Starting phenix.real_space_refine on Fri Feb 23 01:18:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of5_12870/02_2024/7of5_12870_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of5_12870/02_2024/7of5_12870.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of5_12870/02_2024/7of5_12870_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of5_12870/02_2024/7of5_12870_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of5_12870/02_2024/7of5_12870_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of5_12870/02_2024/7of5_12870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of5_12870/02_2024/7of5_12870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of5_12870/02_2024/7of5_12870_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of5_12870/02_2024/7of5_12870_updated.pdb" } resolution = 2.9 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 1451 5.49 5 Mg 70 5.21 5 S 317 5.16 5 C 59699 2.51 5 N 18649 2.21 5 O 22596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "7 PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 102785 Number of models: 1 Model: "" Number of chains: 63 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: 29503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1389, 29503 Classifications: {'RNA': 1389} Modifications used: {'rna2p_pur': 147, 'rna2p_pyr': 106, 'rna3p': 3, 'rna3p_pur': 587, 'rna3p_pyr': 546} Link IDs: {'rna2p': 252, 'rna3p': 1136} Chain breaks: 14 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 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: 2690 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 338, 2685 Classifications: {'peptide': 338} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 338, 2685 Classifications: {'peptide': 338} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 bond proxies already assigned to first conformer: 2740 Chain: "D" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1821 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2405 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 24, 'TRANS': 280} Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "G" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1943 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 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: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1653 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 18, 'TRANS': 180} Chain breaks: 4 Chain: "e" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1599 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 9, 'TRANS': 187} Chain breaks: 2 Chain: "f" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 857 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 113} Chain: "h" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 862 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain breaks: 1 Chain: "i" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 827 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "j" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain: "k" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 627 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "m" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 234 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 3, 'TRANS': 24} Chain: "o" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 786 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "p" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1058 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 3 Chain: "q" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1076 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 14, 'TRANS': 113} Chain: "r" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1203 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 16, 'TRANS': 129} Chain breaks: 2 Chain: "s" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3036 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain breaks: 1 Chain: "u" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 927 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 588 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "w" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "x" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1073 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 6, 'TRANS': 141} 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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 132 Unusual residues: {' MG': 68, 'GTP': 2} Classifications: {'undetermined': 70} Link IDs: {None: 69} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 264 SG CYS 0 110 144.643 40.114 126.497 1.00 86.52 S ATOM 286 SG CYS 0 113 148.005 41.403 124.998 1.00 89.86 S ATOM 366 SG CYS 0 123 145.056 43.401 124.559 1.00 81.08 S ATOM 389 SG CYS 0 126 145.289 39.991 122.752 1.00 86.74 S ATOM 2605 SG CYS 4 76 67.417 110.173 168.592 1.00 88.67 S ATOM 2628 SG CYS 4 79 71.134 109.564 167.980 1.00 85.84 S ATOM 2752 SG CYS 4 92 68.574 106.813 167.210 1.00 84.77 S ATOM 55335 SG CYS I 64 93.404 114.220 197.819 1.00 95.40 S ATOM 95418 SG CYS r 70 91.515 110.648 198.949 1.00 87.94 S ATOM 95439 SG CYS r 73 93.780 112.162 199.714 1.00 87.72 S ATOM 95733 SG CYS r 108 90.570 112.540 196.936 1.00 85.42 S Time building chain proxies: 39.59, per 1000 atoms: 0.39 Number of scatterers: 102785 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 317 16.00 P 1451 15.00 Mg 70 11.99 O 22596 8.00 N 18649 7.00 C 59699 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: 37.82 Conformation dependent library (CDL) restraints added in 10.6 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 0 113 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb=" ZN 4 200 " pdb="ZN ZN 4 200 " - pdb=" ND1 HIS 4 98 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 76 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 79 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 92 " pdb=" ZN r 301 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 73 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 70 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 108 " pdb="ZN ZN r 301 " - pdb=" SG CYS I 64 " Number of angles added : 15 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16620 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 304 helices and 81 sheets defined 42.8% alpha, 13.5% beta 378 base pairs and 677 stacking pairs defined. Time for finding SS restraints: 59.55 Creating SS restraints... Processing helix chain '0' and resid 86 through 95 Processing helix chain '0' and resid 96 through 101 removed outlier: 5.409A pdb=" N ILE 0 101 " --> pdb=" O PRO 0 97 " (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: 3.917A 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: 3.565A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG 3 113 " --> pdb=" O ALA 3 109 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 3.881A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.422A 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: 3.832A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 4.818A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 182 removed outlier: 4.574A pdb=" N ASP 3 182 " --> pdb=" O GLN 3 178 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 40 removed outlier: 5.058A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 52 removed outlier: 4.315A pdb=" N GLU 5 51 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE 5 52 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 47 through 52' Processing helix chain '5' and resid 116 through 125 Processing helix chain '5' and resid 133 through 142 removed outlier: 4.201A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP 5 141 " --> pdb=" O LEU 5 137 " (cutoff:3.500A) removed outlier: 4.312A 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: 4.147A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYS 5 194 " --> pdb=" O SER 5 190 " (cutoff:3.500A) Proline residue: 5 196 - end of helix Processing helix chain '5' and resid 241 through 252 removed outlier: 4.041A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 304 removed outlier: 5.007A 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: 4.097A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 49 removed outlier: 5.284A pdb=" N GLU 6 49 " --> pdb=" O LEU 6 45 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 68 removed outlier: 3.838A pdb=" N TYR 6 57 " --> pdb=" O SER 6 53 " (cutoff:3.500A) Proline residue: 6 68 - end of helix Processing helix chain '6' and resid 73 through 79 removed outlier: 3.832A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 99 through 117 removed outlier: 5.267A 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 244 through 249 removed outlier: 5.016A pdb=" N GLY 6 248 " --> pdb=" O ARG 6 244 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN 6 249 " --> pdb=" O VAL 6 245 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 244 through 249' Processing helix chain '6' and resid 292 through 297 Processing helix chain '6' and resid 299 through 308 removed outlier: 3.633A pdb=" N HIS 6 307 " --> pdb=" O PHE 6 303 " (cutoff:3.500A) Processing helix chain '6' and resid 324 through 333 Processing helix chain '6' and resid 363 through 370 removed outlier: 4.424A pdb=" N ASP 6 367 " --> pdb=" O LEU 6 363 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) Processing helix chain '6' and resid 157 through 163 removed outlier: 4.051A pdb=" N PHE 6 162 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 60 Proline residue: 7 60 - end of helix Processing helix chain '7' and resid 87 through 96 Processing helix chain '7' and resid 97 through 103 Processing helix chain '7' and resid 135 through 157 Processing helix chain '7' and resid 186 through 191 removed outlier: 4.830A pdb=" N GLU 7 191 " --> pdb=" O SER 7 187 " (cutoff:3.500A) 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 321 removed outlier: 3.786A pdb=" N ARG 7 321 " --> pdb=" O LEU 7 317 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 4.792A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) Processing helix chain '8' and resid 107 through 154 removed outlier: 3.533A pdb=" N THR 8 111 " --> pdb=" O THR 8 107 " (cutoff:3.500A) Processing helix chain '8' and resid 155 through 164 removed outlier: 5.355A pdb=" N ALA 8 159 " --> pdb=" O PRO 8 155 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU 8 160 " --> pdb=" O LYS 8 156 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS 8 163 " --> pdb=" O ALA 8 159 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '8' and resid 165 through 170 removed outlier: 4.206A pdb=" N LEU 8 168 " --> pdb=" O ASP 8 165 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE 8 169 " --> pdb=" O PRO 8 166 " (cutoff:3.500A) Proline residue: 8 170 - end of helix No H-bonds generated for 'chain '8' and resid 165 through 170' Processing helix chain '9' and resid 27 through 34 Processing helix chain '9' and resid 53 through 58 removed outlier: 3.582A pdb=" N VAL 9 57 " --> pdb=" O ILE 9 53 " (cutoff:3.500A) Proline residue: 9 58 - end of helix No H-bonds generated for 'chain '9' and resid 53 through 58' Processing helix chain '9' and resid 87 through 96 Processing helix chain '9' and resid 97 through 106 removed outlier: 3.563A pdb=" N ASP 9 106 " --> pdb=" O LYS 9 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 57 removed outlier: 4.623A pdb=" N VAL C 54 " --> pdb=" O MET C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 removed outlier: 4.694A pdb=" N SER C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 97 through 106 removed outlier: 3.553A pdb=" N HIS C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.814A pdb=" N LEU C 163 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Proline residue: C 165 - end of helix removed outlier: 3.559A pdb=" N GLY C 170 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 185A through 195 removed outlier: 4.552A pdb=" N LEU C 189 " --> pdb=" O GLY C 185A" (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 222 through 228 removed outlier: 4.680A pdb=" N GLY C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 245 removed outlier: 3.556A pdb=" N TRP C 241 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLU C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 267 Processing helix chain 'C' and resid 274 through 300 removed outlier: 3.643A pdb=" N LYS C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLU C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) Proline residue: C 285 - end of helix removed outlier: 5.633A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 331 removed outlier: 3.872A pdb=" N TYR C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL C 320 " --> pdb=" O GLN C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 349 Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.747A 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: 3.639A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 297 removed outlier: 3.597A pdb=" N LYS D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N SER D 294 " --> pdb=" O PRO D 290 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 3.643A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 3.883A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.297A pdb=" N LYS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 5.974A 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: 4.624A pdb=" N PHE E 198 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 5.231A 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: 4.792A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 6.067A 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: 3.552A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 3.827A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 5.001A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 3.737A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG F 279 " --> pdb=" O TRP F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 89 removed outlier: 3.884A pdb=" N ALA F 88 " --> pdb=" O HIS F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 103 removed outlier: 3.762A pdb=" N MET G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 116 Processing helix chain 'G' and resid 120 through 135 Processing helix chain 'G' and resid 137 through 149 Proline residue: G 149 - end of helix Processing helix chain 'G' and resid 155 through 170 Processing helix chain 'G' and resid 173 through 183 removed outlier: 3.571A pdb=" N ARG G 178 " --> pdb=" O GLY G 174 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL G 179 " --> pdb=" O LYS G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 203 Processing helix chain 'G' and resid 208 through 219 Processing helix chain 'G' and resid 220 through 226 removed outlier: 4.026A pdb=" N ARG G 224 " --> pdb=" O PRO G 220 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP G 226 " --> pdb=" O VAL G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 239 removed outlier: 5.974A pdb=" N GLU G 231 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 252 removed outlier: 4.585A pdb=" N GLU G 252 " --> pdb=" O ILE G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 272 Processing helix chain 'G' and resid 289 through 294 Processing helix chain 'G' and resid 297 through 304 Processing helix chain 'G' and resid 309 through 328 Processing helix chain 'H' and resid 74 through 79 removed outlier: 3.539A pdb=" N ARG H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 74 through 79' Processing helix chain 'H' and resid 85 through 90 removed outlier: 3.980A 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 removed outlier: 3.773A pdb=" N ARG H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 52 Processing helix chain 'I' and resid 61 through 66 Proline residue: I 66 - end of helix Processing helix chain 'I' and resid 77 through 93 removed outlier: 3.746A pdb=" N GLN I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 120 removed outlier: 3.865A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 139 Proline residue: I 133 - end of helix removed outlier: 3.873A pdb=" N GLU I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 148 removed outlier: 4.141A pdb=" N LEU I 144 " --> pdb=" O TYR I 140 " (cutoff:3.500A) Proline residue: I 145 - end of helix removed outlier: 5.413A pdb=" N VAL I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 