041 " ideal model delta sinusoidal sigma weight residual 147.00 80.11 66.89 1 8.00e+00 1.56e-02 9.11e+01 dihedral pdb=" O4' U A2994 " pdb=" C1' U A2994 " pdb=" N1 U A2994 " pdb=" C2 U A2994 " ideal model delta sinusoidal sigma weight residual 200.00 20.70 179.30 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1689 " pdb=" C1' C A1689 " pdb=" N1 C A1689 " pdb=" C2 C A1689 " ideal model delta sinusoidal sigma weight residual 200.00 22.85 177.15 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 65681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 17127 0.100 - 0.201: 555 0.201 - 0.301: 5 0.301 - 0.402: 0 0.402 - 0.502: 1 Chirality restraints: 17688 Sorted by residual: chirality pdb=" C3' U A3041 " pdb=" C4' U A3041 " pdb=" O3' U A3041 " pdb=" C2' U A3041 " both_signs ideal model delta sigma weight residual False -2.74 -2.24 -0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" C3* GTP C 601 " pdb=" C2* GTP C 601 " pdb=" C4* GTP C 601 " pdb=" O3* GTP C 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' A A2693 " pdb=" C4' A A2693 " pdb=" O3' A A2693 " pdb=" C2' A A2693 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 17685 not shown) Planarity restraints: 13918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2815 " 0.043 2.00e-02 2.50e+03 5.53e-01 6.89e+03 pdb=" C4' OMG A2815 " 0.420 2.00e-02 2.50e+03 pdb=" O4' OMG A2815 " 0.553 2.00e-02 2.50e+03 pdb=" C3' OMG A2815 " -0.593 2.00e-02 2.50e+03 pdb=" O3' OMG A2815 " -0.555 2.00e-02 2.50e+03 pdb=" C2' OMG A2815 " -0.206 2.00e-02 2.50e+03 pdb=" O2' OMG A2815 " 0.917 2.00e-02 2.50e+03 pdb=" C1' OMG A2815 " 0.240 2.00e-02 2.50e+03 pdb=" N9 OMG A2815 " -0.820 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A3040 " -0.026 2.00e-02 2.50e+03 5.50e-01 6.80e+03 pdb=" C4' OMG A3040 " 0.444 2.00e-02 2.50e+03 pdb=" O4' OMG A3040 " 0.715 2.00e-02 2.50e+03 pdb=" C3' OMG A3040 " -0.573 2.00e-02 2.50e+03 pdb=" O3' OMG A3040 " -0.462 2.00e-02 2.50e+03 pdb=" C2' OMG A3040 " -0.254 2.00e-02 2.50e+03 pdb=" O2' OMG A3040 " 0.773 2.00e-02 2.50e+03 pdb=" C1' OMG A3040 " 0.247 2.00e-02 2.50e+03 pdb=" N9 OMG A3040 " -0.863 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A1759 " -0.038 2.00e-02 2.50e+03 2.08e-02 9.78e+00 pdb=" N1 U A1759 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U A1759 " 0.022 2.00e-02 2.50e+03 pdb=" O2 U A1759 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U A1759 " -0.021 2.00e-02 2.50e+03 pdb=" C4 U A1759 " 0.008 2.00e-02 2.50e+03 pdb=" O4 U A1759 " -0.015 2.00e-02 2.50e+03 pdb=" C5 U A1759 " 0.004 2.00e-02 2.50e+03 pdb=" C6 U A1759 " 0.002 2.00e-02 2.50e+03 ... (remaining 13915 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 528 2.45 - 3.06: 66208 3.06 - 3.68: 175099 3.68 - 4.29: 267058 4.29 - 4.90: 401963 Nonbonded interactions: 910856 Sorted by model distance: nonbonded pdb=" OP1 A A2430 " pdb="MG MG A3313 " model vdw 1.840 2.170 nonbonded pdb=" O2B GTP C 601 " pdb="MG MG C 602 " model vdw 1.843 2.170 nonbonded pdb=" OP1 A A1961 " pdb="MG MG A3313 " model vdw 1.844 2.170 nonbonded pdb=" OP2 A A2990 " pdb="MG MG A3364 " model vdw 1.866 2.170 nonbonded pdb=" O2' A A3059 " pdb=" OP1 U A3062 " model vdw 1.868 2.440 ... (remaining 910851 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 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: 0.090 Extract box with map and model: 13.060 Check model and map are aligned: 1.200 Set scattering table: 0.720 Process input model: 307.050 Find NCS groups from input model: 2.920 Set up NCS constraints: 0.320 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:9.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 337.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 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 0.168 106462 Z= 0.198 Angle : 0.538 17.341 150941 Z= 0.270 Chirality : 0.037 0.502 17688 Planarity : 0.008 0.553 13918 Dihedral : 19.109 179.725 49532 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.01 % Allowed : 0.09 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.20 (0.09), residues: 8398 helix: 2.00 (0.10), residues: 2969 sheet: -0.34 (0.16), residues: 1054 loop : 0.36 (0.10), residues: 4375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP 6 235 HIS 0.009 0.001 HIS S 76 PHE 0.023 0.001 PHE s 424 TYR 0.019 0.001 TYR 5 176 ARG 0.010 0.000 ARG m 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2005 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2004 time to evaluate : 7.524 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: 0 155 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8086 (mm-30) REVERT: 1 58 GLU cc_start: 0.8249 (tt0) cc_final: 0.7842 (tt0) REVERT: 4 80 TYR cc_start: 0.8932 (p90) cc_final: 0.8614 (p90) REVERT: 5 153 CYS cc_start: 0.8625 (m) cc_final: 0.8266 (m) REVERT: 5 169 GLU cc_start: 0.7751 (tp30) cc_final: 0.7542 (tp30) REVERT: 6 148 LYS cc_start: 0.9116 (ttmm) cc_final: 0.8884 (ttmt) REVERT: 6 188 TYR cc_start: 0.7979 (m-80) cc_final: 0.7743 (m-80) REVERT: 6 330 ILE cc_start: 0.9603 (mt) cc_final: 0.9372 (mt) REVERT: 7 93 MET cc_start: 0.8852 (mtm) cc_final: 0.8603 (mtm) REVERT: 7 231 GLN cc_start: 0.8227 (pm20) cc_final: 0.7683 (pm20) REVERT: 8 106 LEU cc_start: 0.7876 (mt) cc_final: 0.7463 (mm) REVERT: 8 117 LEU cc_start: 0.9072 (tt) cc_final: 0.8858 (tm) REVERT: 8 147 LEU cc_start: 0.6472 (mm) cc_final: 0.5924 (tm) REVERT: 9 66 THR cc_start: 0.9176 (p) cc_final: 0.8805 (p) REVERT: C 150 LYS cc_start: 0.7491 (mttt) cc_final: 0.6945 (mptt) REVERT: C 418 ASN cc_start: 0.9037 (t0) cc_final: 0.8778 (t0) REVERT: C 480 LYS cc_start: 0.9131 (ptmt) cc_final: 0.8765 (ptmm) REVERT: C 507 TYR cc_start: 0.8848 (t80) cc_final: 0.8383 (t80) REVERT: F 209 TYR cc_start: 0.8901 (t80) cc_final: 0.8698 (t80) REVERT: H 93 ASN cc_start: 0.9030 (m-40) cc_final: 0.8769 (m110) REVERT: H 99 THR cc_start: 0.9210 (p) cc_final: 0.7915 (p) REVERT: H 100 GLN cc_start: 0.8353 (mt0) cc_final: 0.7950 (mp10) REVERT: H 111 LEU cc_start: 0.8971 (mp) cc_final: 0.8677 (mp) REVERT: I 45 GLN cc_start: 0.8757 (tt0) cc_final: 0.8516 (mt0) REVERT: I 61 HIS cc_start: 0.8405 (t-90) cc_final: 0.8192 (t-90) REVERT: I 80 ARG cc_start: 0.9052 (ptp90) cc_final: 0.8678 (ppt170) REVERT: I 86 ILE cc_start: 0.9492 (mm) cc_final: 0.9064 (mm) REVERT: I 90 PHE cc_start: 0.8332 (m-80) cc_final: 0.7866 (m-10) REVERT: I 119 HIS cc_start: 0.7441 (t70) cc_final: 0.7223 (t-90) REVERT: J 66 LEU cc_start: 0.8048 (mt) cc_final: 0.7781 (mm) REVERT: J 69 LYS cc_start: 0.7889 (tptt) cc_final: 0.6878 (tmtt) REVERT: J 116 HIS cc_start: 0.7947 (t70) cc_final: 0.7190 (t70) REVERT: L 37 ARG cc_start: 0.7949 (mtm180) cc_final: 0.7567 (mtm180) REVERT: L 56 ARG cc_start: 0.8538 (mtp85) cc_final: 0.8260 (ttm-80) REVERT: N 114 ASP cc_start: 0.8640 (t0) cc_final: 0.8230 (t0) REVERT: N 197 LYS cc_start: 0.8628 (ttpt) cc_final: 0.7991 (tttp) REVERT: N 201 ASP cc_start: 0.8229 (m-30) cc_final: 0.7821 (m-30) REVERT: P 58 LEU cc_start: 0.9439 (mt) cc_final: 0.9236 (mt) REVERT: P 118 SER cc_start: 0.9006 (t) cc_final: 0.8703 (t) REVERT: T 52 GLU cc_start: 0.8093 (mp0) cc_final: 0.7876 (mp0) REVERT: U 4 ASN cc_start: 0.9148 (m-40) cc_final: 0.8908 (m-40) REVERT: V 53 ASP cc_start: 0.7633 (m-30) cc_final: 0.7378 (m-30) REVERT: V 119 GLN cc_start: 0.9170 (mt0) cc_final: 0.8969 (mt0) REVERT: V 124 ASP cc_start: 0.5861 (t70) cc_final: 0.5392 (t0) REVERT: W 94 GLU cc_start: 0.8068 (tt0) cc_final: 0.7710 (tt0) REVERT: W 104 TYR cc_start: 0.9262 (t80) cc_final: 0.8970 (t80) REVERT: X 9 TRP cc_start: 0.8908 (p-90) cc_final: 0.8572 (p-90) REVERT: Y 70 ASP cc_start: 0.7963 (t70) cc_final: 0.7553 (t70) REVERT: Y 147 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7641 (tp40) REVERT: Z 47 GLN cc_start: 0.8413 (mt0) cc_final: 0.7273 (mt0) REVERT: Z 84 ASP cc_start: 0.8145 (m-30) cc_final: 0.7929 (m-30) REVERT: d 88 TYR cc_start: 0.8693 (t80) cc_final: 0.8402 (t80) REVERT: d 216 MET cc_start: 0.7948 (mtp) cc_final: 0.7609 (mtp) REVERT: d 274 GLN cc_start: 0.8642 (tt0) cc_final: 0.8408 (tt0) REVERT: e 132 LYS cc_start: 0.4965 (mmmt) cc_final: 0.4700 (tptt) REVERT: e 237 LEU cc_start: 0.8543 (pp) cc_final: 0.8339 (tp) REVERT: e 267 LYS cc_start: 0.6689 (pttt) cc_final: 0.6464 (pmtt) REVERT: h 93 ASP cc_start: 0.8202 (t0) cc_final: 0.7985 (t70) REVERT: j 45 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8329 (mt-10) REVERT: j 97 LYS cc_start: 0.8757 (mmtp) cc_final: 0.7651 (mptm) REVERT: k 24 GLU cc_start: 0.6264 (mt-10) cc_final: 0.5722 (mp0) REVERT: k 67 LEU cc_start: 0.8288 (tp) cc_final: 0.8038 (mp) REVERT: l 117 TYR cc_start: 0.8921 (t80) cc_final: 0.7596 (m-10) REVERT: m 77 MET cc_start: 0.3479 (tpt) cc_final: 0.3250 (tmt) REVERT: p 47 LYS cc_start: 0.9302 (mttp) cc_final: 0.9080 (mttm) REVERT: p 117 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8336 (mm110) REVERT: p 149 ASP cc_start: 0.8548 (t0) cc_final: 0.8348 (t0) REVERT: p 152 GLN cc_start: 0.9141 (tp40) cc_final: 0.8572 (tp40) REVERT: p 156 ASP cc_start: 0.8373 (m-30) cc_final: 0.8113 (m-30) REVERT: q 41 ASP cc_start: 0.8150 (p0) cc_final: 0.7797 (p0) REVERT: q 44 ASP cc_start: 0.8445 (t0) cc_final: 0.8104 (t0) REVERT: r 39 VAL cc_start: 0.9111 (t) cc_final: 0.8597 (p) REVERT: r 41 THR cc_start: 0.9188 (m) cc_final: 0.8590 (p) REVERT: r 103 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6466 (mptt) REVERT: u 92 PHE cc_start: 0.8304 (t80) cc_final: 0.8023 (t80) REVERT: u 160 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8536 (mt-10) REVERT: u 166 ASP cc_start: 0.8376 (p0) cc_final: 0.8042 (p0) REVERT: u 177 ILE cc_start: 0.9250 (mp) cc_final: 0.8956 (mm) REVERT: v 21 ARG cc_start: 0.8782 (mmp80) cc_final: 0.8181 (mmt-90) REVERT: v 51 ARG cc_start: 0.8105 (mmt90) cc_final: 0.7712 (mmm160) REVERT: v 59 LEU cc_start: 0.9425 (tp) cc_final: 0.9137 (tt) REVERT: v 63 ASN cc_start: 0.8965 (m-40) cc_final: 0.8329 (m-40) REVERT: w 111 ASP cc_start: 0.7689 (t0) cc_final: 0.7305 (t0) outliers start: 1 outliers final: 4 residues processed: 2005 average time/residue: 1.9217 time to fit residues: 5207.4646 Evaluate side-chains 1392 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1388 time to evaluate : 7.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 153 ILE Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain e residue 245 GLN Chi-restraints excluded: chain v residue 27 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 823 optimal weight: 1.9990 chunk 739 optimal weight: 20.0000 chunk 410 optimal weight: 0.3980 chunk 252 optimal weight: 10.0000 chunk 498 optimal weight: 10.0000 chunk 394 optimal weight: 6.9990 chunk 764 optimal weight: 10.0000 chunk 295 optimal weight: 9.9990 chunk 464 optimal weight: 7.9990 chunk 568 optimal weight: 1.9990 chunk 885 optimal weight: 20.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 GLN 7 49 ASN ** 7 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN C 211 ASN C 232 ASN C 304 ASN C 504 ASN D 156 ASN E 184 ASN E 336 ASN F 184 GLN F 228 GLN F 257 GLN H 126 GLN I 43 GLN I 93 ASN I 128 ASN J 48 GLN J 103 GLN ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN K 160 GLN L 72 GLN L 142 GLN M 219 ASN M 276 ASN N 68 ASN N 98 HIS N 138 HIS N 222 ASN O 100 GLN O 154 GLN O 160 GLN P 176 GLN S 84 ASN S 91 GLN S 118 ASN T 109 ASN T 133 ASN T 195 HIS T 201 GLN T 202 GLN U 84 ASN U 136 GLN Y 73 ASN Y 147 GLN Y 183 GLN Z 62 ASN Z 98 GLN ** d 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 161 HIS d 167 HIS d 193 HIS ** d 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 118 GLN e 156 ASN e 168 GLN e 248 ASN h 99 ASN ** h 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 124 GLN ** o 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 33 GLN o 91 GLN p 125 ASN p 182 ASN p 184 ASN ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 148 HIS u 156 HIS ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 106462 Z= 0.329 Angle : 0.632 19.532 150941 Z= 0.323 Chirality : 0.041 0.302 17688 Planarity : 0.005 0.129 13918 Dihedral : 21.031 179.411 31461 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.54 % Allowed : 11.85 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.09), residues: 8398 helix: 1.86 (0.10), residues: 2983 sheet: -0.32 (0.15), residues: 1107 loop : 0.37 (0.10), residues: 4308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 8 121 HIS 0.013 0.001 HIS d 161 PHE 0.025 0.002 PHE d 185 TYR 0.027 0.002 TYR C 248 ARG 0.011 0.001 ARG k 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1638 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1446 time to evaluate : 7.424 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: 0 128 GLU cc_start: 0.8194 (tp30) cc_final: 0.7811 (tm-30) REVERT: 1 40 LYS cc_start: 0.8895 (tppp) cc_final: 0.8451 (tppp) REVERT: 3 182 ASP cc_start: 0.7947 (m-30) cc_final: 0.7675 (m-30) REVERT: 4 80 TYR cc_start: 0.8933 (p90) cc_final: 0.8677 (p90) REVERT: 5 153 CYS cc_start: 0.8668 (m) cc_final: 0.8345 (m) REVERT: 5 169 GLU cc_start: 0.7753 (tp30) cc_final: 0.7542 (tp30) REVERT: 6 189 CYS cc_start: 0.7280 (m) cc_final: 0.6989 (m) REVERT: 6 305 LYS cc_start: 0.9000 (ttpp) cc_final: 0.8708 (ttpp) REVERT: 6 330 ILE cc_start: 0.9604 (mt) cc_final: 0.9381 (mt) REVERT: 7 93 MET cc_start: 0.8933 (mtm) cc_final: 0.8668 (mtm) REVERT: 7 143 TRP cc_start: 0.9134 (OUTLIER) cc_final: 0.6753 (m-90) REVERT: 7 231 GLN cc_start: 0.8318 (pm20) cc_final: 0.8040 (pm20) REVERT: 7 232 HIS cc_start: 0.8486 (m-70) cc_final: 0.7705 (m-70) REVERT: 8 117 LEU cc_start: 0.9092 (tt) cc_final: 0.8887 (tm) REVERT: 8 147 LEU cc_start: 0.6381 (mm) cc_final: 0.5850 (tm) REVERT: 9 18 MET cc_start: 0.8713 (mmt) cc_final: 0.8126 (mmt) REVERT: C 150 LYS cc_start: 0.7656 (mttt) cc_final: 0.6990 (mppt) REVERT: C 418 ASN cc_start: 0.9122 (t0) cc_final: 0.8782 (t0) REVERT: C 480 LYS cc_start: 0.9072 (ptmt) cc_final: 0.8822 (ptmm) REVERT: C 481 GLU cc_start: 0.7775 (mp0) cc_final: 0.7508 (mp0) REVERT: F 209 TYR cc_start: 0.8928 (t80) cc_final: 0.8654 (t80) REVERT: H 70 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7390 (ptpp) REVERT: H 99 THR cc_start: 0.9312 (p) cc_final: 0.7763 (p) REVERT: H 100 GLN cc_start: 0.8326 (mt0) cc_final: 0.7855 (mp10) REVERT: H 103 GLU cc_start: 0.8577 (tt0) cc_final: 0.8291 (tm-30) REVERT: H 138 LYS cc_start: 0.8549 (tppt) cc_final: 0.8333 (tptp) REVERT: I 40 MET cc_start: 0.8917 (mtt) cc_final: 0.8647 (mtt) REVERT: I 45 GLN cc_start: 0.8812 (tt0) cc_final: 0.8485 (mt0) REVERT: I 99 CYS cc_start: 0.7582 (m) cc_final: 0.6739 (p) REVERT: I 121 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7161 (pt) REVERT: I 157 GLU cc_start: 0.7449 (mp0) cc_final: 0.7214 (mp0) REVERT: J 48 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: J 116 HIS cc_start: 0.7828 (t70) cc_final: 0.7472 (t-90) REVERT: M 218 LYS cc_start: 0.8977 (pttp) cc_final: 0.8757 (pttp) REVERT: N 148 ASP cc_start: 0.8310 (t0) cc_final: 0.8055 (t0) REVERT: N 201 ASP cc_start: 0.8250 (m-30) cc_final: 0.7907 (m-30) REVERT: O 82 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7567 (mt-10) REVERT: P 114 LYS cc_start: 0.9121 (ptmm) cc_final: 0.8898 (tmmm) REVERT: P 118 SER cc_start: 0.8952 (t) cc_final: 0.8708 (t) REVERT: P 146 TYR cc_start: 0.9180 (t80) cc_final: 0.8862 (t80) REVERT: Q 112 TYR cc_start: 0.8822 (m-80) cc_final: 0.8474 (m-80) REVERT: V 31 ASP cc_start: 0.8885 (t70) cc_final: 0.8664 (t0) REVERT: V 53 ASP cc_start: 0.7932 (m-30) cc_final: 0.7566 (m-30) REVERT: V 122 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7837 (tt) REVERT: W 104 TYR cc_start: 0.9231 (t80) cc_final: 0.8981 (t80) REVERT: W 111 THR cc_start: 0.8896 (p) cc_final: 0.8669 (t) REVERT: W 143 LYS cc_start: 0.9087 (mmtp) cc_final: 0.8675 (mmtp) REVERT: X 9 TRP cc_start: 0.8972 (p-90) cc_final: 0.8612 (p-90) REVERT: Y 70 ASP cc_start: 0.8139 (t70) cc_final: 0.7921 (t0) REVERT: Y 169 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8359 (mtt-85) REVERT: Z 43 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6225 (tm-30) REVERT: Z 84 ASP cc_start: 0.8183 (m-30) cc_final: 0.7898 (m-30) REVERT: d 88 TYR cc_start: 0.8721 (t80) cc_final: 0.8408 (t80) REVERT: d 235 GLN cc_start: 0.8415 (mp10) cc_final: 0.7982 (mp10) REVERT: d 274 GLN cc_start: 0.8523 (tt0) cc_final: 0.8240 (tt0) REVERT: e 70 MET cc_start: 0.8548 (mtt) cc_final: 0.8183 (mmm) REVERT: e 79 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8525 (pp) REVERT: e 132 LYS cc_start: 0.5195 (mmmt) cc_final: 0.4955 (tptt) REVERT: f 100 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7490 (tpt) REVERT: j 97 LYS cc_start: 0.8577 (mmtp) cc_final: 0.7198 (mptm) REVERT: j 100 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: j 101 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: k 17 ARG cc_start: 0.8225 (ppp80) cc_final: 0.7383 (tmm-80) REVERT: k 24 GLU cc_start: 0.6478 (mt-10) cc_final: 0.5943 (mp0) REVERT: k 52 ILE cc_start: 0.8538 (pt) cc_final: 0.8251 (mp) REVERT: k 77 ARG cc_start: 0.8076 (mtt-85) cc_final: 0.7637 (mmt-90) REVERT: l 117 TYR cc_start: 0.8938 (t80) cc_final: 0.7628 (m-10) REVERT: p 47 LYS cc_start: 0.9369 (mttp) cc_final: 0.9113 (mttp) REVERT: p 128 ASN cc_start: 0.8401 (t0) cc_final: 0.8070 (t0) REVERT: p 152 GLN cc_start: 0.9162 (tp40) cc_final: 0.8631 (tp40) REVERT: p 184 ASN cc_start: 0.8903 (m110) cc_final: 0.8631 (m-40) REVERT: q 41 ASP cc_start: 0.8307 (p0) cc_final: 0.7948 (p0) REVERT: q 44 ASP cc_start: 0.8519 (t0) cc_final: 0.8220 (t0) REVERT: q 117 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8165 (tpt-90) REVERT: q 143 TRP cc_start: 0.7717 (OUTLIER) cc_final: 0.6989 (t60) REVERT: r 103 LYS cc_start: 0.7084 (mmtt) cc_final: 0.6445 (mttt) REVERT: u 97 MET cc_start: 0.8425 (mtm) cc_final: 0.7337 (mtm) REVERT: u 100 LEU cc_start: 0.9400 (tp) cc_final: 0.9088 (tp) REVERT: u 160 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8351 (mt-10) REVERT: u 166 ASP cc_start: 0.8408 (p0) cc_final: 0.7994 (p0) REVERT: u 183 GLU cc_start: 0.8221 (mp0) cc_final: 0.7223 (mp0) REVERT: u 186 GLU cc_start: 0.7715 (pp20) cc_final: 0.7087 (pp20) REVERT: u 187 ILE cc_start: 0.9195 (tp) cc_final: 0.8654 (mp) REVERT: u 189 GLU cc_start: 0.7773 (pm20) cc_final: 0.7550 (pm20) REVERT: v 17 LEU cc_start: 0.9282 (mm) cc_final: 0.9018 (mm) REVERT: v 21 ARG cc_start: 0.8727 (mmp80) cc_final: 0.8004 (mmt-90) REVERT: v 27 ASP cc_start: 0.8738 (t0) cc_final: 0.8356 (t0) REVERT: v 36 ARG cc_start: 0.8553 (tmt170) cc_final: 0.8281 (tpt-90) REVERT: v 38 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8279 (tm-30) REVERT: v 51 ARG cc_start: 0.8283 (mmt90) cc_final: 0.7791 (mmt180) REVERT: v 56 GLU cc_start: 0.9040 (tp30) cc_final: 0.8805 (tp30) REVERT: v 59 LEU cc_start: 0.9472 (tp) cc_final: 0.9229 (tt) REVERT: v 63 ASN cc_start: 0.9050 (m-40) cc_final: 0.8423 (m-40) REVERT: w 120 MET cc_start: 0.8105 (mmp) cc_final: 0.7669 (tpt) REVERT: w 139 MET cc_start: 0.3868 (tmm) cc_final: 0.2375 (mpp) outliers start: 192 outliers final: 77 residues processed: 1528 average time/residue: 1.8654 time to fit residues: 3913.1491 Evaluate side-chains 1413 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1324 time to evaluate : 7.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 34 ARG Chi-restraints excluded: chain 1 residue 49 VAL Chi-restraints excluded: chain 1 residue 55 LEU Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 123 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain J residue 48 GLN Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain Q residue 131 SER 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 114 ILE Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 169 ARG Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain d residue 192 SER Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 114 ASN Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain j residue 100 GLU Chi-restraints excluded: chain j residue 101 GLU Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain o residue 35 MET Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain q residue 117 ARG Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 51 MET Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 169 CYS Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 198 SER Chi-restraints excluded: chain v residue 9 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 492 optimal weight: 5.9990 chunk 274 optimal weight: 8.9990 chunk 736 optimal weight: 8.9990 chunk 602 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 887 optimal weight: 0.0270 chunk 958 optimal weight: 10.0000 chunk 789 optimal weight: 30.0000 chunk 879 optimal weight: 20.0000 chunk 302 optimal weight: 6.9990 chunk 711 optimal weight: 4.9990 overall best weight: 5.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 178 GLN 5 165 GLN 6 63 GLN 6 243 ASN 6 292 GLN ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN 7 84 ASN C 96 GLN C 177 ASN C 211 ASN C 504 ASN F 184 GLN F 228 GLN F 257 GLN H 126 GLN I 43 GLN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN L 43 ASN L 72 GLN N 68 ASN N 98 HIS ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN O 154 GLN P 142 ASN P 176 GLN S 91 GLN S 118 ASN T 101 GLN T 133 ASN T 201 GLN T 202 GLN U 23 ASN ** U 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 147 GLN Z 98 GLN b 27 GLN b 66 ASN d 47 GLN d 193 HIS d 211 GLN ** e 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 118 GLN ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 99 ASN h 119 GLN k 26 ASN ** k 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 124 GLN ** o 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 33 GLN p 125 ASN p 182 ASN p 184 ASN r 65 ASN u 148 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 106462 Z= 0.399 Angle : 0.641 13.962 150941 Z= 0.329 Chirality : 0.042 0.335 17688 Planarity : 0.005 0.133 13918 Dihedral : 21.023 179.073 31454 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.16 % Allowed : 13.10 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.04 (0.09), residues: 8398 helix: 1.74 (0.10), residues: 2983 sheet: -0.33 (0.15), residues: 1112 loop : 0.34 (0.10), residues: 4303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 193 HIS 0.011 0.001 HIS S 76 PHE 0.021 0.002 PHE I 126 TYR 0.026 0.002 TYR 5 176 ARG 0.026 0.001 ARG k 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1597 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1358 time to evaluate : 7.501 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: 0 128 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: 1 41 LEU cc_start: 0.9263 (tp) cc_final: 0.9059 (tp) REVERT: 2 88 LYS cc_start: 0.8803 (ttpt) cc_final: 0.8407 (ttmt) REVERT: 3 182 ASP cc_start: 0.8022 (m-30) cc_final: 0.7767 (m-30) REVERT: 4 80 TYR cc_start: 0.8942 (p90) cc_final: 0.8627 (p90) REVERT: 5 153 CYS cc_start: 0.8695 (m) cc_final: 0.8318 (m) REVERT: 5 169 GLU cc_start: 0.7776 (tp30) cc_final: 0.7570 (tp30) REVERT: 6 274 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8223 (mttp) REVERT: 6 305 LYS cc_start: 0.9054 (ttpp) cc_final: 0.8763 (ttpp) REVERT: 7 93 MET cc_start: 0.8973 (mtm) cc_final: 0.8713 (mtm) REVERT: 7 143 TRP cc_start: 0.9140 (OUTLIER) cc_final: 0.6912 (m-90) REVERT: 8 117 LEU cc_start: 0.9169 (tt) cc_final: 0.8844 (tm) REVERT: 8 121 TRP cc_start: 0.8613 (t-100) cc_final: 0.8388 (t-100) REVERT: 8 147 LEU cc_start: 0.6509 (mm) cc_final: 0.5941 (tm) REVERT: 8 157 LEU cc_start: 0.7696 (mm) cc_final: 0.7469 (pt) REVERT: 9 18 MET cc_start: 0.8738 (mmt) cc_final: 0.8129 (mmt) REVERT: C 150 LYS cc_start: 0.7681 (mttt) cc_final: 0.7105 (mmpt) REVERT: C 418 ASN cc_start: 0.9203 (t0) cc_final: 0.8818 (t0) REVERT: C 481 GLU cc_start: 0.7839 (mp0) cc_final: 0.7575 (mp0) REVERT: C 488 ASP cc_start: 0.7796 (p0) cc_final: 0.7503 (p0) REVERT: E 81 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8427 (mtpp) REVERT: F 190 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8066 (mpt) REVERT: F 209 TYR cc_start: 0.8953 (t80) cc_final: 0.8722 (t80) REVERT: H 99 THR cc_start: 0.9380 (p) cc_final: 0.8848 (p) REVERT: H 100 GLN cc_start: 0.8449 (mt0) cc_final: 0.8178 (mp10) REVERT: H 138 LYS cc_start: 0.8507 (tppt) cc_final: 0.7766 (tptp) REVERT: I 45 GLN cc_start: 0.8824 (tt0) cc_final: 0.8495 (mt0) REVERT: I 85 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: I 99 CYS cc_start: 0.7803 (m) cc_final: 0.6840 (p) REVERT: I 119 HIS cc_start: 0.6935 (t70) cc_final: 0.6603 (t70) REVERT: J 66 LEU cc_start: 0.7656 (mm) cc_final: 0.7397 (mm) REVERT: J 116 HIS cc_start: 0.7889 (t70) cc_final: 0.7257 (t-90) REVERT: K 153 LYS cc_start: 0.9158 (mtmm) cc_final: 0.8896 (mtpp) REVERT: M 218 LYS cc_start: 0.9003 (pttp) cc_final: 0.8786 (pttp) REVERT: N 114 ASP cc_start: 0.8552 (t0) cc_final: 0.8293 (t0) REVERT: N 148 ASP cc_start: 0.8252 (t0) cc_final: 0.8015 (t0) REVERT: N 201 ASP cc_start: 0.8276 (m-30) cc_final: 0.7929 (m-30) REVERT: O 40 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8165 (mt-10) REVERT: O 82 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7646 (mt-10) REVERT: P 118 SER cc_start: 0.8955 (t) cc_final: 0.8734 (t) REVERT: P 146 TYR cc_start: 0.9186 (t80) cc_final: 0.8902 (t80) REVERT: Q 112 TYR cc_start: 0.8829 (m-80) cc_final: 0.8483 (m-80) REVERT: Q 186 SER cc_start: 0.9161 (OUTLIER) cc_final: 0.8912 (p) REVERT: S 133 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8908 (t) REVERT: U 131 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7479 (tm-30) REVERT: V 31 ASP cc_start: 0.8891 (t70) cc_final: 0.8645 (t0) REVERT: V 53 ASP cc_start: 0.7900 (m-30) cc_final: 0.7559 (m-30) REVERT: V 108 MET cc_start: 0.8439 (ttm) cc_final: 0.7781 (ttm) REVERT: V 181 ASP cc_start: 0.8363 (m-30) cc_final: 0.8136 (m-30) REVERT: W 57 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: W 111 THR cc_start: 0.8897 (p) cc_final: 0.8687 (t) REVERT: W 143 LYS cc_start: 0.9094 (mmtp) cc_final: 0.8886 (mmtm) REVERT: Y 169 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8426 (mtt-85) REVERT: Z 84 ASP cc_start: 0.8192 (m-30) cc_final: 0.7862 (m-30) REVERT: Z 98 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8325 (tp40) REVERT: d 38 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7927 (mtpp) REVERT: d 40 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6473 (mtt90) REVERT: d 88 TYR cc_start: 0.8810 (t80) cc_final: 0.8594 (t80) REVERT: d 235 GLN cc_start: 0.8486 (mp10) cc_final: 0.8074 (mp10) REVERT: d 274 GLN cc_start: 0.8599 (tt0) cc_final: 0.8302 (tt0) REVERT: e 70 MET cc_start: 0.8425 (mtt) cc_final: 0.8049 (mmm) REVERT: e 79 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8607 (pp) REVERT: e 132 LYS cc_start: 0.5175 (mmmt) cc_final: 0.4963 (tptt) REVERT: e 237 LEU cc_start: 0.8498 (pp) cc_final: 0.8216 (tp) REVERT: e 265 LYS cc_start: 0.8114 (mptt) cc_final: 0.7750 (pmtt) REVERT: f 60 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8707 (mtmt) REVERT: f 100 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7454 (tpt) REVERT: h 116 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7307 (mtp85) REVERT: i 42 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8197 (tppp) REVERT: j 97 LYS cc_start: 0.8553 (mmtp) cc_final: 0.8286 (mptm) REVERT: k 24 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6193 (mp0) REVERT: k 33 PHE cc_start: 0.9567 (t80) cc_final: 0.9275 (t80) REVERT: k 56 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.6129 (tpt90) REVERT: k 90 PHE cc_start: 0.8868 (t80) cc_final: 0.8666 (t80) REVERT: l 117 TYR cc_start: 0.8951 (t80) cc_final: 0.7581 (m-10) REVERT: p 47 LYS cc_start: 0.9349 (mttp) cc_final: 0.9099 (mttp) REVERT: p 128 ASN cc_start: 0.8552 (t0) cc_final: 0.8330 (t0) REVERT: p 182 ASN cc_start: 0.8418 (m-40) cc_final: 0.8024 (m110) REVERT: p 183 MET cc_start: 0.8238 (tmm) cc_final: 0.7936 (tmm) REVERT: p 184 ASN cc_start: 0.8986 (m-40) cc_final: 0.8684 (m-40) REVERT: q 41 ASP cc_start: 0.8293 (p0) cc_final: 0.8039 (p0) REVERT: q 44 ASP cc_start: 0.8657 (t0) cc_final: 0.8376 (t0) REVERT: q 117 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8178 (tpt-90) REVERT: q 143 TRP cc_start: 0.7727 (OUTLIER) cc_final: 0.7040 (t60) REVERT: r 37 GLU cc_start: 0.6917 (pp20) cc_final: 0.6151 (pp20) REVERT: r 103 LYS cc_start: 0.7152 (mmtt) cc_final: 0.6539 (mttt) REVERT: u 160 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8256 (mt-10) REVERT: u 166 ASP cc_start: 0.8377 (p0) cc_final: 0.8009 (p0) REVERT: u 183 GLU cc_start: 0.8272 (mp0) cc_final: 0.7345 (mp0) REVERT: u 186 GLU cc_start: 0.7714 (pp20) cc_final: 0.7059 (pp20) REVERT: u 187 ILE cc_start: 0.9203 (tp) cc_final: 0.8692 (mp) REVERT: u 189 GLU cc_start: 0.7733 (pm20) cc_final: 0.7473 (pm20) REVERT: v 21 ARG cc_start: 0.8752 (mmp80) cc_final: 0.8108 (mmt-90) REVERT: v 27 ASP cc_start: 0.8789 (t70) cc_final: 0.8513 (t0) REVERT: v 37 ARG cc_start: 0.8746 (ttm-80) cc_final: 0.8166 (ttm-80) REVERT: v 38 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8357 (tm-30) REVERT: v 51 ARG cc_start: 0.8200 (mmt90) cc_final: 0.7621 (mmt180) REVERT: v 56 GLU cc_start: 0.9019 (tp30) cc_final: 0.8790 (tp30) REVERT: v 59 LEU cc_start: 0.9524 (tp) cc_final: 0.9203 (tt) REVERT: v 63 ASN cc_start: 0.9115 (m-40) cc_final: 0.8452 (m-40) REVERT: w 105 MET cc_start: 0.7534 (mpm) cc_final: 0.6819 (ptt) REVERT: w 120 MET cc_start: 0.7884 (mmp) cc_final: 0.7214 (tpt) outliers start: 239 outliers final: 117 residues processed: 1464 average time/residue: 1.8102 time to fit residues: 3646.8819 Evaluate side-chains 1398 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1263 time to evaluate : 7.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 128 GLU Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 34 ARG Chi-restraints excluded: chain 1 residue 49 VAL Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 6 residue 274 LYS Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 7 residue 43 MET Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 123 LEU Chi-restraints excluded: chain 9 residue 20 LYS Chi-restraints excluded: chain 9 residue 28 ARG Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 131 SER 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 110 SER Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 169 ARG Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain d residue 38 LYS Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 192 SER Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 134 LYS Chi-restraints excluded: chain h residue 114 ASN Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 71 LYS Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 56 ARG Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain p residue 57 THR Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 126 LYS Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 117 ARG Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 51 MET Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain u residue 95 ASP Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 169 CYS Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 198 SER Chi-restraints excluded: chain v residue 26 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 876 optimal weight: 8.9990 chunk 666 optimal weight: 6.9990 chunk 460 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 423 optimal weight: 10.0000 chunk 595 optimal weight: 0.7980 chunk 890 optimal weight: 6.9990 chunk 942 optimal weight: 5.9990 chunk 465 optimal weight: 2.9990 chunk 843 optimal weight: 0.9980 chunk 253 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 GLN 6 63 GLN 6 243 ASN ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN C 96 GLN C 211 ASN C 232 ASN C 304 ASN C 504 ASN D 235 GLN F 184 GLN F 228 GLN F 257 GLN H 126 GLN H 136 ASN I 43 GLN I 150 HIS ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN L 33 GLN L 43 ASN L 72 GLN N 98 HIS O 100 GLN O 154 GLN ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 176 GLN R 27 HIS S 91 GLN S 118 ASN T 101 GLN T 202 GLN V 35 ASN Y 147 GLN Y 179 HIS Z 62 ASN d 193 HIS ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 99 ASN k 26 ASN l 124 GLN o 16 GLN p 125 ASN ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 106462 Z= 0.262 Angle : 0.601 14.331 150941 Z= 0.308 Chirality : 0.040 0.304 17688 Planarity : 0.005 0.126 13918 Dihedral : 21.005 179.854 31454 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.99 % Allowed : 14.76 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.06 (0.09), residues: 8398 helix: 1.77 (0.10), residues: 2971 sheet: -0.28 (0.15), residues: 1119 loop : 0.33 (0.10), residues: 4308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Z 81 HIS 0.010 0.001 HIS k 93 PHE 0.023 0.001 PHE I 126 TYR 0.025 0.001 TYR v 13 ARG 0.015 0.000 ARG 9 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1565 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1339 time to evaluate : 7.358 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: 0 128 GLU cc_start: 0.8155 (tp30) cc_final: 0.7942 (tm-30) REVERT: 1 34 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7657 (ptt-90) REVERT: 3 182 ASP cc_start: 0.7983 (m-30) cc_final: 0.7732 (m-30) REVERT: 4 80 TYR cc_start: 0.8945 (p90) cc_final: 0.8626 (p90) REVERT: 5 153 CYS cc_start: 0.8687 (m) cc_final: 0.8305 (m) REVERT: 5 169 GLU cc_start: 0.7806 (tp30) cc_final: 0.7585 (tp30) REVERT: 6 305 LYS cc_start: 0.9079 (ttpp) cc_final: 0.8804 (ttpp) REVERT: 7 93 MET cc_start: 0.8940 (mtm) cc_final: 0.8677 (mtm) REVERT: 7 143 TRP cc_start: 0.9162 (OUTLIER) cc_final: 0.6968 (m-90) REVERT: 8 121 TRP cc_start: 0.8600 (t-100) cc_final: 0.8316 (t60) REVERT: 9 19 SER cc_start: 0.9031 (p) cc_final: 0.8697 (m) REVERT: 9 116 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8881 (pttp) REVERT: C 150 LYS cc_start: 0.7743 (mttt) cc_final: 0.7232 (mptt) REVERT: C 418 ASN cc_start: 0.9196 (t0) cc_final: 0.8804 (t0) REVERT: C 467 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8558 (ttm170) REVERT: C 481 GLU cc_start: 0.7804 (mp0) cc_final: 0.7570 (mp0) REVERT: F 135 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7541 (mtp180) REVERT: F 209 TYR cc_start: 0.8918 (t80) cc_final: 0.8666 (t80) REVERT: H 89 ARG cc_start: 0.8441 (tpp80) cc_final: 0.7974 (tpp80) REVERT: H 99 THR cc_start: 0.9372 (p) cc_final: 0.8867 (p) REVERT: H 100 GLN cc_start: 0.8358 (mt0) cc_final: 0.8135 (mp10) REVERT: H 137 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8623 (mmmm) REVERT: I 45 GLN cc_start: 0.8764 (tt0) cc_final: 0.8450 (mt0) REVERT: I 99 CYS cc_start: 0.7669 (m) cc_final: 0.6593 (p) REVERT: I 111 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8993 (tm) REVERT: J 21 ARG cc_start: 0.7083 (ttt-90) cc_final: 0.6646 (ttt-90) REVERT: J 91 LEU cc_start: 0.8986 (mt) cc_final: 0.8763 (mp) REVERT: J 116 HIS cc_start: 0.7944 (t70) cc_final: 0.7356 (t-90) REVERT: K 25 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8300 (mmm) REVERT: K 153 LYS cc_start: 0.9166 (mtmm) cc_final: 0.8894 (mtpp) REVERT: M 218 LYS cc_start: 0.9014 (pttp) cc_final: 0.8795 (pttp) REVERT: N 114 ASP cc_start: 0.8526 (t0) cc_final: 0.8320 (t0) REVERT: N 148 ASP cc_start: 0.8213 (t0) cc_final: 0.7925 (t0) REVERT: N 201 ASP cc_start: 0.8271 (m-30) cc_final: 0.7927 (m-30) REVERT: O 40 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8111 (mt-10) REVERT: O 82 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7664 (mt-10) REVERT: P 118 SER cc_start: 0.8914 (t) cc_final: 0.8656 (t) REVERT: P 138 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8339 (OUTLIER) REVERT: P 146 TYR cc_start: 0.9156 (t80) cc_final: 0.8792 (t80) REVERT: Q 186 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8909 (p) REVERT: V 31 ASP cc_start: 0.8879 (t70) cc_final: 0.8645 (t0) REVERT: V 108 MET cc_start: 0.8237 (ttm) cc_final: 0.8037 (ttm) REVERT: V 122 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7886 (tt) REVERT: V 181 ASP cc_start: 0.8352 (m-30) cc_final: 0.8115 (m-30) REVERT: W 57 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: W 143 LYS cc_start: 0.9091 (mmtp) cc_final: 0.8877 (mmtm) REVERT: Y 81 SER cc_start: 0.8872 (t) cc_final: 0.8602 (p) REVERT: Y 169 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8400 (mtt-85) REVERT: Z 84 ASP cc_start: 0.8160 (m-30) cc_final: 0.7828 (m-30) REVERT: d 38 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7941 (mtpp) REVERT: d 235 GLN cc_start: 0.8467 (mp10) cc_final: 0.8049 (mp10) REVERT: d 274 GLN cc_start: 0.8563 (tt0) cc_final: 0.8341 (tt0) REVERT: e 79 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8611 (pp) REVERT: e 132 LYS cc_start: 0.5223 (mmmt) cc_final: 0.4997 (tptt) REVERT: e 139 GLU cc_start: 0.4829 (OUTLIER) cc_final: 0.4327 (mp0) REVERT: e 265 LYS cc_start: 0.8098 (mptt) cc_final: 0.7726 (pmtt) REVERT: f 60 LYS cc_start: 0.8999 (mmmt) cc_final: 0.8690 (mtmt) REVERT: f 100 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7305 (tpt) REVERT: h 116 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7200 (mtp85) REVERT: k 24 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6209 (mp0) REVERT: k 40 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7197 (mm-30) REVERT: l 117 TYR cc_start: 0.8942 (t80) cc_final: 0.7568 (m-10) REVERT: p 47 LYS cc_start: 0.9341 (mttp) cc_final: 0.9071 (mttm) REVERT: p 128 ASN cc_start: 0.8553 (t0) cc_final: 0.8350 (t0) REVERT: p 183 MET cc_start: 0.8170 (tmm) cc_final: 0.7749 (tmm) REVERT: p 184 ASN cc_start: 0.8908 (m-40) cc_final: 0.8665 (m-40) REVERT: q 41 ASP cc_start: 0.8471 (p0) cc_final: 0.8058 (p0) REVERT: q 44 ASP cc_start: 0.8643 (t0) cc_final: 0.8300 (t0) REVERT: q 143 TRP cc_start: 0.7703 (OUTLIER) cc_final: 0.7021 (t60) REVERT: r 37 GLU cc_start: 0.7115 (pp20) cc_final: 0.6892 (pp20) REVERT: r 52 ARG cc_start: 0.8364 (pmm-80) cc_final: 0.8132 (pmm-80) REVERT: r 103 LYS cc_start: 0.7106 (mmtt) cc_final: 0.6485 (mttt) REVERT: u 97 MET cc_start: 0.8395 (mtm) cc_final: 0.7476 (mtm) REVERT: u 101 LEU cc_start: 0.9417 (mt) cc_final: 0.9180 (mp) REVERT: u 160 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8263 (mt-10) REVERT: u 166 ASP cc_start: 0.8406 (p0) cc_final: 0.8036 (p0) REVERT: u 183 GLU cc_start: 0.8272 (mp0) cc_final: 0.7352 (mp0) REVERT: u 186 GLU cc_start: 0.7662 (pp20) cc_final: 0.7078 (pp20) REVERT: u 187 ILE cc_start: 0.9233 (tp) cc_final: 0.8713 (mp) REVERT: u 189 GLU cc_start: 0.7695 (pm20) cc_final: 0.7456 (pm20) REVERT: v 19 GLN cc_start: 0.8545 (tt0) cc_final: 0.8203 (mt0) REVERT: v 24 ARG cc_start: 0.8362 (tmm-80) cc_final: 0.7709 (tmm-80) REVERT: v 27 ASP cc_start: 0.8774 (t70) cc_final: 0.8502 (t0) REVERT: v 38 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8341 (tm-30) REVERT: v 51 ARG cc_start: 0.8173 (mmt90) cc_final: 0.7610 (mmm160) REVERT: v 56 GLU cc_start: 0.8973 (tp30) cc_final: 0.8708 (tp30) REVERT: v 59 LEU cc_start: 0.9509 (tp) cc_final: 0.9172 (tt) REVERT: v 63 ASN cc_start: 0.9098 (m-40) cc_final: 0.8418 (m-40) REVERT: w 105 MET cc_start: 0.7582 (mpm) cc_final: 0.6804 (ptt) outliers start: 226 outliers final: 108 residues processed: 1437 average time/residue: 1.7962 time to fit residues: 3555.4899 Evaluate side-chains 1410 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1284 time to evaluate : 7.