140 through 148' Processing helix chain 'I' and resid 160 through 172 removed outlier: 3.696A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 3.870A 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 31 through 41 removed outlier: 6.781A pdb=" N LEU J 35 " --> pdb=" O PRO J 31 " (cutoff:3.500A) Proline residue: J 37 - end of helix removed outlier: 3.691A pdb=" N GLN J 41 " --> pdb=" O PRO J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 4.410A pdb=" N LYS J 61 " --> pdb=" O THR J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 96 removed outlier: 3.787A pdb=" N PHE J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 125 removed outlier: 4.056A pdb=" N ILE J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA J 125 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 152 removed outlier: 4.124A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER J 143 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 4.116A 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: 4.935A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU K 125 " --> pdb=" O MET K 121 " (cutoff:3.500A) removed outlier: 5.275A 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: 5.482A 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: 4.677A pdb=" N LYS L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 5.991A 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 142 removed outlier: 5.343A pdb=" N GLN L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 20 removed outlier: 3.552A pdb=" N ASP M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 55 through 60 Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.592A 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: 3.583A pdb=" N GLY M 171 " --> pdb=" O ILE M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 190 Proline residue: M 190 - end of helix Processing helix chain 'M' and resid 191 through 197 removed outlier: 3.620A 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: 3.831A 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: 4.104A pdb=" N ASP M 250 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 5.407A 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: 4.771A pdb=" N ILE N 72 " --> pdb=" O ASN N 68 " (cutoff:3.500A) removed outlier: 4.974A 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 184 removed outlier: 3.787A pdb=" N VAL N 172 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) Proline residue: N 184 - end of helix Processing helix chain 'N' and resid 191 through 209 Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 225 through 231 removed outlier: 4.319A pdb=" N VAL N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 4.422A pdb=" N THR N 236 " --> pdb=" O PRO N 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 40 Processing helix chain 'O' and resid 46 through 66 removed outlier: 4.315A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 81 removed outlier: 4.997A pdb=" N THR O 81 " --> pdb=" O ASP O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 98 removed outlier: 4.430A pdb=" N ILE O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 87 - end of helix removed outlier: 3.907A pdb=" N LEU O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 5.272A 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: 4.974A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU P 116 " --> pdb=" O ILE P 112 " (cutoff:3.500A) removed outlier: 5.852A 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: 4.073A 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: 3.824A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 194 removed outlier: 4.655A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASP Q 192 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 removed outlier: 3.809A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 268 removed outlier: 3.672A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Proline residue: Q 263 - end of helix removed outlier: 4.621A pdb=" N GLU Q 266 " --> pdb=" O GLN Q 262 " (cutoff:3.500A) removed outlier: 4.247A 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: 3.902A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 38 removed outlier: 4.589A pdb=" N ARG R 37 " --> pdb=" O GLY R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 44 removed outlier: 4.213A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 64 removed outlier: 3.831A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS R 61 " --> pdb=" O ARG R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 79 Processing helix chain 'R' and resid 82 through 94 Processing helix chain 'R' and resid 98 through 109 Processing helix chain 'R' and resid 110 through 134 Processing helix chain 'S' and resid 68 through 90 Processing helix chain 'S' and resid 150 through 155 removed outlier: 3.544A pdb=" N VAL S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ARG S 155 " --> pdb=" O LYS S 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 150 through 155' Processing helix chain 'T' and resid 49 through 57 removed outlier: 3.686A pdb=" N LYS T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN T 55 " --> pdb=" O TRP T 51 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE T 57 " --> pdb=" O LYS T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 95 removed outlier: 3.776A pdb=" N TYR T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 110 removed outlier: 3.694A pdb=" N PHE T 108 " --> pdb=" O ALA T 104 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN T 109 " --> pdb=" O GLN T 105 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASP T 110 " --> pdb=" O LEU T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 131 removed outlier: 4.163A pdb=" N LYS T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 206 removed outlier: 3.652A 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: 4.715A pdb=" N LYS V 121 " --> pdb=" O HIS V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 184 Processing helix chain 'V' and resid 193 through 203 Processing helix chain 'W' and resid 110 through 121 removed outlier: 3.522A pdb=" N LEU W 120 " --> pdb=" O LEU W 116 " (cutoff:3.500A) Proline residue: W 121 - end of helix Processing helix chain 'X' and resid 7 through 19 removed outlier: 3.752A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 4.649A 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: 5.388A pdb=" N GLU X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 79 removed outlier: 4.022A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG X 77 " --> pdb=" O PRO X 73 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU X 79 " --> pdb=" O SER X 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 72 through 79' Processing helix chain 'X' and resid 128 through 139 Processing helix chain 'X' and resid 140 through 148 Processing helix chain 'X' and resid 149 through 154 Processing helix chain 'X' and resid 155 through 172 Processing helix chain 'X' and resid 180 through 192 Processing helix chain 'X' and resid 197 through 204 removed outlier: 4.572A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL X 204 " --> pdb=" O GLU X 200 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 220 Processing helix chain 'X' and resid 225 through 244 removed outlier: 3.634A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 69 removed outlier: 4.779A pdb=" N PHE Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASP Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 63 through 69' Processing helix chain 'Y' and resid 70 through 75 removed outlier: 3.568A pdb=" N TRP Y 74 " --> pdb=" O ASP Y 70 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLY Y 75 " --> pdb=" O PRO Y 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 70 through 75' Processing helix chain 'Y' and resid 86 through 94 removed outlier: 3.803A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS Y 93 " --> pdb=" O GLN Y 89 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 removed outlier: 3.586A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 129 through 158 removed outlier: 3.792A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 192 removed outlier: 5.265A pdb=" N LYS Y 192 " --> pdb=" O TRP Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 198 removed outlier: 5.076A pdb=" N ARG Y 198 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 238 removed outlier: 4.458A pdb=" N ASP Y 206 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 48 removed outlier: 4.385A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) removed outlier: 5.714A 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: 4.097A pdb=" N THR a 72 " --> pdb=" O PRO a 68 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LYS a 73 " --> pdb=" O TYR a 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 68 through 73' Processing helix chain 'a' and resid 104 through 117 Processing helix chain 'a' and resid 119 through 124 removed outlier: 4.539A pdb=" N TRP a 123 " --> pdb=" O THR a 119 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR a 124 " --> pdb=" O LYS a 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 119 through 124' Processing helix chain 'a' and resid 127 through 134 Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.586A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 4.726A 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: 3.544A pdb=" N ARG b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.200A 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: 5.493A 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: 3.881A 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: 5.426A pdb=" N ASN c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 107 removed outlier: 3.705A pdb=" N GLN c 107 " --> pdb=" O ALA c 103 " (cutoff:3.500A) Processing helix chain 'c' and resid 122 through 146 Proline residue: c 146 - end of helix Processing helix chain 'c' and resid 149 through 162 Processing helix chain 'c' and resid 163 through 174 Processing helix chain 'c' and resid 187 through 206 Processing helix chain 'c' and resid 207 through 224 removed outlier: 3.728A pdb=" N ILE c 220 " --> pdb=" O ARG c 216 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET c 223 " --> pdb=" O LEU c 219 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR c 224 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 3.974A 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: 4.510A pdb=" N THR d 52 " --> pdb=" O PRO d 48 " (cutoff:3.500A) Processing helix chain 'd' and resid 118 through 130 removed outlier: 4.126A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 155 Proline residue: d 138 - end of helix Processing helix chain 'd' and resid 156 through 164 removed outlier: 3.928A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 173 Proline residue: d 170 - end of helix Processing helix chain 'e' and resid 64 through 82 Processing helix chain 'e' and resid 116 through 132 removed outlier: 3.583A pdb=" N LEU e 120 " --> pdb=" O LEU e 116 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE e 131 " --> pdb=" O LYS e 127 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 143 removed outlier: 4.672A pdb=" N GLU e 142 " --> pdb=" O THR e 138 " (cutoff:3.500A) removed outlier: 3.634A 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 197 removed outlier: 4.093A pdb=" N ALA e 193 " --> pdb=" O GLU e 189 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU e 195 " --> pdb=" O THR e 191 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER e 196 " --> pdb=" O LEU e 192 " (cutoff:3.500A) Processing helix chain 'e' and resid 256 through 264 removed outlier: 6.486A pdb=" N LEU e 260 " --> pdb=" O THR e 256 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY e 261 " --> pdb=" O LYS e 257 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 277 removed outlier: 3.590A pdb=" N GLN e 271 " --> pdb=" O LYS e 267 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL e 272 " --> pdb=" O TYR e 268 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ARG e 273 " --> pdb=" O LEU e 269 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER e 277 " --> pdb=" O ARG e 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 64 removed outlier: 3.581A pdb=" N ILE f 63 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 4.885A 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: 3.520A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 53 removed outlier: 4.387A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 3.950A 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 108 Processing helix chain 'h' and resid 113 through 121 removed outlier: 4.385A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 5.106A 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: 4.668A pdb=" N ASN h 147 " --> pdb=" O LEU h 143 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 54 Processing helix chain 'i' and resid 59 through 64 Processing helix chain 'i' and resid 69 through 75 removed outlier: 4.101A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE i 74 " --> pdb=" O PRO i 70 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG i 75 " --> pdb=" O LYS i 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 69 through 75' Processing helix chain 'i' and resid 86 through 98 Processing helix chain 'i' and resid 103 through 123 Processing helix chain 'j' and resid 24 through 32 removed outlier: 3.824A pdb=" N ARG j 28 " --> pdb=" O GLY j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 60 through 105 Processing helix chain 'j' and resid 41 through 46 removed outlier: 4.238A pdb=" N LEU j 46 " --> pdb=" O GLY j 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 41 through 46' Processing helix chain 'k' and resid 27 through 37 removed outlier: 3.823A pdb=" N ARG k 31 " --> pdb=" O VAL k 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 47 removed outlier: 5.121A pdb=" N THR k 45 " --> pdb=" O LYS k 41 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 96 Processing helix chain 'o' and resid 28 through 51 removed outlier: 4.113A pdb=" N MET o 51 " --> pdb=" O TYR o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 removed outlier: 3.560A pdb=" N ARG o 60 " --> pdb=" O ARG o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 81 removed outlier: 3.929A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 removed outlier: 4.121A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS o 99 " --> pdb=" O LEU o 95 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LYS o 100 " --> pdb=" O ASN o 96 " (cutoff:3.500A) Processing helix chain 'p' and resid 44 through 50 Proline residue: p 50 - end of helix Processing helix chain 'p' and resid 54 through 60 removed outlier: 4.260A pdb=" N ALA p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TRP p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 72 through 77 removed outlier: 4.887A pdb=" N THR p 77 " --> pdb=" O LEU p 73 " (cutoff:3.500A) Processing helix chain 'p' and resid 112 through 123 Processing helix chain 'p' and resid 142 through 163 Processing helix chain 'p' and resid 174 through 190 removed outlier: 3.976A pdb=" N ILE p 178 " --> pdb=" O LYS p 174 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLN p 190 " --> pdb=" O GLU p 186 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 53 removed outlier: 3.897A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 48 through 53' Processing helix chain 'q' and resid 54 through 65 Processing helix chain 'q' and resid 71 through 76 removed outlier: 4.291A pdb=" N LEU q 75 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 4.537A 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: 4.179A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 5.780A 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: 4.096A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASP r 183 " --> pdb=" O PRO r 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 178 through 183' Processing helix chain 's' and resid 55 through 73 Processing helix chain 's' and resid 75 through 85 Processing helix chain 's' and resid 101 through 111 Processing helix chain 's' and resid 140 through 155 Processing helix chain 's' and resid 164 through 193 removed outlier: 5.007A pdb=" N SER s 169 " --> pdb=" O ARG s 165 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLU s 170 " --> pdb=" O TYR s 166 " (cutoff:3.500A) removed outlier: 4.114A 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: 4.194A 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 316 through 344 removed outlier: 4.459A pdb=" N ILE s 320 " --> pdb=" O CYS s 316 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU s 321 " --> pdb=" O ALA s 317 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 387 removed outlier: 5.351A pdb=" N ASN s 386 " --> pdb=" O GLN s 382 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN s 387 " --> pdb=" O ALA s 383 " (cutoff:3.500A) Processing helix chain 's' and resid 414 through 427 removed outlier: 3.917A pdb=" N LEU s 418 " --> pdb=" O ASN s 414 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 105 Processing helix chain 'u' and resid 131 through 149 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 23 removed outlier: 4.004A pdb=" N VAL v 9 " --> pdb=" O SER v 5 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU v 10 " --> pdb=" O ARG v 6 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU v 23 " --> pdb=" O GLN v 19 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 41 Processing helix chain 'v' and resid 47 through 64 removed outlier: 3.628A pdb=" N ARG v 51 " --> pdb=" O ASP v 47 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU v 52 " --> pdb=" O ALA v 48 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG v 53 " --> pdb=" O GLU v 49 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 90 removed outlier: 3.612A pdb=" N TYR w 90 " --> pdb=" O VAL w 86 " (cutoff:3.500A) Processing helix chain 'w' and resid 111 through 126 removed outlier: 4.991A pdb=" N GLU w 125 " --> pdb=" O ALA w 121 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 139 removed outlier: 4.335A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) removed outlier: 4.624A 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 helix chain 'x' and resid 191 through 196 removed outlier: 3.680A pdb=" N PHE x 195 " --> pdb=" O GLY x 191 " (cutoff:3.500A) 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: 6.006A 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: 5.962A 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 66 through 69 removed outlier: 5.989A pdb=" N HIS 4 98 " --> pdb=" O CYS 4 92 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N CYS 4 92 " --> pdb=" O HIS 4 98 " (cutoff:3.500A) removed outlier: 6.809A 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: 5.274A pdb=" N VAL 5 351 " --> pdb=" O ASP 5 348 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '5' and resid 200 through 205 removed outlier: 8.821A pdb=" N ARG 5 200 " --> pdb=" O LYS 5 233 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '5' and resid 206 through 214 removed outlier: 5.901A pdb=" N SER 5 207 " --> pdb=" O GLY 5 226 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLY 5 226 " --> pdb=" O SER 5 207 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU 5 219 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '5' and resid 350 through 353 removed outlier: 8.570A 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: 3.714A pdb=" N ASP 6 183 " --> pdb=" O VAL 6 179 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '6' and resid 190 through 193 removed outlier: 4.634A pdb=" N ARG 6 322 " --> pdb=" O VAL 6 193 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG 6 267 " --> pdb=" O LEU 6 221 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR 6 232 " --> pdb=" O SER 6 220 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '6' and resid 215 through 218 removed outlier: 4.072A pdb=" N TRP 6 235 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '6' and resid 272 through 276 removed outlier: 6.579A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR 6 310 " --> pdb=" O ASP 6 276 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '7' and resid 77 through 82 removed outlier: 4.508A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE 7 127 " --> pdb=" O VAL 7 70 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS 7 126 " --> pdb=" O LEU 7 107 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '7' and resid 164 through 167 removed outlier: 7.003A 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: 4.946A 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: 3.763A pdb=" N ARG 9 49 " --> pdb=" O THR 9 45 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'C' and resid 130 through 133 removed outlier: 5.297A pdb=" N ARG C 130 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU C 154 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'C' and resid 230 through 236 removed outlier: 6.828A pdb=" N GLN C 230 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN C 199 " --> pdb=" O ASP C 175 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASP C 255 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ASP C 250 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY C 303 " --> pdb=" O ARG C 382 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LYS C 379 " --> pdb=" O GLU C 339 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLN C 335 " --> pdb=" O LEU C 383 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C' and resid 361 through 365 Processing sheet with id= 22, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.696A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 217 through 220 removed outlier: 3.766A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 139 through 144 Processing sheet with id= 25, first strand: chain 'E' and resid 98 through 101 Processing sheet with id= 26, first strand: chain 'E' and resid 105 through 111 removed outlier: 3.756A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASN E 281 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLU E 330 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'E' and resid 131 through 134 removed outlier: 3.673A pdb=" N LYS E 131 " --> pdb=" O SER E 146 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR E 191 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'E' and resid 265 through 269 removed outlier: 4.369A pdb=" N GLN E 202 " --> pdb=" O VAL E 273 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'E' and resid 142 through 148 No H-bonds generated for sheet with id= 29 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: 6.969A 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 97 Processing sheet with id= 34, first strand: chain 'I' and resid 94 through 100 removed outlier: 4.229A 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: 3.592A pdb=" N ILE J 70 " --> pdb=" O ILE J 20 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA J 22 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL J 24 " --> pdb=" O LEU J 66 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS J 81 " --> pdb=" O LYS J 69 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU J 71 " --> pdb=" O GLU J 79 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU J 79 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'K' and resid 55 through 60 removed outlier: 5.235A pdb=" N ASP K 22 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'L' and resid 38 through 41 Processing sheet with id= 38, first strand: chain 'L' and resid 72 through 76 Processing sheet with id= 39, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 40, first strand: chain 'M' and resid 273 through 277 Processing sheet with id= 41, first strand: chain 'N' and resid 118 through 123 removed outlier: 5.269A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ALA N 186 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'N' and resid 128 through 132 Processing sheet with id= 43, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.118A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N TYR O 104 " --> pdb=" O LYS O 126 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'P' and resid 80 through 85 removed outlier: 6.491A pdb=" N VAL P 90 " --> pdb=" O THR P 107 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Q' and resid 130 through 135 removed outlier: 6.660A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Q' and resid 139 through 142 removed outlier: 7.880A pdb=" N ALA Q 147 " --> pdb=" O LEU Q 166 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'S' and resid 105 through 109 Processing sheet with id= 48, first strand: chain 'S' and resid 112 through 117 removed outlier: 3.839A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU S 126 " --> pdb=" O VAL S 160 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'S' and resid 162 through 165 Processing sheet with id= 50, first strand: chain 'S' and resid 168 through 175 removed outlier: 4.104A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'T' and resid 71 through 78 removed outlier: 4.860A pdb=" N ALA T 71 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS T 177 " --> pdb=" O ALA T 143 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASN T 139 " --> pdb=" O GLY T 181 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'T' and resid 152 through 159 No H-bonds generated for sheet with id= 52 Processing sheet with id= 53, 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: 6.845A pdb=" N ASP U 38 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'V' and resid 92 through 97 removed outlier: 5.974A pdb=" N ASN V 92 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'V' and resid 132 through 135 removed outlier: 7.344A pdb=" N GLU V 132 " --> pdb=" O THR V 148 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG V 145 " --> pdb=" O ILE V 154 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE V 154 " --> pdb=" O ARG V 145 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG V 152 " --> pdb=" O SER V 147 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'W' and resid 81 through 84 removed outlier: 4.475A pdb=" N CYS W 88 " --> pdb=" O GLY W 84 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'W' and resid 97 through 101 Processing sheet with id= 58, first strand: chain 'X' and resid 49 through 52 removed outlier: 5.177A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'X' and resid 85 through 92 removed outlier: 5.031A pdb=" N LYS X 99 " --> pdb=" O ALA X 92 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 61, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.231A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'a' and resid 44 through 52 removed outlier: 5.347A pdb=" N ASN a 44 " --> pdb=" O VAL a 65 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'b' and resid 61 through 68 removed outlier: 4.204A pdb=" N ALA b 83 " --> pdb=" O TYR b 79 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'c' and resid 254 through 257 Processing sheet with id= 65, first strand: chain 'c' and resid 269 through 275 removed outlier: 3.796A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'd' and resid 212 through 219 removed outlier: 3.975A pdb=" N TYR d 245 " --> pdb=" O ILE d 265 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'e' and resid 53 through 57 removed outlier: 5.443A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU e 159 " --> pdb=" O LEU e 53 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG e 162 " --> pdb=" O HIS e 251 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N HIS e 251 " --> pdb=" O ARG e 162 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'e' and resid 201 through 204 removed outlier: 7.066A pdb=" N GLU e 201 " --> pdb=" O LEU e 239 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'f' and resid 123 through 127 removed outlier: 4.869A pdb=" N GLU f 123 " --> pdb=" O GLN f 158 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR f 125 " --> pdb=" O VAL f 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET f 127 " --> pdb=" O GLU f 154 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU f 154 " --> pdb=" O MET f 127 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS f 94 " --> pdb=" O SER f 185 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER f 185 " --> pdb=" O HIS f 94 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR f 96 " --> pdb=" O ARG f 183 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG f 183 " --> pdb=" O THR f 96 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'g' and resid 95 through 101 removed outlier: 5.470A pdb=" N VAL g 137 " --> pdb=" O LYS g 150 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'k' and resid 51 through 56 Processing sheet with id= 72, first strand: chain 'm' and resid 63 through 67 removed outlier: 5.450A pdb=" N ARG m 73 " --> pdb=" O PRO m 53 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU m 55 " --> pdb=" O ARG m 73 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'p' and resid 78 through 82 Processing sheet with id= 74, first strand: chain 'r' and resid 35 through 41 removed outlier: 4.010A pdb=" N PHE r 35 " --> pdb=" O THR r 54 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 's' and resid 90 through 93 removed outlier: 4.260A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N HIS s 281 " --> pdb=" O TYR s 209 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 's' and resid 112 through 116 removed outlier: 6.380A pdb=" N ASN s 391 " --> pdb=" O ASN s 375 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN s 375 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N CYS s 393 " --> pdb=" O GLN s 373 " (cutoff:3.500A) removed outlier: 7.168A 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: 6.834A pdb=" N CYS s 371 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLN s 397 " --> pdb=" O PHE s 369 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE s 369 " --> pdb=" O GLN s 397 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N LYS s 365 " --> pdb=" O LEU s 401 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR s 297 " --> pdb=" O ILE s 241 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 's' and resid 241 through 244 removed outlier: 6.633A pdb=" N ILE s 241 " --> pdb=" O HIS s 296 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'u' and resid 107 through 114 removed outlier: 3.573A pdb=" N ASP u 108 " --> pdb=" O SER u 128 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP u 122 " --> pdb=" O VAL u 114 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'x' and resid 78 through 86 removed outlier: 4.467A pdb=" N ARG x 148 " --> pdb=" O GLU x 138 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLY x 140 " --> pdb=" O PHE x 146 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE x 146 " --> pdb=" O GLY x 140 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'x' and resid 114 through 118 removed outlier: 6.846A pdb=" N VAL x 114 " --> pdb=" O ALA x 182 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP x 178 " --> pdb=" O VAL x 118 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'x' and resid 170 through 174 removed outlier: 3.972A pdb=" N LEU x 173 " --> pdb=" O THR x 161 " (cutoff:3.500A) 2810 hydrogen bonds defined for protein. 