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 34 ARG Chi-restraints excluded: chain 1 residue 49 VAL Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 153 THR Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 7 residue 43 MET Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 123 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain 9 residue 116 LYS Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 135 ARG Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain K residue 25 MET Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 131 SER 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 110 SER Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain X residue 55 LYS Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 169 ARG Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain d residue 38 LYS Chi-restraints excluded: chain d residue 192 SER Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 114 ASN Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 119 GLN Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 71 LYS Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 126 LYS Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 51 MET Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain u residue 95 ASP Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 169 CYS Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 179 LEU Chi-restraints excluded: chain u residue 198 SER Chi-restraints excluded: chain v residue 26 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 784 optimal weight: 10.0000 chunk 534 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 701 optimal weight: 4.9990 chunk 388 optimal weight: 4.9990 chunk 804 optimal weight: 0.0170 chunk 651 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 481 optimal weight: 4.9990 chunk 845 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 146 HIS 5 165 GLN 6 63 GLN 6 243 ASN 7 49 ASN C 96 GLN C 177 ASN C 211 ASN C 232 ASN C 504 ASN D 235 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN F 228 GLN F 257 GLN H 93 ASN H 126 GLN H 136 ASN I 43 GLN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN L 33 GLN L 43 ASN L 72 GLN N 98 HIS N 210 GLN O 100 GLN P 87 GLN P 142 ASN ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 176 GLN S 91 GLN T 101 GLN T 109 ASN T 133 ASN T 201 GLN T 202 GLN U 23 ASN V 35 ASN Z 47 GLN Z 62 ASN Z 98 GLN d 193 HIS ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 99 ASN k 26 ASN p 125 ASN p 182 ASN ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 148 HIS v 42 ASN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 106462 Z= 0.331 Angle : 0.621 14.209 150941 Z= 0.319 Chirality : 0.041 0.327 17688 Planarity : 0.005 0.129 13918 Dihedral : 20.968 179.556 31454 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.04 % Allowed : 15.81 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.04 (0.09), residues: 8398 helix: 1.73 (0.10), residues: 2985 sheet: -0.26 (0.15), residues: 1133 loop : 0.33 (0.10), residues: 4280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Z 81 HIS 0.014 0.001 HIS u 148 PHE 0.027 0.002 PHE k 33 TYR 0.024 0.001 TYR 5 176 ARG 0.015 0.001 ARG g 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1527 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1297 time to evaluate : 7.437 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: 0 128 GLU cc_start: 0.8168 (tp30) cc_final: 0.7951 (tm-30) REVERT: 3 182 ASP cc_start: 0.8032 (m-30) cc_final: 0.7775 (m-30) REVERT: 4 80 TYR cc_start: 0.8948 (p90) cc_final: 0.8635 (p90) REVERT: 5 153 CYS cc_start: 0.8705 (m) cc_final: 0.8310 (m) REVERT: 5 169 GLU cc_start: 0.7761 (tp30) cc_final: 0.7549 (tp30) REVERT: 6 305 LYS cc_start: 0.9105 (ttpp) cc_final: 0.8820 (ttpp) REVERT: 7 93 MET cc_start: 0.8970 (mtm) cc_final: 0.8664 (mtm) REVERT: 7 143 TRP cc_start: 0.9182 (OUTLIER) cc_final: 0.6950 (m-90) REVERT: 8 121 TRP cc_start: 0.8607 (t-100) cc_final: 0.8358 (t60) REVERT: 9 116 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8981 (pttm) REVERT: C 150 LYS cc_start: 0.7753 (mttt) cc_final: 0.7160 (mmpt) REVERT: C 418 ASN cc_start: 0.9195 (t0) cc_final: 0.8796 (t0) REVERT: C 467 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8581 (ttm170) REVERT: C 481 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: E 81 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8401 (mtpp) REVERT: F 135 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7565 (mtp180) REVERT: F 209 TYR cc_start: 0.8940 (t80) cc_final: 0.8696 (t80) REVERT: H 100 GLN cc_start: 0.8372 (mt0) cc_final: 0.8103 (mp-120) REVERT: H 138 LYS cc_start: 0.8450 (tptp) cc_final: 0.7769 (tptp) REVERT: I 45 GLN cc_start: 0.8791 (tt0) cc_final: 0.8466 (mt0) REVERT: I 85 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: I 99 CYS cc_start: 0.7750 (m) cc_final: 0.6436 (p) REVERT: J 91 LEU cc_start: 0.8971 (mt) cc_final: 0.8757 (mp) REVERT: J 116 HIS cc_start: 0.7931 (t70) cc_final: 0.7485 (t-90) REVERT: K 25 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8353 (mmm) REVERT: K 153 LYS cc_start: 0.9183 (mtmm) cc_final: 0.8864 (mtpp) REVERT: M 218 LYS cc_start: 0.9015 (pttp) cc_final: 0.8795 (pttp) REVERT: N 114 ASP cc_start: 0.8573 (t0) cc_final: 0.8281 (t0) REVERT: N 148 ASP cc_start: 0.8158 (t0) cc_final: 0.7854 (t0) REVERT: N 201 ASP cc_start: 0.8280 (m-30) cc_final: 0.7931 (m-30) REVERT: O 40 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8094 (mt-10) REVERT: O 82 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7663 (mt-10) REVERT: P 117 TYR cc_start: 0.8574 (t80) cc_final: 0.8292 (t80) REVERT: P 118 SER cc_start: 0.8894 (t) cc_final: 0.8666 (t) REVERT: P 137 LEU cc_start: 0.9514 (mt) cc_final: 0.9261 (mp) REVERT: P 146 TYR cc_start: 0.9189 (t80) cc_final: 0.8822 (t80) REVERT: Q 186 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8910 (p) REVERT: U 135 GLN cc_start: 0.8696 (tp40) cc_final: 0.8474 (tp40) REVERT: V 31 ASP cc_start: 0.8885 (t70) cc_final: 0.8646 (t0) REVERT: V 53 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: V 122 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7900 (tt) REVERT: V 126 MET cc_start: 0.8645 (ptp) cc_final: 0.8374 (pmm) REVERT: V 199 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8717 (mtm) REVERT: W 57 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: W 143 LYS cc_start: 0.9097 (mmtp) cc_final: 0.8883 (mmtm) REVERT: Y 81 SER cc_start: 0.8856 (t) cc_final: 0.8617 (p) REVERT: Y 147 GLN cc_start: 0.8382 (tp40) cc_final: 0.8121 (tp40) REVERT: Y 169 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8421 (mtt-85) REVERT: Z 47 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8013 (mm110) REVERT: d 38 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7985 (mtpp) REVERT: d 172 MET cc_start: 0.9166 (ttm) cc_final: 0.8840 (ttm) REVERT: d 235 GLN cc_start: 0.8482 (mp10) cc_final: 0.8041 (mp10) REVERT: d 274 GLN cc_start: 0.8562 (tt0) cc_final: 0.8338 (tt0) REVERT: e 54 GLN cc_start: 0.7542 (tp-100) cc_final: 0.6885 (tp-100) REVERT: e 79 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8614 (pp) REVERT: e 132 LYS cc_start: 0.5353 (mmmt) cc_final: 0.5117 (tptt) REVERT: e 139 GLU cc_start: 0.5034 (OUTLIER) cc_final: 0.4422 (mp0) REVERT: e 175 GLN cc_start: 0.5411 (mt0) cc_final: 0.5137 (tt0) REVERT: e 237 LEU cc_start: 0.8412 (pp) cc_final: 0.8117 (tp) REVERT: e 265 LYS cc_start: 0.8191 (mptt) cc_final: 0.7766 (pmtt) REVERT: f 100 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7263 (tpt) REVERT: h 116 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7148 (mtp85) REVERT: k 24 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6146 (mp0) REVERT: k 33 PHE cc_start: 0.9560 (t80) cc_final: 0.9354 (t80) REVERT: k 40 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7160 (mm-30) REVERT: l 117 TYR cc_start: 0.8972 (t80) cc_final: 0.7563 (m-10) REVERT: l 131 ARG cc_start: 0.8671 (mtm110) cc_final: 0.8325 (mtp-110) REVERT: p 47 LYS cc_start: 0.9350 (mttp) cc_final: 0.9079 (mttp) REVERT: p 183 MET cc_start: 0.8226 (tmm) cc_final: 0.7849 (tmm) REVERT: q 41 ASP cc_start: 0.8481 (p0) cc_final: 0.8022 (p0) REVERT: q 44 ASP cc_start: 0.8619 (t0) cc_final: 0.8267 (t0) REVERT: q 117 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8118 (tpt-90) REVERT: q 143 TRP cc_start: 0.7733 (OUTLIER) cc_final: 0.7049 (t60) REVERT: r 37 GLU cc_start: 0.7151 (pp20) cc_final: 0.6911 (pp20) REVERT: r 52 ARG cc_start: 0.8369 (pmm-80) cc_final: 0.8060 (pmm-80) REVERT: r 103 LYS cc_start: 0.7132 (mmtt) cc_final: 0.6534 (mttt) REVERT: u 166 ASP cc_start: 0.8442 (p0) cc_final: 0.8058 (p0) REVERT: u 183 GLU cc_start: 0.8300 (mp0) cc_final: 0.7437 (mp0) REVERT: u 186 GLU cc_start: 0.7654 (pp20) cc_final: 0.7046 (pp20) REVERT: u 187 ILE cc_start: 0.9241 (tp) cc_final: 0.8738 (mp) REVERT: u 189 GLU cc_start: 0.7707 (pm20) cc_final: 0.7444 (pm20) REVERT: v 19 GLN cc_start: 0.8600 (tt0) cc_final: 0.8286 (mt0) REVERT: v 27 ASP cc_start: 0.8810 (t70) cc_final: 0.8561 (t0) REVERT: v 38 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8416 (tm-30) REVERT: v 54 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8418 (tm130) REVERT: v 56 GLU cc_start: 0.8978 (tp30) cc_final: 0.8661 (tp30) REVERT: v 63 ASN cc_start: 0.9136 (m-40) cc_final: 0.8841 (m-40) outliers start: 230 outliers final: 124 residues processed: 1408 average time/residue: 1.8030 time to fit residues: 3496.3625 Evaluate side-chains 1384 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1238 time to evaluate : 7.