8337 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 923 hydrogen bonds 1584 hydrogen bond angles 0 basepair planarities 378 basepair parallelities 677 stacking parallelities Total time for adding SS restraints: 62.68 Time building geometry restraints manager: 41.19 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: 23614 1.33 - 1.45: 29517 1.45 - 1.57: 51555 1.57 - 1.69: 2880 1.69 - 1.81: 496 Bond restraints: 108062 Sorted by residual: bond pdb=" C2 OMU A3039 " pdb=" N3 OMU A3039 " ideal model delta sigma weight residual 1.489 1.330 0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" N3 OMG A3040 " pdb=" C4 OMG A3040 " ideal model delta sigma weight residual 1.492 1.351 0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" N3 OMG A2815 " pdb=" C4 OMG A2815 " ideal model delta sigma weight residual 1.492 1.351 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" N3 OMU A3039 " pdb=" C4 OMU A3039 " ideal model delta sigma weight residual 1.455 1.331 0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" N1 OMG A3040 " pdb=" C2 OMG A3040 " ideal model delta sigma weight residual 1.462 1.339 0.123 2.00e-02 2.50e+03 3.76e+01 ... (remaining 108057 not shown) Histogram of bond angle deviations from ideal: 98.70 - 106.24: 10747 106.24 - 113.78: 62395 113.78 - 121.32: 53072 121.32 - 128.86: 24690 128.86 - 136.40: 2086 Bond angle restraints: 152990 Sorted by residual: angle pdb=" C1' OMG A3040 " pdb=" N9 OMG A3040 " pdb=" C4 OMG A3040 " ideal model delta sigma weight residual 108.29 127.44 -19.15 3.00e+00 1.11e-01 4.07e+01 angle pdb=" O3' U A3038 " pdb=" P OMU A3039 " pdb=" OP2 OMU A3039 " ideal model delta sigma weight residual 108.00 125.19 -17.19 3.00e+00 1.11e-01 3.28e+01 angle pdb=" C1' OMG A2815 " pdb=" N9 OMG A2815 " pdb=" C4 OMG A2815 " ideal model delta sigma weight residual 108.29 124.77 -16.48 3.00e+00 1.11e-01 3.02e+01 angle pdb=" C1' OMG A3040 " pdb=" N9 OMG A3040 " pdb=" C8 OMG A3040 " ideal model delta sigma weight residual 142.82 126.55 16.27 3.00e+00 1.11e-01 2.94e+01 angle pdb=" C1' OMG A2815 " pdb=" N9 OMG A2815 " pdb=" C8 OMG A2815 " ideal model delta sigma weight residual 142.82 126.64 16.18 3.00e+00 1.11e-01 2.91e+01 ... (remaining 152985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 62711 35.75 - 71.49: 3340 71.49 - 107.24: 489 107.24 - 142.98: 28 142.98 - 178.73: 33 Dihedral angle restraints: 66601 sinusoidal: 40915 harmonic: 25686 Sorted by residual: dihedral pdb=" O4' U A2993 " pdb=" C1' U A2993 " pdb=" N1 U A2993 " pdb=" C2 U A2993 " ideal model delta sinusoidal sigma weight residual -160.00 18.73 -178.73 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A2379 " pdb=" C1' C A2379 " pdb=" N1 C A2379 " pdb=" C2 C A2379 " ideal model delta sinusoidal sigma weight residual 200.00 21.37 178.63 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A2898 " pdb=" C1' U A2898 " pdb=" N1 U A2898 " pdb=" C2 U A2898 " ideal model delta sinusoidal sigma weight residual -160.00 13.19 -173.19 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 66598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 14737 0.043 - 0.085: 2256 0.085 - 0.128: 796 0.128 - 0.170: 71 0.170 - 0.213: 8 Chirality restraints: 17868 Sorted by residual: chirality pdb=" C3* GTP A3369 " pdb=" C2* GTP A3369 " pdb=" C4* GTP A3369 " pdb=" O3* GTP A3369 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1' U A3067 " pdb=" O4' U A3067 " pdb=" C2' U A3067 " pdb=" N1 U A3067 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C3' A A1823 " pdb=" C4' A A1823 " pdb=" O3' A A1823 " pdb=" C2' A A1823 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 17865 not shown) Planarity restraints: 14284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A3040 " -0.072 2.00e-02 2.50e+03 5.61e-01 7.07e+03 pdb=" C4' OMG A3040 " 0.512 2.00e-02 2.50e+03 pdb=" O4' OMG A3040 " 0.889 2.00e-02 2.50e+03 pdb=" C3' OMG A3040 " -0.540 2.00e-02 2.50e+03 pdb=" O3' OMG A3040 " -0.446 2.00e-02 2.50e+03 pdb=" C2' OMG A3040 " -0.326 2.00e-02 2.50e+03 pdb=" O2' OMG A3040 " 0.652 2.00e-02 2.50e+03 pdb=" C1' OMG A3040 " 0.177 2.00e-02 2.50e+03 pdb=" N9 OMG A3040 " -0.846 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMU A3039 " 0.026 2.00e-02 2.50e+03 5.46e-01 6.72e+03 pdb=" C4' OMU A3039 " 0.412 2.00e-02 2.50e+03 pdb=" O4' OMU A3039 " 0.502 2.00e-02 2.50e+03 pdb=" C3' OMU A3039 " -0.599 2.00e-02 2.50e+03 pdb=" O3' OMU A3039 " -0.524 2.00e-02 2.50e+03 pdb=" C2' OMU A3039 " -0.184 2.00e-02 2.50e+03 pdb=" O2' OMU A3039 " 0.928 2.00e-02 2.50e+03 pdb=" C1' OMU A3039 " 0.256 2.00e-02 2.50e+03 pdb=" N1 OMU A3039 " -0.818 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2815 " -0.246 2.00e-02 2.50e+03 4.26e-01 4.08e+03 pdb=" C4' OMG A2815 " 0.387 2.00e-02 2.50e+03 pdb=" O4' OMG A2815 " 0.614 2.00e-02 2.50e+03 pdb=" C3' OMG A2815 " -0.514 2.00e-02 2.50e+03 pdb=" O3' OMG A2815 " -0.066 2.00e-02 2.50e+03 pdb=" C2' OMG A2815 " -0.380 2.00e-02 2.50e+03 pdb=" O2' OMG A2815 " 0.443 2.00e-02 2.50e+03 pdb=" C1' OMG A2815 " 0.333 2.00e-02 2.50e+03 pdb=" N9 OMG A2815 " -0.571 2.00e-02 2.50e+03 ... (remaining 14281 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 445 2.42 - 3.04: 63561 3.04 - 3.66: 175089 3.66 - 4.28: 272533 4.28 - 4.90: 411378 Nonbonded interactions: 923006 Sorted by model distance: nonbonded pdb=" OP1 A A1961 " pdb="MG MG A3313 " model vdw 1.796 2.170 nonbonded pdb=" OP1 A A2430 " pdb="MG MG A3313 " model vdw 1.798 2.170 nonbonded pdb=" OP2 G A2692 " pdb="MG MG A3350 " model vdw 1.835 2.170 nonbonded pdb=" OP2 C A2474 " pdb="MG MG A3326 " model vdw 1.866 2.170 nonbonded pdb=" O4 U A2475 " pdb="MG MG A3326 " model vdw 1.866 2.170 ... (remaining 923001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 12.780 Check model and map are aligned: 1.130 Set scattering table: 0.710 Process input model: 298.240 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 330.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 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 0.159 108062 Z= 0.206 Angle : 0.526 19.148 152990 Z= 0.268 Chirality : 0.037 0.213 17868 Planarity : 0.008 0.561 14284 Dihedral : 19.066 178.731 49981 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.09), residues: 8666 helix: 1.94 (0.10), residues: 3068 sheet: -0.45 (0.15), residues: 1101 loop : 0.42 (0.10), residues: 4497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP s 335 HIS 0.009 0.001 HIS S 76 PHE 0.026 0.001 PHE N 87 TYR 0.017 0.001 TYR 5 176 ARG 0.008 0.000 ARG R 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2698 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2698 time to evaluate : 7.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 132 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8292 (mtpp) REVERT: 0 164 THR cc_start: 0.9227 (m) cc_final: 0.9000 (p) REVERT: 1 20 MET cc_start: 0.8659 (mmm) cc_final: 0.7675 (mmm) REVERT: 1 34 ARG cc_start: 0.9025 (ptt90) cc_final: 0.8087 (ptm-80) REVERT: 1 42 THR cc_start: 0.9282 (m) cc_final: 0.9051 (t) REVERT: 5 296 LYS cc_start: 0.8668 (pttt) cc_final: 0.8420 (pttp) REVERT: 6 214 TRP cc_start: 0.8053 (m100) cc_final: 0.7022 (m100) REVERT: 6 239 ASN cc_start: 0.8983 (m-40) cc_final: 0.8672 (m-40) REVERT: 7 50 LYS cc_start: 0.9319 (mmtm) cc_final: 0.9025 (mmtm) REVERT: 7 72 LYS cc_start: 0.8815 (tttt) cc_final: 0.8482 (tttm) REVERT: 7 198 ASN cc_start: 0.9230 (m110) cc_final: 0.8897 (m110) REVERT: 7 231 GLN cc_start: 0.8073 (pm20) cc_final: 0.7332 (pm20) REVERT: 8 117 LEU cc_start: 0.9167 (tt) cc_final: 0.8907 (tp) REVERT: 8 125 LYS cc_start: 0.5816 (pttp) cc_final: 0.3562 (ptmm) REVERT: C 153 MET cc_start: 0.8259 (mmm) cc_final: 0.7842 (mpt) REVERT: C 225 ILE cc_start: 0.8966 (mm) cc_final: 0.8556 (mp) REVERT: C 255 ASP cc_start: 0.8589 (t0) cc_final: 0.8090 (t70) REVERT: C 308 SER cc_start: 0.8448 (t) cc_final: 0.7510 (p) REVERT: C 309 THR cc_start: 0.7694 (m) cc_final: 0.7360 (p) REVERT: C 376 TYR cc_start: 0.8174 (t80) cc_final: 0.7866 (t80) REVERT: D 161 ASP cc_start: 0.8297 (m-30) cc_final: 0.7820 (m-30) REVERT: D 198 SER cc_start: 0.8947 (t) cc_final: 0.8352 (p) REVERT: D 249 ASN cc_start: 0.8688 (t0) cc_final: 0.8482 (t0) REVERT: E 333 TYR cc_start: 0.9035 (m-80) cc_final: 0.8808 (m-80) REVERT: F 75 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7889 (mt-10) REVERT: F 201 GLN cc_start: 0.8400 (tp40) cc_final: 0.8102 (tp40) REVERT: F 205 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8090 (mt-10) REVERT: G 160 ARG cc_start: 0.8949 (mtt180) cc_final: 0.8618 (mtt90) REVERT: G 165 TYR cc_start: 0.8655 (t80) cc_final: 0.8080 (t80) REVERT: G 232 TYR cc_start: 0.8817 (t80) cc_final: 0.8251 (t80) REVERT: G 236 TYR cc_start: 0.8840 (t80) cc_final: 0.8267 (t80) REVERT: G 256 TYR cc_start: 0.8577 (m-80) cc_final: 0.8361 (m-80) REVERT: G 308 THR cc_start: 0.7375 (p) cc_final: 0.7087 (p) REVERT: G 320 LEU cc_start: 0.9614 (tp) cc_final: 0.9330 (tp) REVERT: H 122 ARG cc_start: 0.8328 (mtm110) cc_final: 0.8106 (mtp-110) REVERT: I 99 CYS cc_start: 0.8210 (m) cc_final: 0.7437 (t) REVERT: I 105 SER cc_start: 0.8561 (m) cc_final: 0.8117 (p) REVERT: I 108 ASP cc_start: 0.8464 (m-30) cc_final: 0.8250 (m-30) REVERT: I 144 LEU cc_start: 0.9153 (mm) cc_final: 0.8664 (mm) REVERT: J 35 LEU cc_start: 0.9016 (mt) cc_final: 0.8793 (OUTLIER) REVERT: J 52 GLU cc_start: 0.9055 (tp30) cc_final: 0.8699 (tp30) REVERT: J 54 ASN cc_start: 0.8837 (m-40) cc_final: 0.8378 (m-40) REVERT: J 113 THR cc_start: 0.9084 (p) cc_final: 0.8831 (t) REVERT: J 115 LYS cc_start: 0.7688 (mtpt) cc_final: 0.7480 (tppt) REVERT: K 98 ARG cc_start: 0.8561 (ttm170) cc_final: 0.8349 (ttm170) REVERT: K 135 GLU cc_start: 0.7642 (tp30) cc_final: 0.7400 (tp30) REVERT: K 160 GLN cc_start: 0.8112 (tp40) cc_final: 0.7670 (tp-100) REVERT: K 164 ASP cc_start: 0.8562 (m-30) cc_final: 0.7818 (m-30) REVERT: L 81 LYS cc_start: 0.9181 (mtmt) cc_final: 0.8936 (mttp) REVERT: L 135 SER cc_start: 0.9088 (m) cc_final: 0.8522 (m) REVERT: M 56 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7801 (mt-10) REVERT: M 208 GLU cc_start: 0.7618 (tt0) cc_final: 0.7249 (tt0) REVERT: N 139 ARG cc_start: 0.7249 (mtt180) cc_final: 0.6605 (mtt180) REVERT: N 148 ASP cc_start: 0.8210 (t0) cc_final: 0.7907 (t0) REVERT: N 149 HIS cc_start: 0.6508 (m-70) cc_final: 0.5918 (m170) REVERT: N 171 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6894 (tp30) REVERT: O 40 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8051 (mt-10) REVERT: P 57 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7923 (tm-30) REVERT: P 58 LEU cc_start: 0.9216 (mt) cc_final: 0.8875 (mt) REVERT: P 81 LEU cc_start: 0.9300 (tp) cc_final: 0.9033 (tm) REVERT: P 106 SER cc_start: 0.8892 (p) cc_final: 0.8592 (p) REVERT: P 132 LEU cc_start: 0.9492 (tp) cc_final: 0.8944 (tm) REVERT: P 136 CYS cc_start: 0.8914 (m) cc_final: 0.8548 (m) REVERT: P 147 GLN cc_start: 0.8830 (mt0) cc_final: 0.8520 (mt0) REVERT: P 173 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7765 (mmt-90) REVERT: Q 98 ASP cc_start: 0.8113 (m-30) cc_final: 0.7840 (m-30) REVERT: Q 224 MET cc_start: 0.8837 (mmm) cc_final: 0.8350 (mmp) REVERT: Q 239 ASN cc_start: 0.9028 (t0) cc_final: 0.8558 (t0) REVERT: S 57 SER cc_start: 0.9027 (p) cc_final: 0.8422 (p) REVERT: S 190 GLN cc_start: 0.8884 (mt0) cc_final: 0.8649 (mt0) REVERT: T 59 TYR cc_start: 0.9046 (m-80) cc_final: 0.8842 (m-80) REVERT: T 123 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7536 (mt-10) REVERT: U 56 TYR cc_start: 0.9245 (t80) cc_final: 0.8942 (t80) REVERT: U 128 SER cc_start: 0.8932 (p) cc_final: 0.8254 (p) REVERT: V 73 GLN cc_start: 0.8247 (mt0) cc_final: 0.7901 (mt0) REVERT: V 82 GLN cc_start: 0.9146 (mp10) cc_final: 0.8557 (mp10) REVERT: V 104 TYR cc_start: 0.6971 (t80) cc_final: 0.5927 (t80) REVERT: V 117 HIS cc_start: 0.7866 (p90) cc_final: 0.7437 (p90) REVERT: V 118 ARG cc_start: 0.8510 (mmt-90) cc_final: 0.8294 (mmm-85) REVERT: V 121 LYS cc_start: 0.7842 (mtpt) cc_final: 0.7544 (ttmm) REVERT: V 122 LEU cc_start: 0.8061 (mt) cc_final: 0.7711 (mt) REVERT: V 131 THR cc_start: 0.8780 (p) cc_final: 0.8272 (p) REVERT: X 39 THR cc_start: 0.9428 (m) cc_final: 0.9195 (m) REVERT: X 98 SER cc_start: 0.8855 (t) cc_final: 0.8335 (p) REVERT: X 152 ASP cc_start: 0.8560 (m-30) cc_final: 0.8266 (m-30) REVERT: X 237 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7829 (tm-30) REVERT: Y 70 ASP cc_start: 0.8796 (t70) cc_final: 0.8504 (t0) REVERT: Y 120 LYS cc_start: 0.9305 (mttt) cc_final: 0.9069 (mtmt) REVERT: Z 84 ASP cc_start: 0.8121 (m-30) cc_final: 0.7790 (m-30) REVERT: b 49 ARG cc_start: 0.8083 (mtp180) cc_final: 0.7659 (mtm110) REVERT: b 50 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7968 (mp0) REVERT: c 67 ASP cc_start: 0.8484 (t0) cc_final: 0.8005 (t0) REVERT: d 49 LYS cc_start: 0.8304 (mtpp) cc_final: 0.7608 (mtmt) REVERT: d 51 LYS cc_start: 0.8971 (mttt) cc_final: 0.8737 (mttt) REVERT: d 53 GLU cc_start: 0.7706 (mp0) cc_final: 0.7235 (mp0) REVERT: d 137 PHE cc_start: 0.9062 (t80) cc_final: 0.8790 (t80) REVERT: d 151 CYS cc_start: 0.7797 (m) cc_final: 0.7050 (m) REVERT: d 174 TRP cc_start: 0.7991 (t-100) cc_final: 0.7695 (t60) REVERT: d 196 GLN cc_start: 0.8185 (pt0) cc_final: 0.7777 (pp30) REVERT: d 226 ASP cc_start: 0.7620 (m-30) cc_final: 0.7234 (m-30) REVERT: d 242 VAL cc_start: 0.8879 (t) cc_final: 0.8417 (m) REVERT: d 274 GLN cc_start: 0.9139 (tt0) cc_final: 0.8885 (tt0) REVERT: e 54 GLN cc_start: 0.5283 (mm110) cc_final: 0.4949 (mp10) REVERT: e 61 LYS cc_start: 0.7106 (mttm) cc_final: 0.6769 (pmtt) REVERT: e 120 LEU cc_start: 0.7855 (mt) cc_final: 0.7292 (tm) REVERT: e 155 ARG cc_start: 0.8924 (ptp-110) cc_final: 0.8501 (mtp-110) REVERT: e 168 GLN cc_start: -0.2285 (mt0) cc_final: -0.3365 (tt0) REVERT: e 190 ARG cc_start: 0.8437 (ttp80) cc_final: 0.7963 (ttp-170) REVERT: f 109 TYR cc_start: 0.8243 (t80) cc_final: 0.7951 (t80) REVERT: f 113 LEU cc_start: 0.9051 (mm) cc_final: 0.8567 (tt) REVERT: g 98 LYS cc_start: 0.8414 (mtmm) cc_final: 0.7971 (mtpp) REVERT: h 73 TYR cc_start: 0.9195 (m-80) cc_final: 0.8922 (m-80) REVERT: h 76 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8547 (tm-30) REVERT: h 86 TRP cc_start: 0.8556 (p-90) cc_final: 0.8237 (p-90) REVERT: h 93 ASP cc_start: 0.8071 (t0) cc_final: 0.7831 (t0) REVERT: h 99 ASN cc_start: 0.9456 (m-40) cc_final: 0.9086 (m110) REVERT: h 103 HIS cc_start: 0.8714 (m-70) cc_final: 0.8286 (m170) REVERT: h 135 GLN cc_start: 0.7787 (pt0) cc_final: 0.7067 (pt0) REVERT: j 55 ARG cc_start: 0.8873 (mtp180) cc_final: 0.8410 (mtp180) REVERT: j 81 SER cc_start: 0.8883 (m) cc_final: 0.8634 (p) REVERT: k 19 GLN cc_start: 0.7629 (tm-30) cc_final: 0.6726 (tm-30) REVERT: k 43 ARG cc_start: 0.8772 (mtm180) cc_final: 0.8542 (mtm180) REVERT: k 74 LEU cc_start: 0.8188 (tp) cc_final: 0.7894 (tp) REVERT: k 84 LEU cc_start: 0.9078 (mm) cc_final: 0.8815 (tm) REVERT: k 90 PHE cc_start: 0.8984 (t80) cc_final: 0.8661 (t80) REVERT: m 77 MET cc_start: 0.5440 (tpt) cc_final: 0.5216 (mmp) REVERT: o 29 LEU cc_start: 0.9081 (tp) cc_final: 0.8855 (tp) REVERT: p 149 ASP cc_start: 0.8343 (t0) cc_final: 0.8100 (t70) REVERT: p 152 GLN cc_start: 0.9140 (tp40) cc_final: 0.8174 (tp-100) REVERT: p 156 ASP cc_start: 0.8593 (m-30) cc_final: 0.8014 (m-30) REVERT: p 179 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.7580 (mtm-85) REVERT: p 181 GLU cc_start: 0.8366 (pp20) cc_final: 0.8161 (pp20) REVERT: p 183 MET cc_start: 0.8550 (ttt) cc_final: 0.8219 (tmm) REVERT: q 93 TYR cc_start: 0.8693 (m-80) cc_final: 0.8424 (m-80) REVERT: q 106 LYS cc_start: 0.9037 (mttt) cc_final: 0.8791 (mttt) REVERT: q 112 GLN cc_start: 0.8645 (tp-100) cc_final: 0.8226 (tm-30) REVERT: q 116 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8022 (mm-30) REVERT: q 120 HIS cc_start: 0.8940 (t-90) cc_final: 0.8727 (t-170) REVERT: q 128 MET cc_start: 0.9053 (tpt) cc_final: 0.8797 (tpp) REVERT: q 131 MET cc_start: 0.8633 (mtp) cc_final: 0.8359 (mtm) REVERT: r 39 VAL cc_start: 0.8124 (t) cc_final: 0.7918 (m) REVERT: r 111 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7825 (mp0) REVERT: r 116 GLU cc_start: 0.8017 (tt0) cc_final: 0.7717 (tt0) REVERT: r 130 ASN cc_start: 0.8636 (m-40) cc_final: 0.7907 (m110) REVERT: u 93 ASP cc_start: 0.8561 (p0) cc_final: 0.8267 (p0) REVERT: u 134 HIS cc_start: 0.8447 (t-90) cc_final: 0.7188 (t-170) REVERT: u 138 MET cc_start: 0.8773 (ptm) cc_final: 0.8376 (ptm) REVERT: u 160 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7620 (mt-10) REVERT: u 165 ASP cc_start: 0.8913 (p0) cc_final: 0.8650 (p0) REVERT: v 6 ARG cc_start: 0.7033 (tpt90) cc_final: 0.6772 (mmm160) REVERT: v 17 LEU cc_start: 0.9204 (mm) cc_final: 0.8905 (mm) REVERT: v 35 ILE cc_start: 0.9520 (mm) cc_final: 0.9317 (pp) REVERT: v 51 ARG cc_start: 0.7742 (mmt90) cc_final: 0.7441 (mmp-170) REVERT: w 111 ASP cc_start: 0.8236 (t0) cc_final: 0.7980 (t0) REVERT: w 120 MET cc_start: 0.7779 (mmp) cc_final: 0.6761 (mmm) REVERT: w 145 VAL cc_start: 0.8460 (t) cc_final: 0.8256 (p) REVERT: x 81 CYS cc_start: 0.8312 (t) cc_final: 0.7908 (t) REVERT: x 90 SER cc_start: 0.9059 (t) cc_final: 0.8783 (m) REVERT: x 97 ARG cc_start: 0.8856 (mtt180) cc_final: 0.8613 (mtt180) REVERT: x 104 ASP cc_start: 0.8009 (m-30) cc_final: 0.7778 (m-30) REVERT: x 135 PHE cc_start: 0.9102 (m-80) cc_final: 0.8715 (m-80) REVERT: x 161 THR cc_start: 0.8875 (m) cc_final: 0.8245 (p) outliers start: 0 outliers final: 15 residues processed: 2698 average time/residue: 1.8876 time to fit residues: 6895.2793 Evaluate side-chains 1760 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1746 time to evaluate : 7.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 148 GLU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain N residue 114 ASP Chi-restraints excluded: chain O residue 157 ARG Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 274 ASP Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 227 GLU Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 237 ASP Chi-restraints excluded: chain i residue 74 ILE Chi-restraints excluded: chain j residue 29 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 841 optimal weight: 7.9990 chunk 755 optimal weight: 10.0000 chunk 419 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 chunk 509 optimal weight: 7.9990 chunk 403 optimal weight: 5.9990 chunk 781 optimal weight: 7.9990 chunk 302 optimal weight: 9.9990 chunk 475 optimal weight: 5.9990 chunk 581 optimal weight: 9.9990 chunk 905 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 15 ASN 1 31 ASN 3 154 GLN 3 170 ASN 3 178 GLN 3 185 ASN 4 102 GLN 5 102 GLN 5 165 GLN 6 63 GLN 6 354 GLN ** 7 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN C 314 HIS D 128 GLN D 195 ASN D 235 GLN E 72 GLN E 281 ASN E 336 ASN E 339 GLN F 138 HIS F 184 GLN G 123 GLN ** G 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 GLN I 43 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN I 141 GLN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN ** L 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 ASN L 142 GLN ** M 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 289 ASN N 68 ASN ** N 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 HIS N 149 HIS N 202 GLN O 100 GLN P 176 GLN Q 107 HIS R 89 ASN R 147 GLN T 109 ASN T 133 ASN ** T 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 23 ASN W 70 GLN W 86 ASN X 15 GLN X 53 ASN X 215 GLN Y 92 ASN Y 95 ASN Y 183 GLN Y 225 ASN Z 136 ASN b 24 GLN b 58 ASN b 102 GLN d 47 GLN d 149 HIS d 161 HIS ** g 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN h 147 ASN j 89 GLN k 19 GLN ** k 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 33 GLN q 130 GLN r 79 HIS s 281 HIS s 408 ASN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 ASN x 110 ASN x 199 ASN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 108062 Z= 0.448 Angle : 0.701 18.649 152990 Z= 0.358 Chirality : 0.044 0.262 17868 Planarity : 0.005 0.141 14284 Dihedral : 20.895 179.523 31430 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.45 % Favored : 96.54 % Rotamer: Outliers : 3.74 % Allowed : 15.69 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.09), residues: 8666 helix: 1.59 (0.09), residues: 3067 sheet: -0.37 (0.15), residues: 1121 loop : 0.36 (0.10), residues: 4478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP s 335 HIS 0.016 0.001 HIS u 156 PHE 0.036 0.002 PHE G 316 TYR 0.029 0.002 TYR d 88 ARG 0.012 0.001 ARG h 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2093 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1802 time to evaluate : 7.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 107 ILE cc_start: 0.9631 (OUTLIER) cc_final: 0.9377 (mt) REVERT: 0 128 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7613 (tm-30) REVERT: 0 132 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8525 (mtpp) REVERT: 1 20 MET cc_start: 0.8823 (mmm) cc_final: 0.7728 (mmm) REVERT: 1 38 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7822 (mmm160) REVERT: 5 295 ASP cc_start: 0.8059 (t0) cc_final: 0.7619 (t0) REVERT: 5 313 MET cc_start: 0.9190 (mtm) cc_final: 0.8967 (mtm) REVERT: 6 107 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9041 (tmmt) REVERT: 6 239 ASN cc_start: 0.8912 (m-40) cc_final: 0.8629 (m-40) REVERT: 6 337 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7213 (ppp) REVERT: 7 50 LYS cc_start: 0.9359 (mmtm) cc_final: 0.9050 (mmtm) REVERT: 7 165 ASN cc_start: 0.8588 (t0) cc_final: 0.8019 (t0) REVERT: 7 198 ASN cc_start: 0.9197 (m110) cc_final: 0.8832 (m110) REVERT: 8 125 LYS cc_start: 0.5920 (pttp) cc_final: 0.4774 (ptmm) REVERT: 9 90 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8008 (tm-30) REVERT: 9 94 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7418 (mt-10) REVERT: 9 120 GLU cc_start: 0.8474 (pm20) cc_final: 0.8241 (pm20) REVERT: C 158 MET cc_start: 0.8156 (ppp) cc_final: 0.7680 (ppp) REVERT: C 163 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8982 (mp) REVERT: C 198 ARG cc_start: 0.8483 (mmm-85) cc_final: 0.8256 (mmm-85) REVERT: C 255 ASP cc_start: 0.8609 (t0) cc_final: 0.7875 (t70) REVERT: C 308 SER cc_start: 0.8356 (t) cc_final: 0.7410 (p) REVERT: D 161 ASP cc_start: 0.8340 (m-30) cc_final: 0.7934 (m-30) REVERT: D 199 GLU cc_start: 0.8268 (mp0) cc_final: 0.8058 (mp0) REVERT: F 201 GLN cc_start: 0.8509 (tp40) cc_final: 0.8145 (tp40) REVERT: F 226 MET cc_start: 0.7959 (mtm) cc_final: 0.7662 (mtm) REVERT: G 126 ASP cc_start: 0.8443 (t0) cc_final: 0.7905 (t0) REVERT: G 146 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8064 (pptt) REVERT: G 160 ARG cc_start: 0.9040 (mtt180) cc_final: 0.8581 (mtm-85) REVERT: G 232 TYR cc_start: 0.8878 (t80) cc_final: 0.8307 (t80) REVERT: H 86 THR cc_start: 0.9364 (m) cc_final: 0.9152 (p) REVERT: H 143 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8467 (tm-30) REVERT: I 90 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.8117 (m-10) REVERT: I 105 SER cc_start: 0.8932 (m) cc_final: 0.8316 (p) REVERT: I 108 ASP cc_start: 0.8793 (m-30) cc_final: 0.8305 (m-30) REVERT: I 144 LEU cc_start: 0.9027 (mm) cc_final: 0.8673 (mm) REVERT: J 52 GLU cc_start: 0.8944 (tp30) cc_final: 0.8716 (tp30) REVERT: J 134 ASP cc_start: 0.7751 (t70) cc_final: 0.7534 (t0) REVERT: J 154 ARG cc_start: 0.8282 (ptp90) cc_final: 0.7831 (ptp90) REVERT: K 98 ARG cc_start: 0.8623 (ttm170) cc_final: 0.8300 (ttm170) REVERT: K 160 GLN cc_start: 0.8085 (tp40) cc_final: 0.7772 (tp-100) REVERT: K 164 ASP cc_start: 0.8523 (m-30) cc_final: 0.7524 (m-30) REVERT: L 108 ILE cc_start: 0.9432 (pt) cc_final: 0.9220 (pp) REVERT: L 135 SER cc_start: 0.9201 (m) cc_final: 0.8915 (m) REVERT: M 280 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8971 (mmmm) REVERT: N 65 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8033 (pt0) REVERT: N 68 ASN cc_start: 0.8193 (p0) cc_final: 0.7927 (p0) REVERT: N 86 ASN cc_start: 0.8923 (m-40) cc_final: 0.8708 (m-40) REVERT: N 149 HIS cc_start: 0.6456 (m90) cc_final: 0.5871 (m170) REVERT: N 197 LYS cc_start: 0.9229 (tptm) cc_final: 0.9011 (tptm) REVERT: N 200 LYS cc_start: 0.9127 (mptt) cc_final: 0.8822 (mmtm) REVERT: O 40 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8190 (mt-10) REVERT: O 50 ASP cc_start: 0.8288 (t70) cc_final: 0.8065 (t70) REVERT: P 57 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7894 (tm-30) REVERT: P 58 LEU cc_start: 0.9290 (mt) cc_final: 0.8987 (mt) REVERT: P 81 LEU cc_start: 0.9312 (tp) cc_final: 0.8987 (tm) REVERT: P 132 LEU cc_start: 0.9551 (tp) cc_final: 0.9078 (tp) REVERT: P 138 GLU cc_start: 0.8510 (pt0) cc_final: 0.8059 (pt0) REVERT: P 147 GLN cc_start: 0.8864 (mt0) cc_final: 0.8559 (mt0) REVERT: Q 98 ASP cc_start: 0.8070 (m-30) cc_final: 0.7824 (m-30) REVERT: Q 185 ASP cc_start: 0.8667 (p0) cc_final: 0.8452 (p0) REVERT: Q 239 ASN cc_start: 0.9042 (t0) cc_final: 0.8516 (t0) REVERT: Q 270 MET cc_start: 0.8915 (mmm) cc_final: 0.8705 (mmm) REVERT: R 109 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8027 (mm-30) REVERT: S 68 ASP cc_start: 0.7855 (p0) cc_final: 0.6967 (p0) REVERT: T 119 GLU cc_start: 0.7911 (tp30) cc_final: 0.7392 (tm-30) REVERT: T 123 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7355 (mt-10) REVERT: U 23 ASN cc_start: 0.8509 (t160) cc_final: 0.8257 (t0) REVERT: U 56 TYR cc_start: 0.9335 (t80) cc_final: 0.8992 (t80) REVERT: U 103 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7989 (mp10) REVERT: U 128 SER cc_start: 0.8813 (p) cc_final: 0.8380 (p) REVERT: V 82 GLN cc_start: 0.9210 (mp10) cc_final: 0.8599 (mp10) REVERT: V 104 TYR cc_start: 0.6451 (t80) cc_final: 0.6113 (t80) REVERT: V 117 HIS cc_start: 0.8219 (p90) cc_final: 0.7605 (p90) REVERT: V 118 ARG cc_start: 0.8515 (mmt-90) cc_final: 0.8236 (mmm-85) REVERT: V 131 THR cc_start: 0.8609 (p) cc_final: 0.8325 (p) REVERT: X 36 ARG cc_start: 0.7592 (ptm-80) cc_final: 0.7161 (ptm-80) REVERT: X 98 SER cc_start: 0.9003 (t) cc_final: 0.8521 (p) REVERT: X 152 ASP cc_start: 0.8585 (m-30) cc_final: 0.8322 (m-30) REVERT: Y 120 LYS cc_start: 0.9252 (mttt) cc_final: 0.9048 (mtmt) REVERT: Y 150 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: Z 61 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8027 (mm110) REVERT: Z 84 ASP cc_start: 0.8164 (m-30) cc_final: 0.7825 (m-30) REVERT: a 56 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8277 (mtp180) REVERT: b 45 GLU cc_start: 0.8242 (tp30) cc_final: 0.7882 (tp30) REVERT: b 49 ARG cc_start: 0.8174 (mtp180) cc_final: 0.7740 (mtm-85) REVERT: c 67 ASP cc_start: 0.8647 (t0) cc_final: 0.8011 (t0) REVERT: c 277 ASP cc_start: 0.7828 (p0) cc_final: 0.7592 (p0) REVERT: d 151 CYS cc_start: 0.7822 (m) cc_final: 0.7153 (m) REVERT: d 242 VAL cc_start: 0.9170 (t) cc_final: 0.8967 (m) REVERT: e 120 LEU cc_start: 0.7580 (mt) cc_final: 0.7370 (tm) REVERT: e 190 ARG cc_start: 0.8413 (ttp80) cc_final: 0.7939 (ttp-170) REVERT: f 100 MET cc_start: 0.8634 (ttm) cc_final: 0.8300 (mmm) REVERT: f 109 TYR cc_start: 0.8441 (t80) cc_final: 0.7696 (t80) REVERT: f 113 LEU cc_start: 0.9110 (mm) cc_final: 0.8688 (tt) REVERT: f 117 LEU cc_start: 0.9047 (mt) cc_final: 0.8800 (mp) REVERT: g 46 GLN cc_start: 0.8566 (pm20) cc_final: 0.8286 (pm20) REVERT: g 98 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8179 (mtpp) REVERT: h 56 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.8071 (mtm-85) REVERT: h 73 TYR cc_start: 0.9172 (m-80) cc_final: 0.8760 (m-80) REVERT: h 76 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8595 (tm-30) REVERT: h 99 ASN cc_start: 0.9459 (m-40) cc_final: 0.9176 (m110) REVERT: h 103 HIS cc_start: 0.8778 (m-70) cc_final: 0.8403 (m170) REVERT: h 116 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7748 (mtp180) REVERT: h 153 LYS cc_start: 0.9270 (mmtm) cc_final: 0.8994 (mmmt) REVERT: k 17 ARG cc_start: 0.8803 (ttp80) cc_final: 0.8593 (ttp80) REVERT: k 43 ARG cc_start: 0.8644 (mtm180) cc_final: 0.8095 (mtm180) REVERT: k 76 MET cc_start: 0.8134 (tpp) cc_final: 0.7818 (mmm) REVERT: k 84 LEU cc_start: 0.9123 (mm) cc_final: 0.8769 (tt) REVERT: k 90 PHE cc_start: 0.9083 (t80) cc_final: 0.8677 (t80) REVERT: m 77 MET cc_start: 0.5298 (tpt) cc_final: 0.5013 (mmp) REVERT: o 91 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: p 118 LYS cc_start: 0.8921 (mtmp) cc_final: 0.8665 (mtmp) REVERT: p 149 ASP cc_start: 0.8309 (t0) cc_final: 0.8058 (t70) REVERT: p 152 GLN cc_start: 0.9148 (tp40) cc_final: 0.8389 (tp40) REVERT: p 156 ASP cc_start: 0.8583 (m-30) cc_final: 0.8117 (m-30) REVERT: p 179 ARG cc_start: 0.8048 (ttp-110) cc_final: 0.7750 (mtm110) REVERT: p 183 MET cc_start: 0.8542 (ttt) cc_final: 0.8211 (tmm) REVERT: q 83 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7990 (ttp-170) REVERT: q 99 MET cc_start: 0.8773 (mtt) cc_final: 0.7851 (mtm) REVERT: q 103 LEU cc_start: 0.9355 (mt) cc_final: 0.9116 (mt) REVERT: q 112 GLN cc_start: 0.8781 (tp-100) cc_final: 0.8364 (tm-30) REVERT: q 116 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8173 (mm-30) REVERT: q 127 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8638 (mtmm) REVERT: q 128 MET cc_start: 0.8977 (tpt) cc_final: 0.8719 (tpp) REVERT: q 134 ASN cc_start: 0.9060 (m110) cc_final: 0.8770 (m-40) REVERT: r 113 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7787 (mpt-90) REVERT: r 117 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7842 (mm-30) REVERT: u 101 LEU cc_start: 0.9218 (mt) cc_final: 0.8910 (mp) REVERT: u 158 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8443 (ttpt) REVERT: u 160 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7848 (mt-10) REVERT: u 188 TYR cc_start: 0.8863 (m-80) cc_final: 0.8558 (m-80) REVERT: v 12 LEU cc_start: 0.9012 (tm) cc_final: 0.8652 (tp) REVERT: v 13 TYR cc_start: 0.8592 (t80) cc_final: 0.8378 (t80) REVERT: v 27 ASP cc_start: 0.7924 (t0) cc_final: 0.7721 (t0) REVERT: v 38 GLU cc_start: 0.7513 (tt0) cc_final: 0.7280 (tt0) REVERT: v 56 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8403 (tp30) REVERT: w 145 VAL cc_start: 0.8455 (t) cc_final: 0.8204 (p) REVERT: x 81 CYS cc_start: 0.8506 (t) cc_final: 0.8132 (t) REVERT: x 90 SER cc_start: 0.9107 (t) cc_final: 0.8792 (m) REVERT: x 104 ASP cc_start: 0.8360 (m-30) cc_final: 0.8156 (m-30) REVERT: x 161 THR cc_start: 0.8974 (m) cc_final: 0.8574 (p) outliers start: 291 outliers final: 127 residues processed: 1931 average time/residue: 1.7417 time to fit residues: 4661.1816 Evaluate side-chains 1752 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1606 time to evaluate : 7.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 107 ILE Chi-restraints excluded: chain 1 residue 22 SER Chi-restraints excluded: chain 1 residue 29 CYS Chi-restraints excluded: chain 1 residue 40 LYS Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 4 residue 70 THR Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 6 residue 107 LYS Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 337 MET Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 52 GLN Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 339 GLN Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 324 GLU Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 147 SER Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain M residue 14 ASP Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 157 ARG Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 156 ASP Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 202 VAL Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 276 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 111 GLU Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain U residue 103 GLN Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 86 ASN Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 116 LEU Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 150 GLU Chi-restraints excluded: chain Y residue 177 ILE Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 137 THR Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 136 LYS Chi-restraints excluded: chain c residue 136 CYS Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain d residue 86 ASP Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain e residue 55 ARG Chi-restraints excluded: chain e residue 192 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain g residue 157 LEU Chi-restraints excluded: chain h residue 85 ASN Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 88 THR Chi-restraints excluded: chain k residue 94 ILE Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain r residue 117 GLU Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 254 ASP Chi-restraints excluded: chain s residue 266 CYS Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 158 LYS Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain v residue 9 VAL Chi-restraints excluded: chain v residue 29 ASP Chi-restraints excluded: chain v residue 56 GLU Chi-restraints excluded: chain x residue 124 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 503 optimal weight: 9.9990 chunk 280 optimal weight: 8.9990 chunk 753 optimal weight: 30.0000 chunk 616 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 chunk 907 optimal weight: 9.9990 chunk 979 optimal weight: 30.0000 chunk 807 optimal weight: 50.0000 chunk 899 optimal weight: 0.9980 chunk 309 optimal weight: 1.9990 chunk 727 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 15 ASN 3 154 GLN 3 185 ASN 5 191 GLN ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN F 74 GLN ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 GLN ** G 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 ASN I 43 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN M 289 ASN ** N 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 HIS N 202 GLN P 176 GLN R 89 ASN R 147 GLN T 109 ASN T 133 ASN V 119 GLN W 70 GLN X 53 ASN Y 92 ASN Z 136 ASN b 120 HIS d 149 HIS d 161 HIS d 196 GLN ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 271 GLN f 61 HIS ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 147 ASN k 19 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 182 ASN r 130 ASN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 ASN x 93 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 108062 Z= 0.339 Angle : 0.653 14.873 152990 Z= 0.335 Chirality : 0.041 0.247 17868 Planarity : 0.005 0.124 14284 Dihedral : 20.839 179.914 31406 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.36 % Favored : 96.63 % Rotamer: Outliers : 3.71 % Allowed : 18.23 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.09), residues: 8666 helix: 1.51 (0.09), residues: 3073 sheet: -0.36 (0.15), residues: 1114 loop : 0.33 (0.10), residues: 4479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Z 81 HIS 0.010 0.001 HIS C 218 PHE 0.026 0.002 PHE I 90 TYR 0.025 0.002 TYR C 376 ARG 0.012 0.001 ARG h 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1972 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1683 time to evaluate : 7.133 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: 0 107 ILE cc_start: 0.9619 (OUTLIER) cc_final: 0.9357 (mt) REVERT: 0 128 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7478 (tm-30) REVERT: 0 132 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8453 (mtpp) REVERT: 0 144 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8316 (tm-30) REVERT: 1 20 MET cc_start: 0.8772 (mmm) cc_final: 0.7586 (mmm) REVERT: 1 38 ARG cc_start: 0.8305 (mmm160) cc_final: 0.7677 (mmm160) REVERT: 3 146 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: 5 295 ASP cc_start: 0.8013 (t0) cc_final: 0.7714 (t0) REVERT: 5 313 MET cc_start: 0.9169 (mtm) cc_final: 0.8914 (mtm) REVERT: 6 107 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9069 (tmmt) REVERT: 6 148 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8739 (mmmm) REVERT: 7 50 LYS cc_start: 0.9358 (mmtm) cc_final: 0.9033 (mmtm) REVERT: 7 143 TRP cc_start: 0.8850 (OUTLIER) cc_final: 0.7997 (m-90) REVERT: 7 181 TYR cc_start: 0.8775 (t80) cc_final: 0.8152 (t80) REVERT: 7 235 TYR cc_start: 0.8313 (m-80) cc_final: 0.8043 (m-80) REVERT: 8 125 LYS cc_start: 0.5600 (pttp) cc_final: 0.4339 (ptmm) REVERT: 9 90 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8108 (tm-30) REVERT: C 158 MET cc_start: 0.8243 (ppp) cc_final: 0.7689 (ppp) REVERT: C 191 LEU cc_start: 0.9436 (mt) cc_final: 0.9197 (mt) REVERT: C 243 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8020 (pp20) REVERT: C 255 ASP cc_start: 0.8456 (t0) cc_final: 0.7817 (t70) REVERT: C 308 SER cc_start: 0.8324 (t) cc_final: 0.6986 (p) REVERT: C 309 THR cc_start: 0.7977 (m) cc_final: 0.7718 (p) REVERT: D 161 ASP cc_start: 0.8327 (m-30) cc_final: 0.7929 (m-30) REVERT: D 197 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: D 199 GLU cc_start: 0.8199 (mp0) cc_final: 0.7994 (mp0) REVERT: F 201 GLN cc_start: 0.8510 (tp40) cc_final: 0.8143 (tp40) REVERT: G 123 GLN cc_start: 0.8899 (tp40) cc_final: 0.8563 (pt0) REVERT: G 126 ASP cc_start: 0.8480 (t0) cc_final: 0.8118 (t0) REVERT: G 147 LYS cc_start: 0.8868 (mmmt) cc_final: 0.8600 (mmmt) REVERT: G 160 ARG cc_start: 0.9056 (mtt180) cc_final: 0.8592 (mtm-85) REVERT: G 232 TYR cc_start: 0.8866 (t80) cc_final: 0.8320 (t80) REVERT: H 143 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8449 (tm-30) REVERT: I 105 SER cc_start: 0.8942 (m) cc_final: 0.8288 (p) REVERT: I 108 ASP cc_start: 0.8711 (m-30) cc_final: 0.8216 (m-30) REVERT: I 119 HIS cc_start: 0.8336 (t70) cc_final: 0.8036 (t70) REVERT: I 144 LEU cc_start: 0.9013 (mm) cc_final: 0.8601 (mm) REVERT: J 52 GLU cc_start: 0.8943 (tp30) cc_final: 0.8742 (tp30) REVERT: J 54 ASN cc_start: 0.8609 (m-40) cc_final: 0.8304 (m-40) REVERT: J 142 ARG cc_start: 0.8921 (mtm180) cc_final: 0.8446 (mtm180) REVERT: J 154 ARG cc_start: 0.8303 (ptp90) cc_final: 0.7633 (ptp90) REVERT: K 98 ARG cc_start: 0.8634 (ttm170) cc_final: 0.8347 (ttm170) REVERT: K 156 ASP cc_start: 0.8279 (m-30) cc_final: 0.7979 (m-30) REVERT: K 160 GLN cc_start: 0.8076 (tp40) cc_final: 0.7576 (tp-100) REVERT: K 164 ASP cc_start: 0.8492 (m-30) cc_final: 0.7574 (m-30) REVERT: L 108 ILE cc_start: 0.9443 (pt) cc_final: 0.9237 (pp) REVERT: L 135 SER cc_start: 0.9148 (m) cc_final: 0.8719 (m) REVERT: M 218 LYS cc_start: 0.8929 (ptpp) cc_final: 0.8504 (ptpp) REVERT: M 238 ARG cc_start: 0.8065 (mtt90) cc_final: 0.7741 (mtt90) REVERT: M 280 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8895 (mmmm) REVERT: M 292 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8542 (pttm) REVERT: N 65 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7978 (pt0) REVERT: N 76 SER cc_start: 0.9159 (t) cc_final: 0.8928 (t) REVERT: N 83 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8808 (p) REVERT: N 149 HIS cc_start: 0.6242 (m90) cc_final: 0.6000 (m-70) REVERT: N 173 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7951 (mm-40) REVERT: N 197 LYS cc_start: 0.9269 (tptm) cc_final: 0.8993 (tptm) REVERT: N 200 LYS cc_start: 0.9194 (mptt) cc_final: 0.8870 (mmtm) REVERT: O 40 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8182 (mt-10) REVERT: O 50 ASP cc_start: 0.8309 (t70) cc_final: 0.8090 (t70) REVERT: P 57 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7833 (tm-30) REVERT: P 58 LEU cc_start: 0.9324 (mt) cc_final: 0.9034 (mt) REVERT: P 81 LEU cc_start: 0.9277 (tp) cc_final: 0.8966 (tm) REVERT: P 113 LYS cc_start: 0.9185 (ptmt) cc_final: 0.8697 (ptpt) REVERT: P 138 GLU cc_start: 0.8523 (pt0) cc_final: 0.8152 (pt0) REVERT: P 147 GLN cc_start: 0.8893 (mt0) cc_final: 0.8575 (mt0) REVERT: P 158 MET cc_start: 0.9273 (mmp) cc_final: 0.8781 (mmt) REVERT: P 162 GLN cc_start: 0.9288 (mt0) cc_final: 0.9009 (mt0) REVERT: Q 98 ASP cc_start: 0.8136 (m-30) cc_final: 0.7868 (m-30) REVERT: Q 123 ASP cc_start: 0.8560 (t0) cc_final: 0.8338 (t0) REVERT: Q 224 MET cc_start: 0.9137 (mmm) cc_final: 0.8423 (mmp) REVERT: Q 239 ASN cc_start: 0.9028 (t0) cc_final: 0.8505 (t0) REVERT: R 26 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8721 (pttm) REVERT: R 29 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7741 (mmt180) REVERT: R 58 TYR cc_start: 0.9001 (m-80) cc_final: 0.8786 (m-80) REVERT: R 109 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8050 (mm-30) REVERT: T 119 GLU cc_start: 0.7934 (tp30) cc_final: 0.7425 (tm-30) REVERT: T 123 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7099 (mt-10) REVERT: U 23 ASN cc_start: 0.8492 (t160) cc_final: 0.8274 (t0) REVERT: U 56 TYR cc_start: 0.9249 (t80) cc_final: 0.8974 (t80) REVERT: U 103 GLN cc_start: 0.8267 (mp10) cc_final: 0.7997 (mp10) REVERT: U 128 SER cc_start: 0.8791 (p) cc_final: 0.8538 (p) REVERT: V 55 TYR cc_start: 0.8669 (p90) cc_final: 0.7891 (p90) REVERT: V 82 GLN cc_start: 0.9208 (mp10) cc_final: 0.8632 (mp10) REVERT: V 104 TYR cc_start: 0.6325 (t80) cc_final: 0.6113 (t80) REVERT: V 117 HIS cc_start: 0.8037 (p90) cc_final: 0.7531 (p90) REVERT: V 118 ARG cc_start: 0.8470 (mmt-90) cc_final: 0.8155 (mmm-85) REVERT: V 119 GLN cc_start: 0.9025 (mt0) cc_final: 0.8682 (mt0) REVERT: W 57 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: W 119 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8259 (mtp85) REVERT: W 139 GLU cc_start: 0.8643 (pm20) cc_final: 0.8421 (pm20) REVERT: X 6 TYR cc_start: 0.9325 (m-80) cc_final: 0.9096 (m-80) REVERT: X 36 ARG cc_start: 0.7628 (ptm-80) cc_final: 0.7188 (ptm-80) REVERT: X 98 SER cc_start: 0.9010 (t) cc_final: 0.8554 (p) REVERT: Y 143 ASP cc_start: 0.8367 (t70) cc_final: 0.8009 (t0) REVERT: Y 150 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: Z 59 ASP cc_start: 0.8663 (t0) cc_final: 0.8222 (t0) REVERT: Z 61 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8196 (mm110) REVERT: Z 134 MET cc_start: 0.8765 (tpp) cc_final: 0.7657 (tpp) REVERT: a 41 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7575 (t70) REVERT: a 46 ASN cc_start: 0.8841 (m-40) cc_final: 0.8283 (m-40) REVERT: a 56 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8296 (mtp180) REVERT: b 45 GLU cc_start: 0.8258 (tp30) cc_final: 0.7889 (tp30) REVERT: b 49 ARG cc_start: 0.8300 (mtp180) cc_final: 0.7599 (mtm-85) REVERT: c 46 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: c 67 ASP cc_start: 0.8641 (t0) cc_final: 0.8076 (t0) REVERT: c 105 ARG cc_start: 0.7739 (ptm160) cc_final: 0.7122 (tpm170) REVERT: d 84 ILE cc_start: 0.7743 (mt) cc_final: 0.7450 (pp) REVERT: d 151 CYS cc_start: 0.7978 (m) cc_final: 0.7583 (m) REVERT: d 196 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7203 (pp30) REVERT: e 70 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.8011 (mmm) REVERT: f 100 MET cc_start: 0.8612 (ttm) cc_final: 0.8356 (mmm) REVERT: f 109 TYR cc_start: 0.8202 (t80) cc_final: 0.7886 (t80) REVERT: f 113 LEU cc_start: 0.9091 (mm) cc_final: 0.8662 (tt) REVERT: f 117 LEU cc_start: 0.9022 (mt) cc_final: 0.8767 (mp) REVERT: g 76 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8472 (ptp-110) REVERT: g 98 LYS cc_start: 0.8622 (mtmm) cc_final: 0.8225 (mtpp) REVERT: h 73 TYR cc_start: 0.9170 (m-80) cc_final: 0.8848 (m-80) REVERT: h 76 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8558 (tm-30) REVERT: h 93 ASP cc_start: 0.8214 (t0) cc_final: 0.8002 (t0) REVERT: h 99 ASN cc_start: 0.9459 (m-40) cc_final: 0.9138 (m110) REVERT: h 103 HIS cc_start: 0.8773 (m-70) cc_final: 0.8241 (m170) REVERT: h 116 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7802 (mtp180) REVERT: h 153 LYS cc_start: 0.9326 (mmtm) cc_final: 0.9008 (mmmt) REVERT: j 61 LYS cc_start: 0.9260 (mmmm) cc_final: 0.9048 (mmtp) REVERT: k 14 LYS cc_start: 0.7665 (mmtp) cc_final: 0.7220 (mtpt) REVERT: k 43 ARG cc_start: 0.8607 (mtm180) cc_final: 0.8005 (mtm180) REVERT: k 56 ARG cc_start: 0.6455 (tmt170) cc_final: 0.6218 (tpt-90) REVERT: k 67 LEU cc_start: 0.8320 (mt) cc_final: 0.8103 (mm) REVERT: k 84 LEU cc_start: 0.9114 (mm) cc_final: 0.8758 (tt) REVERT: k 90 PHE cc_start: 0.9090 (t80) cc_final: 0.8679 (t80) REVERT: m 77 MET cc_start: 0.5319 (tpt) cc_final: 0.5021 (mmp) REVERT: o 91 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: p 118 LYS cc_start: 0.8919 (mtmp) cc_final: 0.8655 (mtmp) REVERT: p 124 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.8841 (ptpp) REVERT: p 156 ASP cc_start: 0.8552 (m-30) cc_final: 0.8279 (m-30) REVERT: p 179 ARG cc_start: 0.8038 (ttp-110) cc_final: 0.7589 (mtm-85) REVERT: p 181 GLU cc_start: 0.8301 (pp20) cc_final: 0.8098 (pp20) REVERT: p 183 MET cc_start: 0.8555 (ttt) cc_final: 0.8223 (tmm) REVERT: q 108 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9273 (tp) REVERT: q 112 GLN cc_start: 0.8767 (tp-100) cc_final: 0.8346 (tm-30) REVERT: q 116 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8194 (mm-30) REVERT: q 134 ASN cc_start: 0.9163 (m110) cc_final: 0.8829 (m-40) REVERT: r 117 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7865 (mm-30) REVERT: r 164 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.6810 (mmtt) REVERT: s 265 LYS cc_start: 0.8380 (mppt) cc_final: 0.8171 (mmtm) REVERT: s 385 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7756 (pm20) REVERT: u 93 ASP cc_start: 0.8661 (p0) cc_final: 0.8439 (p0) REVERT: u 158 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8379 (ttpt) REVERT: u 160 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7742 (mt-10) REVERT: u 186 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7539 (pp20) REVERT: u 188 TYR cc_start: 0.8892 (m-80) cc_final: 0.8630 (m-80) REVERT: v 12 LEU cc_start: 0.9005 (tm) cc_final: 0.8622 (tp) REVERT: v 27 ASP cc_start: 0.8022 (t0) cc_final: 0.7759 (t0) REVERT: x 81 CYS cc_start: 0.8489 (t) cc_final: 0.8102 (t) REVERT: x 90 SER cc_start: 0.9111 (t) cc_final: 0.8743 (m) REVERT: x 161 THR cc_start: 0.8945 (m) cc_final: 0.8558 (p) REVERT: x 164 LYS cc_start: 0.8824 (ptpp) cc_final: 0.8197 (mptt) outliers start: 289 outliers final: 135 residues processed: 1818 average time/residue: 1.7279 time to fit residues: 4389.3828 Evaluate side-chains 1748 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1581 time to evaluate : 7.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 107 ILE Chi-restraints excluded: chain 0 residue 140 GLN Chi-restraints excluded: chain 0 residue 155 GLU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 29 CYS Chi-restraints excluded: chain 1 residue 41 LEU Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 3 residue 146 GLU Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 4 residue 70 THR Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 6 residue 107 LYS Chi-restraints excluded: chain 6 residue 148 LYS Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 226 LEU Chi-restraints excluded: chain 6 residue 353 LYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 8 residue 154 SER Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 52 GLN Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 324 GLU Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 147 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 143 ASN Chi-restraints excluded: chain M residue 14 ASP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 114 ASP Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 157 ARG Chi-restraints excluded: chain P residue 127 SER Chi-restraints excluded: chain P residue 156 ASP Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 202 VAL Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 276 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 111 GLU Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain V residue 51 ASP Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 119 ARG Chi-restraints excluded: chain X residue 53 ASN Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 150 GLU Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 136 LYS Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 136 CYS Chi-restraints excluded: chain d residue 86 ASP Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 196 GLN Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain e residue 55 ARG Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 192 LEU Chi-restraints excluded: chain e residue 239 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 157 LEU Chi-restraints excluded: chain h residue 85 ASN Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 94 ILE Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 124 LYS Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 117 GLU Chi-restraints excluded: chain r residue 164 LYS Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 254 ASP Chi-restraints excluded: chain s residue 264 ILE Chi-restraints excluded: chain s residue 266 CYS Chi-restraints excluded: chain s residue 385 GLN Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 158 LYS Chi-restraints excluded: chain u residue 186 GLU Chi-restraints excluded: chain u residue 196 LEU Chi-restraints excluded: chain v residue 29 ASP Chi-restraints excluded: chain v residue 42 ASN Chi-restraints excluded: chain w residue 87 LEU Chi-restraints excluded: chain x residue 124 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 896 optimal weight: 2.9990 chunk 681 optimal weight: 6.9990 chunk 470 optimal weight: 0.9980 chunk 100 optimal weight: 0.0050 chunk 432 optimal weight: 10.0000 chunk 609 optimal weight: 0.9980 chunk 910 optimal weight: 8.9990 chunk 963 optimal weight: 5.9990 chunk 475 optimal weight: 2.9990 chunk 862 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 15 ASN 3 154 GLN 3 170 ASN 3 185 ASN ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN C 218 HIS ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS G 167 GLN G 195 ASN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 289 ASN N 68 ASN N 110 ASN N 138 HIS N 202 GLN P 176 GLN Q 261 ASN R 89 ASN R 147 GLN T 109 ASN T 202 GLN W 70 GLN Y 92 ASN Z 136 ASN b 25 GLN d 47 GLN d 149 HIS d 161 HIS d 196 GLN d 274 GLN f 94 HIS ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 108062 Z= 0.187 Angle : 0.615 14.265 152990 Z= 0.314 Chirality : 0.039 0.223 17868 Planarity : 0.005 0.115 14284 Dihedral : 20.791 179.090 31404 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.29 % Favored : 96.70 % Rotamer: Outliers : 3.43 % Allowed : 19.64 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.09), residues: 8666 helix: 1.56 (0.09), residues: 3070 sheet: -0.33 (0.15), residues: 1100 loop : 0.37 (0.10), residues: 4496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP V 135 HIS 0.013 0.001 HIS k 93 PHE 0.022 0.001 PHE d 132 TYR 0.047 0.001 TYR C 376 ARG 0.024 0.001 ARG e 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2008 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1741 time to evaluate : 7.297 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: 0 107 ILE cc_start: 0.9593 (OUTLIER) cc_final: 