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 34 ARG Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 153 THR Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 6 residue 300 THR Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 123 LEU Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain 9 residue 116 LYS Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 135 ARG Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain K residue 25 MET Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 131 SER 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 110 SER Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 199 MET Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 169 ARG Chi-restraints excluded: chain Z residue 47 GLN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 140 LYS Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain d residue 38 LYS Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 192 SER Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 114 ASN Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 119 GLN Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 71 LYS Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain p residue 57 THR Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 126 LYS Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 117 ARG Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 51 MET Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain u residue 95 ASP Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 135 LEU Chi-restraints excluded: chain u residue 143 VAL Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 169 CYS Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 179 LEU Chi-restraints excluded: chain u residue 198 SER Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 53 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 317 optimal weight: 6.9990 chunk 848 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 553 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 943 optimal weight: 2.9990 chunk 783 optimal weight: 10.0000 chunk 436 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 312 optimal weight: 2.9990 chunk 495 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 GLN 6 63 GLN 7 49 ASN C 96 GLN C 211 ASN C 232 ASN C 304 ASN C 504 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN F 228 GLN F 257 GLN H 126 GLN H 136 ASN I 43 GLN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN L 33 GLN L 43 ASN L 72 GLN N 98 HIS O 100 GLN P 142 ASN ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 176 GLN S 91 GLN T 101 GLN T 201 GLN T 202 GLN V 35 ASN Y 92 ASN Z 47 GLN Z 98 GLN ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 118 GLN ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 99 ASN k 26 ASN p 125 ASN p 182 ASN ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 148 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 106462 Z= 0.317 Angle : 0.623 14.195 150941 Z= 0.320 Chirality : 0.041 0.368 17688 Planarity : 0.005 0.128 13918 Dihedral : 20.966 179.997 31454 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.21 % Allowed : 16.57 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 8398 helix: 1.73 (0.10), residues: 2980 sheet: -0.26 (0.15), residues: 1141 loop : 0.33 (0.10), residues: 4277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP d 183 HIS 0.010 0.001 HIS k 93 PHE 0.022 0.002 PHE I 126 TYR 0.025 0.001 TYR d 88 ARG 0.014 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1526 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1283 time to evaluate : 7.437 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: 3 182 ASP cc_start: 0.8013 (m-30) cc_final: 0.7767 (m-30) REVERT: 4 80 TYR cc_start: 0.8944 (p90) cc_final: 0.8647 (p90) REVERT: 5 153 CYS cc_start: 0.8725 (m) cc_final: 0.8310 (m) REVERT: 5 169 GLU cc_start: 0.7765 (tp30) cc_final: 0.7537 (tp30) REVERT: 6 116 ASN cc_start: 0.8818 (t0) cc_final: 0.8417 (p0) REVERT: 6 305 LYS cc_start: 0.9119 (ttpp) cc_final: 0.8849 (ttpp) REVERT: 7 93 MET cc_start: 0.8968 (mtm) cc_final: 0.8690 (mtm) REVERT: 7 143 TRP cc_start: 0.9196 (OUTLIER) cc_final: 0.6922 (m-90) REVERT: 8 121 TRP cc_start: 0.8576 (t-100) cc_final: 0.8282 (t60) REVERT: C 150 LYS cc_start: 0.7740 (mttt) cc_final: 0.7161 (mmpt) REVERT: C 418 ASN cc_start: 0.9179 (t0) cc_final: 0.8789 (t0) REVERT: C 481 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: D 158 GLN cc_start: 0.7778 (mp10) cc_final: 0.7440 (mp10) REVERT: E 81 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8386 (mtpp) REVERT: F 135 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7552 (mtp180) REVERT: F 209 TYR cc_start: 0.8931 (t80) cc_final: 0.8683 (t80) REVERT: H 100 GLN cc_start: 0.8398 (mt0) cc_final: 0.8129 (mp-120) REVERT: I 45 GLN cc_start: 0.8774 (tt0) cc_final: 0.8459 (mt0) REVERT: I 85 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: I 99 CYS cc_start: 0.7737 (m) cc_final: 0.6477 (p) REVERT: I 115 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8515 (mm110) REVERT: J 102 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7982 (mpp-170) REVERT: J 116 HIS cc_start: 0.8072 (t70) cc_final: 0.7396 (t-90) REVERT: K 25 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8356 (mmm) REVERT: K 153 LYS cc_start: 0.9183 (mtmm) cc_final: 0.8868 (mtpp) REVERT: K 162 GLU cc_start: 0.8167 (mp0) cc_final: 0.7962 (pm20) REVERT: M 218 LYS cc_start: 0.9016 (pttp) cc_final: 0.8795 (pttp) REVERT: N 65 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8283 (mt-10) REVERT: N 104 MET cc_start: 0.8988 (tmm) cc_final: 0.8768 (ttp) REVERT: N 114 ASP cc_start: 0.8587 (t0) cc_final: 0.8288 (t0) REVERT: N 148 ASP cc_start: 0.8168 (t0) cc_final: 0.7860 (t0) REVERT: N 201 ASP cc_start: 0.8279 (m-30) cc_final: 0.7930 (m-30) REVERT: O 40 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8077 (mt-10) REVERT: O 82 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7662 (mt-10) REVERT: P 117 TYR cc_start: 0.8602 (t80) cc_final: 0.8315 (t80) REVERT: P 118 SER cc_start: 0.8858 (t) cc_final: 0.8621 (t) REVERT: P 146 TYR cc_start: 0.9198 (t80) cc_final: 0.8844 (t80) REVERT: Q 186 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8921 (p) REVERT: V 122 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7903 (tt) REVERT: V 126 MET cc_start: 0.8747 (ptp) cc_final: 0.8434 (mtm) REVERT: V 199 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8723 (mtm) REVERT: W 57 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: W 143 LYS cc_start: 0.9093 (mmtp) cc_final: 0.8883 (mmtm) REVERT: Y 81 SER cc_start: 0.8898 (t) cc_final: 0.8658 (p) REVERT: Y 169 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8411 (mtt-85) REVERT: Z 47 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8468 (mm-40) REVERT: d 38 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7994 (mtpp) REVERT: d 172 MET cc_start: 0.9200 (ttm) cc_final: 0.8885 (ttm) REVERT: d 235 GLN cc_start: 0.8491 (mp10) cc_final: 0.8063 (mp10) REVERT: d 274 GLN cc_start: 0.8595 (tt0) cc_final: 0.8343 (tt0) REVERT: e 79 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8646 (pp) REVERT: e 132 LYS cc_start: 0.5389 (mmmt) cc_final: 0.5116 (tptt) REVERT: e 139 GLU cc_start: 0.5042 (OUTLIER) cc_final: 0.4450 (mp0) REVERT: e 265 LYS cc_start: 0.8207 (mptt) cc_final: 0.7760 (pmtt) REVERT: f 100 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7245 (tpt) REVERT: h 116 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7119 (mtp85) REVERT: i 84 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8811 (ttpt) REVERT: k 24 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6120 (mp0) REVERT: k 33 PHE cc_start: 0.9566 (t80) cc_final: 0.9105 (t80) REVERT: k 40 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6960 (mm-30) REVERT: l 117 TYR cc_start: 0.8980 (t80) cc_final: 0.7563 (m-10) REVERT: l 131 ARG cc_start: 0.8653 (mtm110) cc_final: 0.8296 (mtp-110) REVERT: p 47 LYS cc_start: 0.9351 (mttp) cc_final: 0.9084 (mttp) REVERT: p 183 MET cc_start: 0.8273 (tmm) cc_final: 0.7851 (tmm) REVERT: q 117 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8138 (tpt-90) REVERT: q 143 TRP cc_start: 0.7735 (OUTLIER) cc_final: 0.7033 (t60) REVERT: r 37 GLU cc_start: 0.7287 (pp20) cc_final: 0.7072 (pp20) REVERT: r 103 LYS cc_start: 0.7129 (mmtt) cc_final: 0.6542 (mttt) REVERT: u 92 PHE cc_start: 0.8524 (t80) cc_final: 0.8279 (t80) REVERT: u 105 ASN cc_start: 0.9046 (p0) cc_final: 0.8829 (p0) REVERT: u 118 MET cc_start: 0.8332 (mpp) cc_final: 0.8063 (mtm) REVERT: u 138 MET cc_start: 0.8556 (mtm) cc_final: 0.8191 (mtm) REVERT: u 166 ASP cc_start: 0.8457 (p0) cc_final: 0.8060 (p0) REVERT: u 183 GLU cc_start: 0.8326 (mp0) cc_final: 0.7456 (mp0) REVERT: u 186 GLU cc_start: 0.7689 (pp20) cc_final: 0.7100 (pp20) REVERT: u 187 ILE cc_start: 0.9242 (tp) cc_final: 0.8741 (mp) REVERT: u 189 GLU cc_start: 0.7728 (pm20) cc_final: 0.7460 (pm20) REVERT: v 19 GLN cc_start: 0.8659 (tt0) cc_final: 0.8322 (mt0) REVERT: v 27 ASP cc_start: 0.8831 (t70) cc_final: 0.8585 (t0) REVERT: v 38 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8521 (tm-30) REVERT: v 56 GLU cc_start: 0.9010 (tp30) cc_final: 0.8680 (tp30) REVERT: v 59 LEU cc_start: 0.9543 (mt) cc_final: 0.9233 (mp) REVERT: v 62 LEU cc_start: 0.9425 (tm) cc_final: 0.9142 (tm) REVERT: v 63 ASN cc_start: 0.9189 (m-40) cc_final: 0.8765 (m-40) REVERT: w 105 MET cc_start: 0.7569 (mpm) cc_final: 0.6720 (ptt) REVERT: w 139 MET cc_start: 0.3469 (tpt) cc_final: 0.1580 (mpp) outliers start: 243 outliers final: 130 residues processed: 1404 average time/residue: 1.8029 time to fit residues: 3497.9549 Evaluate side-chains 1402 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1249 time to evaluate : 7.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 153 THR Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 5 residue 55 LEU Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 6 residue 300 THR Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 123 LEU Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 135 ARG Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 102 ARG Chi-restraints excluded: chain K residue 25 MET Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain N residue 51 ARG Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 199 MET Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 169 ARG Chi-restraints excluded: chain Z residue 47 GLN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 140 LYS Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain c residue 277 ASP Chi-restraints excluded: chain d residue 38 LYS Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 192 SER Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 114 ASN Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 119 GLN Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 71 LYS Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 19 GLN Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain p residue 57 THR Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 126 LYS Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 117 ARG Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 51 MET Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 112 THR Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain u residue 95 ASP Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 143 VAL Chi-restraints excluded: chain u residue 169 CYS Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 179 LEU Chi-restraints excluded: chain u residue 198 SER Chi-restraints excluded: chain v residue 26 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 909 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 537 optimal weight: 0.7980 chunk 688 optimal weight: 9.9990 chunk 533 optimal weight: 6.9990 chunk 794 optimal weight: 50.0000 chunk 526 optimal weight: 3.9990 chunk 939 optimal weight: 8.9990 chunk 588 optimal weight: 4.9990 chunk 572 optimal weight: 7.9990 chunk 433 optimal weight: 0.0970 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 GLN 7 49 ASN C 96 GLN C 177 ASN C 211 ASN C 232 ASN C 504 ASN D 158 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN F 228 GLN F 257 GLN H 126 GLN H 136 ASN I 43 GLN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 HIS K 94 GLN L 33 GLN L 43 ASN L 72 GLN M 26 ASN ** M 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS O 100 GLN P 142 ASN ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 GLN P 176 GLN S 91 GLN T 101 GLN T 201 GLN T 202 GLN V 35 ASN Y 92 ASN Z 47 GLN Z 98 GLN d 77 HIS d 193 HIS ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 99 ASN k 26 ASN p 125 ASN p 182 ASN r 96 HIS ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 148 HIS ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 106462 Z= 0.206 Angle : 0.600 14.360 150941 Z= 0.307 Chirality : 0.039 0.373 17688 Planarity : 0.004 0.123 13918 Dihedral : 20.942 179.149 31454 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.80 % Allowed : 17.22 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.09), residues: 8398 helix: 1.78 (0.10), residues: 2972 sheet: -0.20 (0.15), residues: 1119 loop : 0.37 (0.10), residues: 4307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP d 183 HIS 0.012 0.001 HIS u 148 PHE 0.026 0.001 PHE I 126 TYR 0.026 0.001 TYR d 88 ARG 0.014 0.000 ARG J 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1521 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1309 time to evaluate : 7.582 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: 0 127 TYR cc_start: 0.9206 (t80) cc_final: 0.8979 (t80) REVERT: 1 39 GLU cc_start: 0.7759 (pm20) cc_final: 0.7554 (pm20) REVERT: 3 182 ASP cc_start: 0.7957 (m-30) cc_final: 0.7693 (m-30) REVERT: 4 80 TYR cc_start: 0.8935 (p90) cc_final: 0.8590 (p90) REVERT: 5 153 CYS cc_start: 0.8711 (m) cc_final: 0.8302 (m) REVERT: 5 169 GLU cc_start: 0.7727 (tp30) cc_final: 0.7501 (tp30) REVERT: 6 116 ASN cc_start: 0.8891 (t0) cc_final: 0.8435 (p0) REVERT: 6 305 LYS cc_start: 0.9132 (ttpp) cc_final: 0.8830 (ttpp) REVERT: 7 93 MET cc_start: 0.8925 (mtm) cc_final: 0.8648 (mtm) REVERT: 7 143 TRP cc_start: 0.9175 (OUTLIER) cc_final: 0.7138 (m-90) REVERT: 8 121 TRP cc_start: 0.8572 (t-100) cc_final: 0.8248 (t60) REVERT: C 150 LYS cc_start: 0.7755 (mttt) cc_final: 0.7180 (mmpt) REVERT: C 418 ASN cc_start: 0.9140 (t0) cc_final: 0.8759 (t0) REVERT: C 481 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: D 158 GLN cc_start: 0.7776 (mp-120) cc_final: 0.7519 (mp10) REVERT: F 135 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7510 (mtp180) REVERT: F 209 TYR cc_start: 0.8903 (t80) cc_final: 0.8668 (t80) REVERT: H 100 GLN cc_start: 0.8385 (mt0) cc_final: 0.8172 (mp-120) REVERT: H 138 LYS cc_start: 0.8280 (tptp) cc_final: 0.7619 (tptp) REVERT: I 45 GLN cc_start: 0.8742 (tt0) cc_final: 0.8428 (mt0) REVERT: I 85 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: I 93 ASN cc_start: 0.8555 (t0) cc_final: 0.8248 (t0) REVERT: I 99 CYS cc_start: 0.7721 (m) cc_final: 0.6495 (p) REVERT: I 115 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8527 (mm110) REVERT: J 21 ARG cc_start: 0.7083 (ttt-90) cc_final: 0.6593 (ttm-80) REVERT: J 102 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.8053 (mpp-170) REVERT: J 116 HIS cc_start: 0.8108 (t70) cc_final: 0.7667 (t-90) REVERT: K 153 LYS cc_start: 0.9175 (mtmm) cc_final: 0.8890 (mtpp) REVERT: L 128 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7639 (ttp-170) REVERT: M 218 LYS cc_start: 0.9016 (pttp) cc_final: 0.8809 (pttp) REVERT: N 65 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8236 (mt-10) REVERT: N 104 MET cc_start: 0.8948 (tmm) cc_final: 0.8697 (ttp) REVERT: N 114 ASP cc_start: 0.8576 (t0) cc_final: 0.8236 (t0) REVERT: N 148 ASP cc_start: 0.8140 (t0) cc_final: 0.7814 (t0) REVERT: N 201 ASP cc_start: 0.8258 (m-30) cc_final: 0.7910 (m-30) REVERT: O 40 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8024 (mt-10) REVERT: O 82 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7637 (mt-10) REVERT: P 117 TYR cc_start: 0.8597 (t80) cc_final: 0.8267 (t80) REVERT: P 118 SER cc_start: 0.8837 (t) cc_final: 0.8606 (t) REVERT: P 134 GLN cc_start: 0.9045 (tt0) cc_final: 0.8665 (tm-30) REVERT: P 146 TYR cc_start: 0.9155 (t80) cc_final: 0.8737 (t80) REVERT: Q 186 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8932 (p) REVERT: V 31 ASP cc_start: 0.8856 (t70) cc_final: 0.8634 (t0) REVERT: V 111 SER cc_start: 0.8736 (m) cc_final: 0.8515 (p) REVERT: V 122 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7919 (tt) REVERT: V 126 MET cc_start: 0.8717 (ptp) cc_final: 0.8383 (mtm) REVERT: V 199 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8729 (mtm) REVERT: W 57 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: W 143 LYS cc_start: 0.9087 (mmtp) cc_final: 0.8879 (mmtm) REVERT: Y 81 SER cc_start: 0.8853 (t) cc_final: 0.8598 (p) REVERT: Y 169 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8367 (mtt-85) REVERT: d 38 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7998 (mtpp) REVERT: d 40 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6225 (pmt170) REVERT: d 172 MET cc_start: 0.9199 (ttm) cc_final: 0.8975 (ttm) REVERT: d 235 GLN cc_start: 0.8473 (mp10) cc_final: 0.8062 (mp10) REVERT: d 274 GLN cc_start: 0.8559 (tt0) cc_final: 0.8310 (tt0) REVERT: e 79 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8661 (pp) REVERT: e 132 LYS cc_start: 0.5482 (mmmt) cc_final: 0.5181 (tptt) REVERT: e 139 GLU cc_start: 0.5104 (OUTLIER) cc_final: 0.4574 (mp0) REVERT: f 100 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7264 (tpt) REVERT: h 116 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7060 (mtp85) REVERT: j 101 GLU cc_start: 0.7839 (pp20) cc_final: 0.7622 (pp20) REVERT: k 24 GLU cc_start: 0.6658 (mt-10) cc_final: 0.6151 (mp0) REVERT: k 40 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6948 (mm-30) REVERT: l 117 TYR cc_start: 0.8952 (t80) cc_final: 0.7543 (m-10) REVERT: l 128 ARG cc_start: 0.8618 (ttt-90) cc_final: 0.8403 (tmm-80) REVERT: l 131 ARG cc_start: 0.8633 (mtm110) cc_final: 0.8382 (mtm-85) REVERT: p 38 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6792 (mm-30) REVERT: p 47 LYS cc_start: 0.9343 (mttp) cc_final: 0.9069 (mttp) REVERT: p 183 MET cc_start: 0.8306 (tmm) cc_final: 0.7857 (tmm) REVERT: q 143 TRP cc_start: 0.7622 (OUTLIER) cc_final: 0.6933 (t60) REVERT: r 103 LYS cc_start: 0.7092 (mmtt) cc_final: 0.6479 (mttt) REVERT: u 118 MET cc_start: 0.8290 (mpp) cc_final: 0.8025 (mtm) REVERT: u 141 TYR cc_start: 0.8795 (t80) cc_final: 0.8244 (t80) REVERT: u 166 ASP cc_start: 0.8423 (p0) cc_final: 0.8025 (p0) REVERT: u 183 GLU cc_start: 0.8328 (mp0) cc_final: 0.7982 (mp0) REVERT: u 187 ILE cc_start: 0.9211 (tp) cc_final: 0.8766 (mp) REVERT: u 189 GLU cc_start: 0.7694 (pm20) cc_final: 0.7447 (pm20) REVERT: v 19 GLN cc_start: 0.8622 (tt0) cc_final: 0.8349 (mt0) REVERT: v 27 ASP cc_start: 0.8834 (t70) cc_final: 0.8590 (t0) REVERT: v 38 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8476 (tm-30) REVERT: v 54 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8275 (tm130) REVERT: v 56 GLU cc_start: 0.8969 (tp30) cc_final: 0.8648 (tp30) REVERT: v 59 LEU cc_start: 0.9504 (mt) cc_final: 0.9288 (mm) REVERT: v 62 LEU cc_start: 0.9399 (tm) cc_final: 0.9123 (tm) REVERT: v 63 ASN cc_start: 0.9160 (m-40) cc_final: 0.8715 (m-40) REVERT: w 105 MET cc_start: 0.7429 (mpm) cc_final: 0.6690 (ptt) outliers start: 212 outliers final: 120 residues processed: 1413 average time/residue: 1.7613 time to fit residues: 3452.9666 Evaluate side-chains 1407 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1267 time to evaluate : 7.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 183 SER Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 6 residue 300 THR Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 123 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 135 ARG Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 102 ARG Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 128 ARG Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain N residue 51 ARG Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain S residue 164 THR Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 127 TYR Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 199 MET Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 169 ARG Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain c residue 277 ASP Chi-restraints excluded: chain d residue 38 LYS Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 192 SER Chi-restraints excluded: chain d residue 193 HIS Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 114 ASN Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 119 GLN Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain k residue 19 GLN Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 51 MET Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain u residue 95 ASP Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 169 CYS Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 198 SER Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 39 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 581 optimal weight: 10.0000 chunk 375 optimal weight: 4.9990 chunk 561 optimal weight: 0.9990 chunk 283 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 597 optimal weight: 0.9980 chunk 640 optimal weight: 0.0770 chunk 464 optimal weight: 0.3980 chunk 87 optimal weight: 0.0370 chunk 738 optimal weight: 9.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 GLN 7 49 ASN 8 143 GLN C 96 GLN C 211 ASN C 232 ASN C 356 GLN C 504 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN F 228 GLN F 257 GLN H 136 ASN I 43 GLN I 151 ASN ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 43 ASN M 170 ASN N 98 HIS O 100 GLN P 142 ASN ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 GLN P 176 GLN R 125 HIS S 91 GLN T 101 GLN T 201 GLN T 202 GLN U 23 ASN V 35 ASN Z 98 GLN d 77 HIS d 193 HIS ** e 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 99 ASN k 26 ASN o 33 GLN p 125 ASN p 182 ASN ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 106462 Z= 0.151 Angle : 0.593 17.511 150941 Z= 0.303 Chirality : 0.038 0.372 17688 Planarity : 0.004 0.118 13918 Dihedral : 20.849 178.346 31454 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.00 % Allowed : 18.57 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.16 (0.09), residues: 8398 helix: 1.80 (0.10), residues: 2971 sheet: -0.16 (0.15), residues: 1127 loop : 0.42 (0.10), residues: 4300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP d 183 HIS 0.050 0.001 HIS d 193 PHE 0.019 0.001 PHE v 30 TYR 0.039 0.001 TYR 9 117 ARG 0.018 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1495 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1344 time to evaluate : 7.334 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: 0 127 TYR cc_start: 0.9124 (t80) cc_final: 0.8879 (t80) REVERT: 0 128 GLU cc_start: 0.8026 (tp30) cc_final: 0.7783 (tm-30) REVERT: 2 88 LYS cc_start: 0.8682 (ttpt) cc_final: 0.7959 (ttpt) REVERT: 3 182 ASP cc_start: 0.7924 (m-30) cc_final: 0.7675 (m-30) REVERT: 4 80 TYR cc_start: 0.8931 (p90) cc_final: 0.8595 (p90) REVERT: 5 153 CYS cc_start: 0.8687 (m) cc_final: 0.8287 (m) REVERT: 5 169 GLU cc_start: 0.7718 (tp30) cc_final: 0.7497 (tp30) REVERT: 6 116 ASN cc_start: 0.8861 (t0) cc_final: 0.8451 (p0) REVERT: 6 305 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8808 (ttpp) REVERT: 7 93 MET cc_start: 0.8881 (mtm) cc_final: 0.8608 (mtm) REVERT: 7 143 TRP cc_start: 0.9117 (OUTLIER) cc_final: 0.7152 (m-90) REVERT: 8 121 TRP cc_start: 0.8504 (t-100) cc_final: 0.8226 (t60) REVERT: 9 18 MET cc_start: 0.8710 (mmt) cc_final: 0.8185 (mmt) REVERT: 9 90 GLN cc_start: 0.8872 (tt0) cc_final: 0.8658 (tt0) REVERT: 9 117 TYR cc_start: 0.7446 (m-80) cc_final: 0.7001 (m-80) REVERT: C 150 LYS cc_start: 0.7761 (mttt) cc_final: 0.7282 (mptt) REVERT: C 418 ASN cc_start: 0.9070 (t0) cc_final: 0.8708 (t0) REVERT: C 481 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: D 158 GLN cc_start: 0.7771 (mp-120) cc_final: 0.7560 (mp10) REVERT: I 45 GLN cc_start: 0.8696 (tt0) cc_final: 0.8389 (mt0) REVERT: I 85 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: I 93 ASN cc_start: 0.8639 (t0) cc_final: 0.8307 (t0) REVERT: I 99 CYS cc_start: 0.7660 (m) cc_final: 0.5663 (p) REVERT: J 21 ARG cc_start: 0.7059 (ttt-90) cc_final: 0.6574 (ttt-90) REVERT: J 116 HIS cc_start: 0.8017 (t70) cc_final: 0.7509 (t-90) REVERT: K 162 GLU cc_start: 0.8306 (mp0) cc_final: 0.8046 (pm20) REVERT: M 218 LYS cc_start: 0.9017 (pttp) cc_final: 0.8744 (pttp) REVERT: N 65 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: N 114 ASP cc_start: 0.8486 (t0) cc_final: 0.8172 (t0) REVERT: N 148 ASP cc_start: 0.8086 (t0) cc_final: 0.7753 (t0) REVERT: N 201 ASP cc_start: 0.8239 (m-30) cc_final: 0.7901 (m-30) REVERT: O 40 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7923 (mt-10) REVERT: O 82 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7594 (mt-10) REVERT: P 117 TYR cc_start: 0.8570 (t80) cc_final: 0.8283 (t80) REVERT: P 118 SER cc_start: 0.8782 (t) cc_final: 0.8544 (t) REVERT: P 134 GLN cc_start: 0.9032 (tt0) cc_final: 0.8646 (tm-30) REVERT: Q 186 SER cc_start: 0.9161 (t) cc_final: 0.8958 (p) REVERT: V 31 ASP cc_start: 0.8867 (t70) cc_final: 0.8652 (t0) REVERT: V 108 MET cc_start: 0.8318 (ttm) cc_final: 0.8001 (ttm) REVERT: V 111 SER cc_start: 0.8790 (m) cc_final: 0.8538 (p) REVERT: V 122 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7996 (tt) REVERT: V 126 MET cc_start: 0.8618 (ptp) cc_final: 0.8379 (mtm) REVERT: V 199 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8652 (mtm) REVERT: W 143 LYS cc_start: 0.9070 (mmtp) cc_final: 0.8611 (mmtp) REVERT: Y 81 SER cc_start: 0.8705 (t) cc_final: 0.8416 (p) REVERT: Y 169 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8326 (mtt-85) REVERT: Z 43 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6841 (tm-30) REVERT: Z 85 ILE cc_start: 0.9355 (mt) cc_final: 0.9144 (mt) REVERT: c 231 MET cc_start: 0.8849 (mtm) cc_final: 0.8537 (mtp) REVERT: d 38 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7973 (mtpp) REVERT: d 40 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6176 (pmt170) REVERT: d 118 SER cc_start: 0.8377 (p) cc_final: 0.8168 (p) REVERT: d 172 MET cc_start: 0.9168 (ttm) cc_final: 0.8836 (ttm) REVERT: d 235 GLN cc_start: 0.8411 (mp10) cc_final: 0.7995 (mp10) REVERT: d 274 GLN cc_start: 0.8467 (tt0) cc_final: 0.8265 (tt0) REVERT: e 79 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8642 (pp) REVERT: e 132 LYS cc_start: 0.5500 (mmmt) cc_final: 0.5194 (tptt) REVERT: e 139 GLU cc_start: 0.5079 (OUTLIER) cc_final: 0.4752 (tp30) REVERT: e 265 LYS cc_start: 0.8207 (mptt) cc_final: 0.7769 (pmtt) REVERT: f 60 LYS cc_start: 0.8737 (mtpm) cc_final: 0.8507 (mtpm) REVERT: f 100 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7138 (tpt) REVERT: h 116 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.6995 (mtp85) REVERT: i 84 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8670 (ttpt) REVERT: j 101 GLU cc_start: 0.7930 (pp20) cc_final: 0.7728 (pp20) REVERT: k 24 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6053 (mp0) REVERT: k 33 PHE cc_start: 0.9537 (t80) cc_final: 0.9179 (t80) REVERT: k 40 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7001 (mm-30) REVERT: k 86 MET cc_start: 0.8867 (mmm) cc_final: 0.8044 (mtm) REVERT: l 117 TYR cc_start: 0.8930 (t80) cc_final: 0.7501 (m-10) REVERT: l 131 ARG cc_start: 0.8597 (mtm110) cc_final: 0.8391 (mtm-85) REVERT: p 38 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6774 (mm-30) REVERT: p 47 LYS cc_start: 0.9348 (mttp) cc_final: 0.9079 (mttp) REVERT: p 152 GLN cc_start: 0.9082 (tp40) cc_final: 0.8297 (tp40) REVERT: p 156 ASP cc_start: 0.8186 (m-30) cc_final: 0.7553 (m-30) REVERT: p 183 MET cc_start: 0.8318 (tmm) cc_final: 0.7853 (tmm) REVERT: q 59 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8673 (mptt) REVERT: q 143 TRP cc_start: 0.7643 (OUTLIER) cc_final: 0.6898 (t60) REVERT: r 37 GLU cc_start: 0.7166 (pp20) cc_final: 0.6903 (pp20) REVERT: r 52 ARG cc_start: 0.8422 (pmm-80) cc_final: 0.7908 (pmm-80) REVERT: r 103 LYS cc_start: 0.7053 (mmtt) cc_final: 0.6443 (mttt) REVERT: r 188 SER cc_start: 0.9256 (OUTLIER) cc_final: 0.9054 (p) REVERT: u 118 MET cc_start: 0.8254 (mpp) cc_final: 0.7988 (mtm) REVERT: u 166 ASP cc_start: 0.8411 (p0) cc_final: 0.7983 (p0) REVERT: u 177 ILE cc_start: 0.9256 (mm) cc_final: 0.9047 (mp) REVERT: u 183 GLU cc_start: 0.8299 (mp0) cc_final: 0.7950 (mp0) REVERT: u 187 ILE cc_start: 0.9133 (tp) cc_final: 0.8718 (mp) REVERT: v 27 ASP cc_start: 0.8817 (t70) cc_final: 0.8571 (t0) REVERT: v 38 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8399 (tm-30) REVERT: v 39 PHE cc_start: 0.9263 (m-10) cc_final: 0.9013 (m-10) REVERT: v 40 ARG cc_start: 0.7945 (ppt170) cc_final: 0.7713 (ppt170) REVERT: v 56 GLU cc_start: 0.8944 (tp30) cc_final: 0.8655 (tp30) REVERT: v 59 LEU cc_start: 0.9491 (mt) cc_final: 0.9290 (mm) REVERT: v 63 ASN cc_start: 0.9142 (m-40) cc_final: 0.8685 (m-40) REVERT: w 139 MET cc_start: 0.3688 (tpt) cc_final: 0.1878 (mpp) outliers start: 151 outliers final: 73 residues processed: 1417 average time/residue: 1.7869 time to fit residues: 3524.1144 Evaluate side-chains 1358 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1268 time to evaluate : 8.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 174 ILE Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 6 residue 300 THR Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 8 residue 123 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 127 TYR Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 199 MET Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 169 ARG Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain d residue 38 LYS Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 192 SER Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain f residue 96 THR Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 114 ASN Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 119 GLN Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain k residue 49 CYS Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain q residue 59 LYS Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain u residue 95 ASP Chi-restraints excluded: chain u residue 198 SER Chi-restraints excluded: chain v residue 12 LEU Chi-restraints excluded: chain v residue 26 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 854 optimal weight: 10.0000 chunk 900 optimal weight: 5.9990 chunk 821 optimal weight: 4.9990 chunk 875 optimal weight: 9.9990 chunk 527 optimal weight: 0.9980 chunk 381 optimal weight: 8.9990 chunk 687 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 791 optimal weight: 7.9990 chunk 828 optimal weight: 8.9990 chunk 872 optimal weight: 2.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 GLN 6 37 ASN 6 63 GLN 8 143 GLN C 96 GLN C 211 ASN C 304 ASN C 504 ASN F 103 GLN F 184 GLN F 228 GLN F 257 GLN H 136 ASN I 43 GLN ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN L 43 ASN L 113 ASN N 68 ASN N 98 HIS O 100 GLN P 142 ASN ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 GLN P 176 GLN Q 261 ASN T 101 GLN T 201 GLN T 202 GLN U 23 ASN V 35 ASN X 53 ASN Z 98 GLN ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 HIS d 193 HIS ** e 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 99 ASN k 26 ASN p 125 ASN p 182 ASN s 164 HIS ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 106462 Z= 0.379 Angle : 0.654 15.912 150941 Z= 0.333 Chirality : 0.042 0.381 17688 Planarity : 0.005 0.129 13918 Dihedral : 20.807 179.246 31454 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.17 % Allowed : 19.17 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.09), residues: 8398 helix: 1.75 (0.10), residues: 2974 sheet: -0.19 (0.15), residues: 1149 loop : 0.41 (0.10), residues: 4275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP d 183 HIS 0.018 0.001 HIS d 193 PHE 0.021 0.002 PHE v 30 TYR 0.030 0.002 TYR d 88 ARG 0.015 0.001 ARG 1 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1273 time to evaluate : 7.441 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: 0 178 ASP cc_start: 0.7621 (p0) cc_final: 0.7341 (p0) REVERT: 2 88 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8368 (ttpp) REVERT: 3 182 ASP cc_start: 0.8042 (m-30) cc_final: 0.7788 (m-30) REVERT: 4 80 TYR cc_start: 0.8955 (p90) cc_final: 0.8659 (p90) REVERT: 5 153 CYS cc_start: 0.8728 (m) cc_final: 0.8316 (m) REVERT: 5 169 GLU cc_start: 0.7760 (tp30) cc_final: 0.7543 (tp30) REVERT: 6 116 ASN cc_start: 0.8806 (t0) cc_final: 0.8353 (p0) REVERT: 6 305 LYS cc_start: 0.9125 (ttpp) cc_final: 0.8820 (ttpp) REVERT: 6 317 SER cc_start: 0.8875 (t) cc_final: 0.8511 (m) REVERT: 7 93 MET cc_start: 0.8939 (mtm) cc_final: 0.8623 (mtm) REVERT: 7 143 TRP cc_start: 0.9224 (OUTLIER) cc_final: 0.6938 (m-90) REVERT: 8 121 TRP cc_start: 0.8501 (t-100) cc_final: 0.8251 (t60) REVERT: C 150 LYS cc_start: 0.7787 (mttt) cc_final: 0.7197 (mmpt) REVERT: C 418 ASN cc_start: 0.9164 (t0) cc_final: 0.8780 (t0) REVERT: C 481 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: D 158 GLN cc_start: 0.7821 (mp-120) cc_final: 0.7553 (mp10) REVERT: F 135 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7532 (mtp180) REVERT: H 70 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.6893 (ptpp) REVERT: H 103 GLU cc_start: 0.8547 (tt0) cc_final: 0.8279 (tm-30) REVERT: I 45 GLN cc_start: 0.8806 (tt0) cc_final: 0.8477 (mt0) REVERT: I 85 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: I 93 ASN cc_start: 0.8743 (t0) cc_final: 0.8360 (t0) REVERT: I 115 GLN cc_start: 0.9005 (mp10) cc_final: 0.8620 (mm110) REVERT: J 116 HIS cc_start: 0.8082 (t70) cc_final: 0.7544 (t-90) REVERT: K 25 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8332 (mmm) REVERT: K 162 GLU cc_start: 0.8278 (mp0) cc_final: 0.8005 (pm20) REVERT: L 128 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7605 (ttp-170) REVERT: M 170 ASN cc_start: 0.8383 (m-40) cc_final: 0.8101 (m-40) REVERT: M 218 LYS cc_start: 0.9018 (pttp) cc_final: 0.8789 (pttp) REVERT: N 104 MET cc_start: 0.8979 (tmm) cc_final: 0.8717 (ttp) REVERT: N 114 ASP cc_start: 0.8571 (t0) cc_final: 0.8218 (t0) REVERT: N 148 ASP cc_start: 0.8105 (t0) cc_final: 0.7736 (t0) REVERT: N 201 ASP cc_start: 0.8285 (m-30) cc_final: 0.7940 (m-30) REVERT: O 40 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8088 (mt-10) REVERT: O 82 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7662 (mt-10) REVERT: P 117 TYR cc_start: 0.8581 (t80) cc_final: 0.8287 (t80) REVERT: P 118 SER cc_start: 0.8829 (t) cc_final: 0.8596 (t) REVERT: P 134 GLN cc_start: 0.9034 (tt0) cc_final: 0.8643 (tm-30) REVERT: Q 125 TYR cc_start: 0.8415 (m-80) cc_final: 0.7857 (m-80) REVERT: Q 186 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8933 (p) REVERT: V 31 ASP cc_start: 0.8921 (t70) cc_final: 0.8661 (t0) REVERT: V 122 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7992 (tt) REVERT: V 126 MET cc_start: 0.8673 (ptp) cc_final: 0.8437 (mtm) REVERT: V 199 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8665 (mtm) REVERT: W 57 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: Y 169 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8449 (mtt-85) REVERT: d 38 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8013 (mtpp) REVERT: d 154 ASN cc_start: 0.8871 (t0) cc_final: 0.8300 (t0) REVERT: d 172 MET cc_start: 0.9203 (ttm) cc_final: 0.8849 (ttm) REVERT: d 235 GLN cc_start: 0.8502 (mp10) cc_final: 0.8079 (mp10) REVERT: d 274 GLN cc_start: 0.8560 (tt0) cc_final: 0.8360 (tt0) REVERT: e 79 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8664 (pp) REVERT: e 132 LYS cc_start: 0.5507 (mmmt) cc_final: 0.5198 (tptt) REVERT: e 265 LYS cc_start: 0.8198 (mptt) cc_final: 0.7935 (mppt) REVERT: f 100 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7170 (tpt) REVERT: h 116 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7001 (mtp85) REVERT: i 84 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8813 (ttpt) REVERT: k 24 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6212 (mp0) REVERT: k 40 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6718 (mm-30) REVERT: k 43 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8224 (mtm-85) REVERT: l 117 TYR cc_start: 0.8960 (t80) cc_final: 0.7523 (m-10) REVERT: p 38 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6811 (mm-30) REVERT: p 47 LYS cc_start: 0.9347 (mttp) cc_final: 0.9087 (mttp) REVERT: p 183 MET cc_start: 0.8345 (tmm) cc_final: 0.7885 (tmm) REVERT: q 59 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8673 (mptt) REVERT: q 128 MET cc_start: 0.9118 (tpt) cc_final: 0.8883 (tpp) REVERT: q 131 MET cc_start: 0.9073 (mtp) cc_final: 0.8849 (ptp) REVERT: q 143 TRP cc_start: 0.7638 (OUTLIER) cc_final: 0.6941 (t60) REVERT: r 37 GLU cc_start: 0.7331 (pp20) cc_final: 0.7058 (pp20) REVERT: r 52 ARG cc_start: 0.8425 (pmm-80) cc_final: 0.8073 (pmm-80) REVERT: r 103 LYS cc_start: 0.7277 (mmtt) cc_final: 0.6707 (mttt) REVERT: u 118 MET cc_start: 0.8315 (mpp) cc_final: 0.8045 (mtm) REVERT: u 141 TYR cc_start: 0.8872 (t80) cc_final: 0.8452 (t80) REVERT: u 145 MET cc_start: 0.7755 (tmm) cc_final: 0.7478 (tmt) REVERT: u 166 ASP cc_start: 0.8425 (p0) cc_final: 0.8015 (p0) REVERT: u 183 GLU cc_start: 0.8319 (mp0) cc_final: 0.7965 (mp0) REVERT: u 187 ILE cc_start: 0.9239 (tp) cc_final: 0.8745 (mp) REVERT: v 27 ASP cc_start: 0.8832 (t70) cc_final: 0.8584 (t0) REVERT: v 38 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8430 (tm-30) REVERT: v 39 PHE cc_start: 0.9303 (m-10) cc_final: 0.9054 (m-10) REVERT: v 40 ARG cc_start: 0.8082 (ppt170) cc_final: 0.7814 (ppt170) REVERT: v 54 GLN cc_start: 0.8273 (tm-30) cc_final: 0.8045 (tm130) REVERT: v 56 GLU cc_start: 0.8982 (tp30) cc_final: 0.8665 (tp30) REVERT: v 59 LEU cc_start: 0.9539 (mt) cc_final: 0.9310 (mm) REVERT: v 63 ASN cc_start: 0.9171 (m-40) cc_final: 0.8757 (m-40) REVERT: w 139 MET cc_start: 0.3234 (tpt) cc_final: 0.1689 (mpp) outliers start: 164 outliers final: 99 residues processed: 1348 average time/residue: 1.8021 time to fit residues: 3369.4300 Evaluate side-chains 1361 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1243 time to evaluate : 7.