0.9327 (mt) REVERT: 0 128 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7549 (tm-30) REVERT: 0 132 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8453 (mtpp) REVERT: 0 143 LYS cc_start: 0.8864 (mtpp) cc_final: 0.8561 (mtmm) REVERT: 0 144 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8399 (tm-30) REVERT: 1 20 MET cc_start: 0.8565 (mmm) cc_final: 0.7336 (mmm) REVERT: 1 38 ARG cc_start: 0.8361 (mmm160) cc_final: 0.7563 (mmm160) REVERT: 1 39 GLU cc_start: 0.7912 (pm20) cc_final: 0.7115 (pm20) REVERT: 3 146 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: 4 74 LYS cc_start: 0.9290 (mtpt) cc_final: 0.9051 (mtpm) REVERT: 5 295 ASP cc_start: 0.7894 (t0) cc_final: 0.7606 (t0) REVERT: 6 107 LYS cc_start: 0.9471 (ttpt) cc_final: 0.9030 (tmmt) REVERT: 6 148 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8733 (mmmm) REVERT: 6 214 TRP cc_start: 0.8083 (m100) cc_final: 0.7830 (m100) REVERT: 6 274 LYS cc_start: 0.7382 (tptt) cc_final: 0.7156 (tptm) REVERT: 6 334 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8395 (pt) REVERT: 7 50 LYS cc_start: 0.9339 (mmtm) cc_final: 0.9034 (mmtm) REVERT: 7 181 TYR cc_start: 0.8572 (t80) cc_final: 0.8150 (t80) REVERT: 7 235 TYR cc_start: 0.8289 (m-80) cc_final: 0.7986 (m-80) REVERT: 8 125 LYS cc_start: 0.5523 (pttp) cc_final: 0.4503 (ptmm) REVERT: 9 55 GLU cc_start: 0.8884 (mp0) cc_final: 0.8680 (mp0) REVERT: C 31 TRP cc_start: 0.9147 (m100) cc_final: 0.8081 (m100) REVERT: C 163 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8839 (mt) REVERT: C 179 ASP cc_start: 0.8085 (m-30) cc_final: 0.7840 (m-30) REVERT: C 243 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7995 (pp20) REVERT: C 255 ASP cc_start: 0.8392 (t0) cc_final: 0.8135 (t70) REVERT: C 308 SER cc_start: 0.8269 (t) cc_final: 0.7996 (m) REVERT: D 78 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8368 (tppt) REVERT: D 161 ASP cc_start: 0.8327 (m-30) cc_final: 0.7839 (m-30) REVERT: D 197 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7999 (pt0) REVERT: F 201 GLN cc_start: 0.8471 (tp40) cc_final: 0.8065 (tp-100) REVERT: F 209 TYR cc_start: 0.9001 (t80) cc_final: 0.8758 (t80) REVERT: G 123 GLN cc_start: 0.8848 (tp40) cc_final: 0.8590 (tp40) REVERT: G 159 MET cc_start: 0.9036 (tmm) cc_final: 0.8751 (tmm) REVERT: G 232 TYR cc_start: 0.8813 (t80) cc_final: 0.8223 (t80) REVERT: G 236 TYR cc_start: 0.8844 (t80) cc_final: 0.8624 (t80) REVERT: H 67 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7238 (mm-30) REVERT: H 91 LYS cc_start: 0.8829 (mttp) cc_final: 0.8550 (mptt) REVERT: H 93 ASN cc_start: 0.8982 (m-40) cc_final: 0.8742 (t0) REVERT: H 100 GLN cc_start: 0.8314 (mm110) cc_final: 0.8082 (mm-40) REVERT: I 105 SER cc_start: 0.8960 (m) cc_final: 0.8393 (p) REVERT: I 108 ASP cc_start: 0.8731 (m-30) cc_final: 0.8336 (m-30) REVERT: I 114 HIS cc_start: 0.9175 (t70) cc_final: 0.8913 (t-170) REVERT: I 119 HIS cc_start: 0.8432 (t70) cc_final: 0.8166 (t70) REVERT: I 144 LEU cc_start: 0.8967 (mm) cc_final: 0.8559 (mm) REVERT: J 52 GLU cc_start: 0.8874 (tp30) cc_final: 0.8655 (tp30) REVERT: J 54 ASN cc_start: 0.8621 (m-40) cc_final: 0.8301 (m-40) REVERT: J 142 ARG cc_start: 0.8960 (mtm180) cc_final: 0.8629 (mtm-85) REVERT: J 154 ARG cc_start: 0.8323 (ptp90) cc_final: 0.7835 (ptp90) REVERT: K 98 ARG cc_start: 0.8623 (ttm170) cc_final: 0.8338 (ttm170) REVERT: K 160 GLN cc_start: 0.8016 (tp40) cc_final: 0.7638 (tp-100) REVERT: K 164 ASP cc_start: 0.8480 (m-30) cc_final: 0.7521 (m-30) REVERT: L 133 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: L 135 SER cc_start: 0.9082 (m) cc_final: 0.8861 (m) REVERT: M 99 ASN cc_start: 0.9130 (m110) cc_final: 0.8781 (m110) REVERT: M 218 LYS cc_start: 0.8889 (ptpp) cc_final: 0.8452 (ptpp) REVERT: M 238 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7696 (mtt90) REVERT: M 292 LYS cc_start: 0.8783 (ttpp) cc_final: 0.8565 (pttm) REVERT: N 65 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7992 (pt0) REVERT: N 173 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7915 (mm-40) REVERT: N 197 LYS cc_start: 0.9283 (tptm) cc_final: 0.8982 (tptm) REVERT: N 200 LYS cc_start: 0.9160 (mptt) cc_final: 0.8814 (mmtm) REVERT: O 40 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8106 (mt-10) REVERT: O 69 ASN cc_start: 0.9222 (t0) cc_final: 0.8952 (t0) REVERT: P 57 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7756 (tm-30) REVERT: P 58 LEU cc_start: 0.9292 (mt) cc_final: 0.8860 (mt) REVERT: P 100 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8704 (mtmm) REVERT: P 138 GLU cc_start: 0.8476 (pt0) cc_final: 0.8203 (pt0) REVERT: P 147 GLN cc_start: 0.8928 (mt0) cc_final: 0.8631 (mt0) REVERT: P 162 GLN cc_start: 0.9269 (mt0) cc_final: 0.8998 (mt0) REVERT: Q 98 ASP cc_start: 0.7995 (m-30) cc_final: 0.7723 (m-30) REVERT: Q 123 ASP cc_start: 0.8602 (t0) cc_final: 0.8322 (t0) REVERT: Q 224 MET cc_start: 0.9073 (mmm) cc_final: 0.8382 (mmp) REVERT: Q 239 ASN cc_start: 0.8989 (t0) cc_final: 0.8454 (t0) REVERT: R 40 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.8156 (ttm-80) REVERT: R 109 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8179 (mm-30) REVERT: T 119 GLU cc_start: 0.7918 (tp30) cc_final: 0.7592 (tm-30) REVERT: U 23 ASN cc_start: 0.8457 (t160) cc_final: 0.8206 (t0) REVERT: U 56 TYR cc_start: 0.9154 (t80) cc_final: 0.8869 (t80) REVERT: U 128 SER cc_start: 0.8891 (p) cc_final: 0.8626 (p) REVERT: V 78 GLN cc_start: 0.8442 (tt0) cc_final: 0.8226 (tt0) REVERT: V 82 GLN cc_start: 0.9198 (mp10) cc_final: 0.8561 (mp10) REVERT: V 92 ASN cc_start: 0.9100 (t0) cc_final: 0.8255 (t0) REVERT: V 117 HIS cc_start: 0.8125 (p90) cc_final: 0.7917 (p90) REVERT: W 49 ARG cc_start: 0.8235 (mtm180) cc_final: 0.8008 (mpp-170) REVERT: W 57 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: W 60 TYR cc_start: 0.8989 (t80) cc_final: 0.8782 (t80) REVERT: W 139 GLU cc_start: 0.8557 (pm20) cc_final: 0.8308 (pm20) REVERT: X 98 SER cc_start: 0.8963 (t) cc_final: 0.8583 (p) REVERT: X 115 TYR cc_start: 0.8540 (t80) cc_final: 0.8233 (t80) REVERT: Y 143 ASP cc_start: 0.8354 (t70) cc_final: 0.8012 (t0) REVERT: Y 150 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7709 (tp30) REVERT: Z 61 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8255 (mm-40) REVERT: Z 134 MET cc_start: 0.8788 (tpp) cc_final: 0.7607 (tpp) REVERT: a 41 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7552 (t70) REVERT: a 46 ASN cc_start: 0.8761 (m-40) cc_final: 0.8202 (m-40) REVERT: a 56 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8242 (mtp180) REVERT: a 110 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7459 (tp30) REVERT: a 114 LYS cc_start: 0.8642 (tppp) cc_final: 0.8065 (tppp) REVERT: b 49 ARG cc_start: 0.8372 (mtp180) cc_final: 0.7805 (mtm-85) REVERT: c 46 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: c 67 ASP cc_start: 0.8591 (t0) cc_final: 0.8014 (t0) REVERT: c 105 ARG cc_start: 0.7942 (ptm160) cc_final: 0.7289 (tpm170) REVERT: d 84 ILE cc_start: 0.7644 (mt) cc_final: 0.7345 (pp) REVERT: d 196 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7197 (pp30) REVERT: d 251 GLN cc_start: 0.8493 (tp40) cc_final: 0.8286 (tp40) REVERT: f 60 LYS cc_start: 0.9226 (mtpm) cc_final: 0.8882 (mtpp) REVERT: f 100 MET cc_start: 0.8613 (ttm) cc_final: 0.8358 (mmm) REVERT: f 109 TYR cc_start: 0.8140 (t80) cc_final: 0.7807 (t80) REVERT: f 113 LEU cc_start: 0.9096 (mm) cc_final: 0.8636 (tt) REVERT: f 117 LEU cc_start: 0.9058 (mt) cc_final: 0.8804 (mp) REVERT: g 56 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7755 (ttm110) REVERT: g 98 LYS cc_start: 0.8519 (mtmm) cc_final: 0.8196 (mtpp) REVERT: h 73 TYR cc_start: 0.9183 (m-80) cc_final: 0.8844 (m-80) REVERT: h 76 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8579 (tm-30) REVERT: h 99 ASN cc_start: 0.9452 (m-40) cc_final: 0.9094 (m110) REVERT: h 103 HIS cc_start: 0.8771 (m-70) cc_final: 0.8295 (m170) REVERT: h 116 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7675 (mtp180) REVERT: h 137 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7565 (ppt-90) REVERT: h 153 LYS cc_start: 0.9307 (mmtm) cc_final: 0.9023 (mmmt) REVERT: j 61 LYS cc_start: 0.9139 (mmmm) cc_final: 0.8834 (mttp) REVERT: k 14 LYS cc_start: 0.7669 (mmtp) cc_final: 0.7409 (mtpt) REVERT: k 43 ARG cc_start: 0.8647 (mtm180) cc_final: 0.8279 (mtm180) REVERT: k 84 LEU cc_start: 0.9070 (mm) cc_final: 0.8688 (tt) REVERT: k 90 PHE cc_start: 0.9064 (t80) cc_final: 0.8688 (t80) REVERT: m 77 MET cc_start: 0.5300 (tpt) cc_final: 0.5002 (mmp) REVERT: o 91 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: p 118 LYS cc_start: 0.8921 (mtmp) cc_final: 0.8679 (mtmp) REVERT: p 136 THR cc_start: 0.9134 (p) cc_final: 0.8906 (p) REVERT: p 156 ASP cc_start: 0.8529 (m-30) cc_final: 0.8259 (m-30) REVERT: p 179 ARG cc_start: 0.8040 (ttp-110) cc_final: 0.7560 (mtm-85) REVERT: p 183 MET cc_start: 0.8522 (ttt) cc_final: 0.8138 (tmm) REVERT: q 112 GLN cc_start: 0.8747 (tp-100) cc_final: 0.8388 (tm-30) REVERT: q 116 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8227 (mm-30) REVERT: q 134 ASN cc_start: 0.9241 (m110) cc_final: 0.8972 (m-40) REVERT: r 110 GLU cc_start: 0.7853 (pm20) cc_final: 0.7649 (pm20) REVERT: r 111 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8024 (mp0) REVERT: r 113 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7650 (mpt-90) REVERT: r 117 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7886 (mm-30) REVERT: s 265 LYS cc_start: 0.8324 (mppt) cc_final: 0.8116 (mmtm) REVERT: u 93 ASP cc_start: 0.8617 (p0) cc_final: 0.8413 (p0) REVERT: u 158 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8550 (ttpt) REVERT: u 160 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7899 (mt-10) REVERT: u 186 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7622 (pp20) REVERT: u 187 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8527 (mm) REVERT: v 12 LEU cc_start: 0.8968 (tm) cc_final: 0.8580 (tp) REVERT: v 27 ASP cc_start: 0.8362 (t0) cc_final: 0.8028 (t0) REVERT: w 139 MET cc_start: 0.7534 (mpm) cc_final: 0.7303 (tpt) REVERT: x 81 CYS cc_start: 0.8542 (t) cc_final: 0.8258 (t) REVERT: x 90 SER cc_start: 0.9074 (t) cc_final: 0.8729 (m) REVERT: x 104 ASP cc_start: 0.8205 (m-30) cc_final: 0.7967 (m-30) REVERT: x 135 PHE cc_start: 0.8935 (m-80) cc_final: 0.8545 (m-80) REVERT: x 161 THR cc_start: 0.9017 (m) cc_final: 0.8725 (p) outliers start: 267 outliers final: 116 residues processed: 1867 average time/residue: 1.6828 time to fit residues: 4406.3820 Evaluate side-chains 1736 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1595 time to evaluate : 7.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 107 ILE Chi-restraints excluded: chain 0 residue 140 GLN Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 41 LEU Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 1 residue 51 LYS Chi-restraints excluded: chain 3 residue 146 GLU Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 4 residue 70 THR Chi-restraints excluded: chain 5 residue 148 GLU Chi-restraints excluded: chain 5 residue 274 LYS Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 6 residue 148 LYS Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 18 MET Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 52 GLN Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 100 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 324 GLU Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 133 GLU Chi-restraints excluded: chain M residue 14 ASP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 157 ARG Chi-restraints excluded: chain O residue 160 GLN Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 202 VAL Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 187 GLU Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain Y residue 70 ASP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 150 GLU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 136 LYS Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 136 CYS Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 184 SER Chi-restraints excluded: chain d residue 196 GLN Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 192 LEU Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 85 ASN Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 137 ARG Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 94 ILE Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain r residue 117 GLU Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 266 CYS Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 158 LYS Chi-restraints excluded: chain u residue 186 GLU Chi-restraints excluded: chain u residue 187 ILE Chi-restraints excluded: chain u residue 196 LEU Chi-restraints excluded: chain w residue 87 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 802 optimal weight: 6.9990 chunk 547 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 717 optimal weight: 0.4980 chunk 397 optimal weight: 3.9990 chunk 822 optimal weight: 40.0000 chunk 666 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 492 optimal weight: 5.9990 chunk 864 optimal weight: 4.9990 chunk 243 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 118 GLN 0 170 GLN 1 15 ASN 1 35 ASN 3 154 GLN 3 170 ASN 3 185 ASN ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN G 167 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN L 52 HIS ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 289 ASN N 68 ASN N 86 ASN N 138 HIS N 202 GLN ** O 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 GLN P 176 GLN Q 261 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 147 GLN T 109 ASN T 202 GLN U 23 ASN U 136 GLN ** V 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 GLN Y 92 ASN b 25 GLN ** b 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 135 ASN d 149 HIS d 161 HIS d 167 HIS d 196 GLN d 220 GLN d 274 GLN ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 182 ASN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 ASN x 199 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 108062 Z= 0.270 Angle : 0.632 14.294 152990 Z= 0.323 Chirality : 0.040 0.238 17868 Planarity : 0.005 0.116 14284 Dihedral : 20.695 178.616 31404 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.50 % Favored : 96.49 % Rotamer: Outliers : 3.83 % Allowed : 20.95 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.09), residues: 8666 helix: 1.50 (0.09), residues: 3072 sheet: -0.35 (0.15), residues: 1139 loop : 0.35 (0.10), residues: 4455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP 8 121 HIS 0.009 0.001 HIS h 110 PHE 0.033 0.002 PHE G 316 TYR 0.037 0.001 TYR C 376 ARG 0.011 0.000 ARG d 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1933 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1635 time to evaluate : 8.131 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: 0 128 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7599 (tm-30) REVERT: 0 132 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8465 (mtpp) REVERT: 0 144 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8469 (tm-30) REVERT: 1 20 MET cc_start: 0.8511 (mmm) cc_final: 0.7202 (mmm) REVERT: 1 38 ARG cc_start: 0.8363 (mmm160) cc_final: 0.7830 (mmm160) REVERT: 1 39 GLU cc_start: 0.8054 (pm20) cc_final: 0.7709 (pm20) REVERT: 1 58 GLU cc_start: 0.7492 (tt0) cc_final: 0.7289 (tt0) REVERT: 3 146 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: 4 73 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8297 (mttp) REVERT: 4 74 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8973 (mtpm) REVERT: 5 295 ASP cc_start: 0.7967 (t0) cc_final: 0.7673 (t0) REVERT: 6 107 LYS cc_start: 0.9484 (ttpt) cc_final: 0.9060 (tmmt) REVERT: 6 148 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8707 (mmmm) REVERT: 6 334 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8395 (pt) REVERT: 7 50 LYS cc_start: 0.9347 (mmtm) cc_final: 0.9040 (mmtm) REVERT: 7 143 TRP cc_start: 0.8905 (OUTLIER) cc_final: 0.8138 (m-90) REVERT: 7 181 TYR cc_start: 0.8688 (t80) cc_final: 0.8202 (t80) REVERT: 7 235 TYR cc_start: 0.8260 (m-80) cc_final: 0.7976 (m-80) REVERT: 8 125 LYS cc_start: 0.5570 (pttp) cc_final: 0.4799 (ptmm) REVERT: 9 55 GLU cc_start: 0.8882 (mp0) cc_final: 0.8679 (mp0) REVERT: C 243 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8011 (pp20) REVERT: C 255 ASP cc_start: 0.8378 (t0) cc_final: 0.7718 (t70) REVERT: C 308 SER cc_start: 0.8364 (t) cc_final: 