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 174 ILE Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 6 residue 300 THR Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 8 residue 123 LEU Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 135 ARG Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain K residue 25 MET Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 128 ARG Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain N residue 51 ARG Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 199 MET Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain X residue 55 LYS Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 169 ARG Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 140 LYS Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain d residue 38 LYS Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 114 ASN Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 119 GLN Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 45 ASP Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 19 GLN Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 49 CYS Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain p residue 126 LYS Chi-restraints excluded: chain q residue 59 LYS Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain u residue 95 ASP Chi-restraints excluded: chain u residue 125 VAL Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 198 SER Chi-restraints excluded: chain v residue 26 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 575 optimal weight: 7.9990 chunk 926 optimal weight: 10.0000 chunk 565 optimal weight: 7.9990 chunk 439 optimal weight: 9.9990 chunk 643 optimal weight: 4.9990 chunk 971 optimal weight: 20.0000 chunk 894 optimal weight: 1.9990 chunk 773 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 597 optimal weight: 0.8980 chunk 474 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 37 ASN 6 63 GLN 7 49 ASN ** 7 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 143 GLN C 211 ASN C 232 ASN C 304 ASN C 504 ASN F 103 GLN ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN H 136 ASN I 43 GLN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 43 ASN L 113 ASN N 98 HIS ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 142 ASN ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 176 GLN T 101 GLN T 201 GLN T 202 GLN U 23 ASN V 35 ASN ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 HIS ** e 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 99 ASN k 26 ASN ** k 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 135 ASN p 125 ASN p 182 ASN ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 148 HIS ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 106462 Z= 0.316 Angle : 0.686 61.599 150941 Z= 0.346 Chirality : 0.040 0.525 17688 Planarity : 0.005 0.129 13918 Dihedral : 20.816 179.317 31454 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.93 % Allowed : 19.80 % Favored : 78.27 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.09), residues: 8398 helix: 1.76 (0.10), residues: 2974 sheet: -0.20 (0.15), residues: 1149 loop : 0.41 (0.10), residues: 4275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP d 183 HIS 0.016 0.001 HIS k 93 PHE 0.028 0.002 PHE H 140 TYR 0.024 0.001 TYR 5 176 ARG 0.020 0.000 ARG D 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16796 Ramachandran restraints generated. 8398 Oldfield, 0 Emsley, 8398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1247 time to evaluate : 7.711 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: 0 178 ASP cc_start: 0.7615 (p0) cc_final: 0.7338 (p0) REVERT: 2 88 LYS cc_start: 0.8765 (ttpt) cc_final: 0.8363 (ttpp) REVERT: 3 182 ASP cc_start: 0.8032 (m-30) cc_final: 0.7778 (m-30) REVERT: 4 80 TYR cc_start: 0.8951 (p90) cc_final: 0.8658 (p90) REVERT: 5 153 CYS cc_start: 0.8725 (m) cc_final: 0.8311 (m) REVERT: 5 169 GLU cc_start: 0.7757 (tp30) cc_final: 0.7538 (tp30) REVERT: 6 116 ASN cc_start: 0.8804 (t0) cc_final: 0.8350 (p0) REVERT: 6 305 LYS cc_start: 0.9138 (ttpp) cc_final: 0.8833 (ttpp) REVERT: 6 317 SER cc_start: 0.8870 (t) cc_final: 0.8507 (m) REVERT: 7 43 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8761 (pp-130) REVERT: 7 93 MET cc_start: 0.8933 (mtm) cc_final: 0.8618 (mtm) REVERT: 7 143 TRP cc_start: 0.9220 (OUTLIER) cc_final: 0.6935 (m-90) REVERT: 8 121 TRP cc_start: 0.8497 (t-100) cc_final: 0.8261 (t60) REVERT: C 150 LYS cc_start: 0.7784 (mttt) cc_final: 0.7194 (mmpt) REVERT: C 418 ASN cc_start: 0.9161 (t0) cc_final: 0.8776 (t0) REVERT: C 481 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: D 158 GLN cc_start: 0.7815 (mp-120) cc_final: 0.7544 (mp10) REVERT: E 81 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8381 (mtpp) REVERT: F 135 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7521 (mtp180) REVERT: H 103 GLU cc_start: 0.8547 (tt0) cc_final: 0.8279 (tm-30) REVERT: I 45 GLN cc_start: 0.8795 (tt0) cc_final: 0.8468 (mt0) REVERT: I 85 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: I 93 ASN cc_start: 0.8671 (t0) cc_final: 0.8370 (t0) REVERT: I 115 GLN cc_start: 0.9026 (mp10) cc_final: 0.8647 (mm110) REVERT: J 116 HIS cc_start: 0.8034 (t70) cc_final: 0.7547 (t-90) REVERT: L 128 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7600 (ttp-170) REVERT: M 170 ASN cc_start: 0.8374 (m-40) cc_final: 0.8090 (m-40) REVERT: M 218 LYS cc_start: 0.9015 (pttp) cc_final: 0.8785 (pttp) REVERT: N 104 MET cc_start: 0.8973 (tmm) cc_final: 0.8710 (ttp) REVERT: N 114 ASP cc_start: 0.8548 (t0) cc_final: 0.8213 (t0) REVERT: N 148 ASP cc_start: 0.8098 (t0) cc_final: 0.7733 (t0) REVERT: N 201 ASP cc_start: 0.8281 (m-30) cc_final: 0.7932 (m-30) REVERT: O 40 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8091 (mt-10) REVERT: O 82 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7652 (mt-10) REVERT: P 117 TYR cc_start: 0.8579 (t80) cc_final: 0.8284 (t80) REVERT: P 118 SER cc_start: 0.8824 (t) cc_final: 0.8593 (t) REVERT: P 134 GLN cc_start: 0.9032 (tt0) cc_final: 0.8640 (tm-30) REVERT: Q 125 TYR cc_start: 0.8414 (m-80) cc_final: 0.7845 (m-80) REVERT: Q 186 SER cc_start: 0.9158 (t) cc_final: 0.8927 (p) REVERT: V 31 ASP cc_start: 0.8917 (t70) cc_final: 0.8657 (t0) REVERT: V 122 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7990 (tt) REVERT: V 199 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8663 (mtm) REVERT: W 57 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: Y 169 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8441 (mtt-85) REVERT: d 38 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8008 (mtpp) REVERT: d 154 ASN cc_start: 0.8868 (t0) cc_final: 0.8296 (t0) REVERT: d 172 MET cc_start: 0.9200 (ttm) cc_final: 0.8846 (ttm) REVERT: d 235 GLN cc_start: 0.8499 (mp10) cc_final: 0.8076 (mp10) REVERT: e 70 MET cc_start: 0.8509 (mtt) cc_final: 0.8297 (mmt) REVERT: e 79 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8662 (pp) REVERT: e 132 LYS cc_start: 0.5507 (mmmt) cc_final: 0.5198 (tptt) REVERT: e 265 LYS cc_start: 0.8197 (mptt) cc_final: 0.7934 (mppt) REVERT: f 100 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7169 (tpt) REVERT: h 116 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7023 (mtp85) REVERT: i 84 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8804 (ttpt) REVERT: k 24 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6208 (mp0) REVERT: k 40 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6712 (mm-30) REVERT: k 43 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.8207 (mtm-85) REVERT: k 86 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8602 (mtt) REVERT: l 117 TYR cc_start: 0.8960 (t80) cc_final: 0.7523 (m-10) REVERT: p 38 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6812 (mm-30) REVERT: p 47 LYS cc_start: 0.9345 (mttp) cc_final: 0.9082 (mttp) REVERT: p 183 MET cc_start: 0.8343 (tmm) cc_final: 0.7879 (tmm) REVERT: q 59 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8670 (mptt) REVERT: q 128 MET cc_start: 0.9112 (tpt) cc_final: 0.8883 (tpp) REVERT: q 131 MET cc_start: 0.9068 (mtp) cc_final: 0.8846 (ptp) REVERT: q 143 TRP cc_start: 0.7637 (OUTLIER) cc_final: 0.6939 (t60) REVERT: r 37 GLU cc_start: 0.7322 (pp20) cc_final: 0.7033 (pp20) REVERT: r 52 ARG cc_start: 0.8420 (pmm-80) cc_final: 0.8045 (pmm-80) REVERT: r 103 LYS cc_start: 0.7267 (mmtt) cc_final: 0.6692 (mttt) REVERT: u 118 MET cc_start: 0.8312 (mpp) cc_final: 0.8040 (mtm) REVERT: u 148 HIS cc_start: 0.8539 (OUTLIER) cc_final: 0.8306 (t70) REVERT: u 166 ASP cc_start: 0.8447 (p0) cc_final: 0.8032 (p0) REVERT: u 183 GLU cc_start: 0.8314 (mp0) cc_final: 0.7962 (mp0) REVERT: u 187 ILE cc_start: 0.9226 (tp) cc_final: 0.8744 (mp) REVERT: v 27 ASP cc_start: 0.8829 (t70) cc_final: 0.8582 (t0) REVERT: v 38 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8426 (tm-30) REVERT: v 39 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.9047 (m-10) REVERT: v 40 ARG cc_start: 0.8076 (ppt170) cc_final: 0.7810 (ppt170) REVERT: v 54 GLN cc_start: 0.8280 (tm-30) cc_final: 0.8064 (tm130) REVERT: v 56 GLU cc_start: 0.8980 (tp30) cc_final: 0.8665 (tp30) REVERT: v 59 LEU cc_start: 0.9535 (mt) cc_final: 0.9308 (mm) REVERT: v 63 ASN cc_start: 0.9160 (m-40) cc_final: 0.8757 (m-40) outliers start: 146 outliers final: 104 residues processed: 1310 average time/residue: 1.8248 time to fit residues: 3311.7819 Evaluate side-chains 1366 residues out of total 7561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1241 time to evaluate : 7.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 55 LEU Chi-restraints excluded: chain 1 residue 58 GLU Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 5 residue 273 VAL Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 184 LEU Chi-restraints excluded: chain 6 residue 300 THR Chi-restraints excluded: chain 7 residue 43 MET Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 78 VAL Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 189 LEU Chi-restraints excluded: chain 8 residue 123 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 135 ARG Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 128 ARG Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain N residue 51 ARG Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 107 MET Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain P residue 144 MET Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 161 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 199 MET Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain X residue 55 LYS Chi-restraints excluded: chain X residue 98 SER Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain Y residue 169 ARG Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 140 LYS Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain d residue 38 LYS Chi-restraints excluded: chain d residue 88 TYR Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 114 ASN Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 119 GLN Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 19 GLN Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 39 SER Chi-restraints excluded: chain k residue 49 CYS Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 65 ASP Chi-restraints excluded: chain k residue 84 LEU Chi-restraints excluded: chain k residue 86 MET Chi-restraints excluded: chain p residue 81 CYS Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain p residue 126 LYS Chi-restraints excluded: chain q residue 59 LYS Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain q residue 143 TRP Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 201 ASP Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain u residue 95 ASP 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 170 VAL Chi-restraints excluded: chain u residue 198 SER Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 39 PHE Chi-restraints excluded: chain v residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 975 random chunks: chunk 614 optimal weight: 7.9990 chunk 823 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 chunk 713 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 774 optimal weight: 3.9990 chunk 324 optimal weight: 7.9990 chunk 795 optimal weight: 50.0000 chunk 98 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 37 ASN 6 63 GLN 7 49 ASN 8 143 GLN C 96 GLN C 211 ASN C 304 ASN C 504 ASN F 103 GLN F 184 GLN F 228 GLN F 257 GLN H 136 ASN I 43 GLN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 43 ASN N 98 HIS ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 142 ASN ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 GLN P 176 GLN T 101 GLN T 201 GLN T 202 GLN U 23 ASN V 35 ASN Y 76 GLN Z 62 ASN ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 HIS ** e 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 99 ASN k 26 ASN ** k 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 123 HIS p 125 ASN p 182 ASN ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 148 HIS ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.076421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.049985 restraints weight = 236698.011| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 1.77 r_work: 0.2504 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2395 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 106462 Z= 0.389 Angle : 0.671 14.109 150941 Z= 0.344 Chirality : 0.043 0.347 17688 Planarity : 0.005 0.130 13918 Dihedral : 20.889 179.535 31454 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.26 % Allowed : 19.52 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 8398 helix: 1.64 (0.10), residues: 2971 sheet: -0.25 (0.15), residues: 1131 loop : 0.36 (0.10), residues: 4296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP d 183 HIS 0.031 0.001 HIS u 148 PHE 0.021 0.002 PHE 6 273 TYR 0.035 0.002 TYR d 88 ARG 0.021 0.001 ARG D 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47966.81 seconds wall clock time: 830 minutes 36.52 seconds (49836.52 seconds total)