0.7156 (p) REVERT: C 349 MET cc_start: 0.8678 (tpp) cc_final: 0.8386 (tpp) REVERT: D 78 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8399 (tppt) REVERT: D 161 ASP cc_start: 0.8352 (m-30) cc_final: 0.7863 (m-30) REVERT: D 197 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7987 (pt0) REVERT: F 103 GLN cc_start: 0.8959 (mt0) cc_final: 0.8647 (mt0) REVERT: F 201 GLN cc_start: 0.8509 (tp40) cc_final: 0.8098 (tp-100) REVERT: G 123 GLN cc_start: 0.8815 (tp40) cc_final: 0.8575 (tp40) REVERT: G 267 TYR cc_start: 0.9091 (t80) cc_final: 0.8775 (t80) REVERT: H 100 GLN cc_start: 0.8409 (mm110) cc_final: 0.8111 (mp-120) REVERT: I 108 ASP cc_start: 0.8789 (m-30) cc_final: 0.8497 (m-30) REVERT: I 114 HIS cc_start: 0.9169 (t70) cc_final: 0.8720 (t-170) REVERT: I 119 HIS cc_start: 0.8527 (t70) cc_final: 0.8244 (t70) REVERT: I 144 LEU cc_start: 0.8996 (mm) cc_final: 0.8560 (mm) REVERT: J 52 GLU cc_start: 0.8881 (tp30) cc_final: 0.8644 (tp30) REVERT: J 54 ASN cc_start: 0.8720 (m-40) cc_final: 0.8342 (m-40) REVERT: J 142 ARG cc_start: 0.8995 (mtm180) cc_final: 0.8608 (mtm-85) REVERT: J 154 ARG cc_start: 0.8371 (ptp90) cc_final: 0.7841 (ptp90) REVERT: K 26 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8791 (mm110) REVERT: K 98 ARG cc_start: 0.8633 (ttm170) cc_final: 0.8332 (ttm170) REVERT: K 135 GLU cc_start: 0.7552 (tp30) cc_final: 0.7284 (tp30) REVERT: K 139 LYS cc_start: 0.9256 (mttt) cc_final: 0.8782 (mmtp) REVERT: K 160 GLN cc_start: 0.8038 (tp40) cc_final: 0.7660 (tp-100) REVERT: K 164 ASP cc_start: 0.8502 (m-30) cc_final: 0.7647 (m-30) REVERT: L 135 SER cc_start: 0.9124 (m) cc_final: 0.8895 (m) REVERT: M 99 ASN cc_start: 0.9121 (m110) cc_final: 0.8757 (m-40) REVERT: M 218 LYS cc_start: 0.8910 (ptpp) cc_final: 0.8485 (ptpp) REVERT: M 238 ARG cc_start: 0.8045 (mtt90) cc_final: 0.7723 (mtt90) REVERT: M 280 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8888 (mmmm) REVERT: N 65 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8022 (pt0) REVERT: N 98 HIS cc_start: 0.8002 (m170) cc_final: 0.7789 (m-70) REVERT: N 173 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7783 (mm-40) REVERT: N 177 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8244 (m-30) REVERT: N 197 LYS cc_start: 0.9285 (tptm) cc_final: 0.8967 (tptm) REVERT: N 200 LYS cc_start: 0.9214 (mptt) cc_final: 0.8834 (mmtm) REVERT: O 40 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8107 (mt-10) REVERT: O 69 ASN cc_start: 0.9240 (t0) cc_final: 0.8916 (t0) REVERT: O 73 MET cc_start: 0.9505 (tpt) cc_final: 0.9289 (mmm) REVERT: P 57 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7750 (tm-30) REVERT: P 58 LEU cc_start: 0.9326 (mt) cc_final: 0.8899 (mt) REVERT: P 81 LEU cc_start: 0.9262 (tp) cc_final: 0.8946 (tm) REVERT: P 138 GLU cc_start: 0.8505 (pt0) cc_final: 0.8239 (pt0) REVERT: P 147 GLN cc_start: 0.8938 (mt0) cc_final: 0.8641 (mt0) REVERT: P 158 MET cc_start: 0.9252 (mmp) cc_final: 0.8695 (mmt) REVERT: P 162 GLN cc_start: 0.9298 (mt0) cc_final: 0.9061 (mt0) REVERT: Q 98 ASP cc_start: 0.7992 (m-30) cc_final: 0.7728 (m-30) REVERT: Q 101 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: Q 123 ASP cc_start: 0.8591 (t0) cc_final: 0.8338 (t0) REVERT: Q 239 ASN cc_start: 0.8997 (t0) cc_final: 0.8465 (t0) REVERT: R 40 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.8131 (ttm-80) REVERT: R 109 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8146 (mm-30) REVERT: T 119 GLU cc_start: 0.7945 (tp30) cc_final: 0.7456 (tm-30) REVERT: U 56 TYR cc_start: 0.9159 (t80) cc_final: 0.8887 (t80) REVERT: U 128 SER cc_start: 0.8856 (p) cc_final: 0.8564 (p) REVERT: V 18 HIS cc_start: 0.8488 (m-70) cc_final: 0.8147 (m170) REVERT: V 75 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8746 (tppp) REVERT: V 82 GLN cc_start: 0.9227 (mp10) cc_final: 0.8592 (mp10) REVERT: V 92 ASN cc_start: 0.9112 (t0) cc_final: 0.8259 (t0) REVERT: W 49 ARG cc_start: 0.8218 (mtm180) cc_final: 0.7954 (mpp-170) REVERT: W 57 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: W 60 TYR cc_start: 0.8996 (t80) cc_final: 0.8790 (t80) REVERT: W 122 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8259 (mtpm) REVERT: W 139 GLU cc_start: 0.8563 (pm20) cc_final: 0.8278 (pm20) REVERT: X 98 SER cc_start: 0.8976 (t) cc_final: 0.8595 (p) REVERT: X 115 TYR cc_start: 0.8584 (t80) cc_final: 0.8310 (t80) REVERT: X 175 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8441 (mp10) REVERT: Y 143 ASP cc_start: 0.8367 (t70) cc_final: 0.8035 (t0) REVERT: Y 150 GLU cc_start: 0.8138 (tp30) cc_final: 0.7732 (tp30) REVERT: Z 84 ASP cc_start: 0.8044 (m-30) cc_final: 0.7719 (m-30) REVERT: Z 134 MET cc_start: 0.8798 (tpp) cc_final: 0.7602 (tpp) REVERT: Z 136 ASN cc_start: 0.8004 (t0) cc_final: 0.7632 (t0) REVERT: a 41 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7533 (t70) REVERT: a 46 ASN cc_start: 0.8766 (m-40) cc_final: 0.8224 (m-40) REVERT: a 56 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8268 (mtp180) REVERT: b 45 GLU cc_start: 0.8157 (tp30) cc_final: 0.7368 (tp30) REVERT: b 49 ARG cc_start: 0.8301 (mtp180) cc_final: 0.7953 (mtm-85) REVERT: c 46 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: c 67 ASP cc_start: 0.8633 (t0) cc_final: 0.8051 (t0) REVERT: c 105 ARG cc_start: 0.7735 (ptm160) cc_final: 0.7284 (tpm170) REVERT: d 53 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7557 (mp0) REVERT: d 196 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7331 (pp30) REVERT: e 139 GLU cc_start: 0.4884 (OUTLIER) cc_final: 0.4625 (mm-30) REVERT: f 109 TYR cc_start: 0.8192 (t80) cc_final: 0.7862 (t80) REVERT: f 113 LEU cc_start: 0.9103 (mm) cc_final: 0.8664 (tt) REVERT: f 117 LEU cc_start: 0.9049 (mt) cc_final: 0.8778 (mp) REVERT: g 49 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8094 (mm-30) REVERT: g 98 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8196 (mtpp) REVERT: g 116 ASP cc_start: 0.8257 (t0) cc_final: 0.8048 (t70) REVERT: h 76 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8568 (tm-30) REVERT: h 99 ASN cc_start: 0.9466 (m-40) cc_final: 0.9093 (m110) REVERT: h 103 HIS cc_start: 0.8773 (m-70) cc_final: 0.8404 (m170) REVERT: h 116 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7715 (mtp180) REVERT: h 153 LYS cc_start: 0.9326 (mmtm) cc_final: 0.9042 (mmmt) REVERT: i 58 ASP cc_start: 0.8584 (m-30) cc_final: 0.8370 (m-30) REVERT: j 61 LYS cc_start: 0.9132 (mmmm) cc_final: 0.8859 (mttp) REVERT: k 43 ARG cc_start: 0.8639 (mtm180) cc_final: 0.8341 (mtm180) REVERT: k 56 ARG cc_start: 0.6352 (tmt170) cc_final: 0.6133 (tpt-90) REVERT: k 84 LEU cc_start: 0.9128 (mm) cc_final: 0.8753 (tt) REVERT: k 90 PHE cc_start: 0.9061 (t80) cc_final: 0.8742 (t80) REVERT: o 91 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: p 156 ASP cc_start: 0.8514 (m-30) cc_final: 0.8260 (m-30) REVERT: p 179 ARG cc_start: 0.8046 (ttp-110) cc_final: 0.7760 (mtm110) REVERT: p 183 MET cc_start: 0.8542 (ttt) cc_final: 0.8158 (tmm) REVERT: q 134 ASN cc_start: 0.9229 (m110) cc_final: 0.8982 (m110) REVERT: q 143 TRP cc_start: 0.7860 (m100) cc_final: 0.7397 (t60) REVERT: r 104 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9205 (mp) REVERT: r 113 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7735 (mpt-90) REVERT: u 158 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8502 (ttpt) REVERT: u 160 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7859 (mt-10) REVERT: u 186 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7682 (pp20) REVERT: u 187 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8625 (mm) REVERT: v 12 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8579 (tp) REVERT: v 27 ASP cc_start: 0.8365 (t0) cc_final: 0.8092 (t0) REVERT: v 44 LYS cc_start: 0.8367 (mmmt) cc_final: 0.6926 (mmmm) REVERT: x 81 CYS cc_start: 0.8439 (t) cc_final: 0.8016 (t) REVERT: x 90 SER cc_start: 0.9061 (t) cc_final: 0.8695 (m) REVERT: x 104 ASP cc_start: 0.8141 (m-30) cc_final: 0.7857 (m-30) REVERT: x 135 PHE cc_start: 0.8965 (m-80) cc_final: 0.8635 (m-80) REVERT: x 161 THR cc_start: 0.8960 (m) cc_final: 0.8660 (p) REVERT: x 164 LYS cc_start: 0.8784 (ptpt) cc_final: 0.8168 (mptt) REVERT: x 179 GLU cc_start: 0.7814 (pp20) cc_final: 0.7308 (mt-10) outliers start: 298 outliers final: 135 residues processed: 1781 average time/residue: 1.7097 time to fit residues: 4259.1637 Evaluate side-chains 1705 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1541 time to evaluate : 7.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 140 GLN Chi-restraints excluded: chain 0 residue 155 GLU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 41 LEU Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 3 residue 146 GLU Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 4 residue 70 THR Chi-restraints excluded: chain 5 residue 148 GLU Chi-restraints excluded: chain 5 residue 274 LYS Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 148 LYS Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 353 LYS Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 52 GLN Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 100 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 324 GLU Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 143 ASN Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain M residue 14 ASP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 251 GLU Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain N residue 177 ASP Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 157 ARG Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 202 VAL Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 111 GLU Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 75 LYS Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain W residue 122 LYS Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 175 GLN Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 227 GLU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 136 CYS Chi-restraints excluded: chain d residue 118 SER Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 196 GLN Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain j residue 97 LYS Chi-restraints excluded: chain j residue 101 GLU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 94 ILE Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 266 CYS Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 158 LYS Chi-restraints excluded: chain u residue 186 GLU Chi-restraints excluded: chain u residue 187 ILE Chi-restraints excluded: chain v residue 12 LEU Chi-restraints excluded: chain x residue 124 SER Chi-restraints excluded: chain x residue 204 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 324 optimal weight: 3.9990 chunk 867 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 565 optimal weight: 6.9990 chunk 237 optimal weight: 10.0000 chunk 964 optimal weight: 3.9990 chunk 800 optimal weight: 20.0000 chunk 446 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 319 optimal weight: 10.0000 chunk 506 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 15 ASN 3 154 GLN 3 185 ASN ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS F 184 GLN G 195 ASN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 289 ASN N 98 HIS N 138 HIS N 202 GLN P 176 GLN Q 261 ASN R 77 GLN R 89 ASN R 147 GLN T 109 ASN T 202 GLN U 23 ASN ** V 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 GLN W 86 ASN X 53 ASN X 76 GLN Y 92 ASN b 129 GLN c 139 GLN d 149 HIS d 161 HIS d 196 GLN d 274 GLN ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 152 GLN r 130 ASN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 108062 Z= 0.291 Angle : 0.643 14.280 152990 Z= 0.328 Chirality : 0.040 0.360 17868 Planarity : 0.005 0.117 14284 Dihedral : 20.674 179.190 31402 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.51 % Favored : 96.48 % Rotamer: Outliers : 3.89 % Allowed : 21.71 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.09), residues: 8666 helix: 1.40 (0.09), residues: 3079 sheet: -0.35 (0.15), residues: 1140 loop : 0.33 (0.10), residues: 4447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP 8 121 HIS 0.018 0.001 HIS w 103 PHE 0.032 0.002 PHE G 316 TYR 0.035 0.001 TYR C 376 ARG 0.012 0.000 ARG g 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1912 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1609 time to evaluate : 7.323 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: 0.8162 (tm-30) cc_final: 0.7231 (tm-30) REVERT: 0 132 LYS cc_start: 0.8797 (mtpp) cc_final: 0.8414 (mttp) REVERT: 0 143 LYS cc_start: 0.8876 (mtpp) cc_final: 0.8581 (mtmm) REVERT: 0 144 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8509 (tm-30) REVERT: 1 38 ARG cc_start: 0.8427 (mmm160) cc_final: 0.7754 (mmm160) REVERT: 1 39 GLU cc_start: 0.8033 (pm20) cc_final: 0.7694 (pm20) REVERT: 1 40 LYS cc_start: 0.9182 (tptm) cc_final: 0.8829 (tptt) REVERT: 1 58 GLU cc_start: 0.7578 (tt0) cc_final: 0.7263 (tt0) REVERT: 3 146 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: 4 78 ASP cc_start: 0.9115 (m-30) cc_final: 0.8912 (m-30) REVERT: 6 107 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9062 (tmmt) REVERT: 6 148 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8705 (mmmm) REVERT: 7 50 LYS cc_start: 0.9370 (mmtm) cc_final: 0.9044 (mmtm) REVERT: 7 143 TRP cc_start: 0.8970 (OUTLIER) cc_final: 0.8219 (m-90) REVERT: 7 181 TYR cc_start: 0.8709 (t80) cc_final: 0.8203 (t80) REVERT: 7 235 TYR cc_start: 0.8279 (m-80) cc_final: 0.7999 (m-80) REVERT: 9 55 GLU cc_start: 0.8866 (mp0) cc_final: 0.8657 (mp0) REVERT: C 243 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8045 (pp20) REVERT: C 255 ASP cc_start: 0.8332 (t0) cc_final: 0.7438 (t70) REVERT: C 308 SER cc_start: 0.8320 (t) cc_final: 0.7163 (p) REVERT: C 349 MET cc_start: 0.8702 (tpp) cc_final: 0.8424 (tpp) REVERT: D 78 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8414 (tppt) REVERT: D 161 ASP cc_start: 0.8360 (m-30) cc_final: 0.7878 (m-30) REVERT: F 103 GLN cc_start: 0.8945 (mt0) cc_final: 0.8638 (mt0) REVERT: F 201 GLN cc_start: 0.8526 (tp40) cc_final: 0.8094 (tp-100) REVERT: G 147 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8670 (mmpt) REVERT: G 158 GLN cc_start: 0.7954 (mp10) cc_final: 0.7652 (mp10) REVERT: G 267 TYR cc_start: 0.9073 (t80) cc_final: 0.8806 (t80) REVERT: H 93 ASN cc_start: 0.8917 (m-40) cc_final: 0.8702 (t0) REVERT: H 100 GLN cc_start: 0.8405 (mm110) cc_final: 0.8105 (mp-120) REVERT: H 116 LYS cc_start: 0.9070 (mttm) cc_final: 0.8758 (mttp) REVERT: I 108 ASP cc_start: 0.8890 (m-30) cc_final: 0.8544 (m-30) REVERT: I 114 HIS cc_start: 0.8988 (t70) cc_final: 0.8669 (t-170) REVERT: I 119 HIS cc_start: 0.8532 (t70) cc_final: 0.8242 (t70) REVERT: I 144 LEU cc_start: 0.8970 (mm) cc_final: 0.8526 (mm) REVERT: J 52 GLU cc_start: 0.8869 (tp30) cc_final: 0.8627 (tp30) REVERT: J 54 ASN cc_start: 0.8831 (m-40) cc_final: 0.8460 (m-40) REVERT: J 154 ARG cc_start: 0.8338 (ptp90) cc_final: 0.7816 (ptp90) REVERT: K 98 ARG cc_start: 0.8634 (ttm170) cc_final: 0.8328 (ttm170) REVERT: K 139 LYS cc_start: 0.9269 (mttt) cc_final: 0.9036 (mmmm) REVERT: K 160 GLN cc_start: 0.8059 (tp40) cc_final: 0.7702 (tp-100) REVERT: K 164 ASP cc_start: 0.8505 (m-30) cc_final: 0.7728 (m-30) REVERT: L 135 SER cc_start: 0.9133 (m) cc_final: 0.8912 (m) REVERT: M 99 ASN cc_start: 0.9117 (m110) cc_final: 0.8757 (m110) REVERT: M 218 LYS cc_start: 0.8922 (ptpp) cc_final: 0.8508 (ptpp) REVERT: M 238 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7728 (mtt90) REVERT: M 280 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8842 (mmmm) REVERT: M 292 LYS cc_start: 0.8786 (ttpp) cc_final: 0.8513 (pttm) REVERT: N 65 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8029 (pt0) REVERT: N 116 LYS cc_start: 0.8749 (pptt) cc_final: 0.8397 (mtmm) REVERT: N 117 ASN cc_start: 0.8029 (t0) cc_final: 0.7582 (t0) REVERT: N 171 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7184 (mt-10) REVERT: N 173 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7844 (mm-40) REVERT: N 177 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8261 (m-30) REVERT: N 197 LYS cc_start: 0.9277 (tptm) cc_final: 0.8954 (tptm) REVERT: N 200 LYS cc_start: 0.9215 (mptt) cc_final: 0.8869 (mmtm) REVERT: N 207 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7439 (ptp-110) REVERT: O 40 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8109 (mt-10) REVERT: O 69 ASN cc_start: 0.9247 (t0) cc_final: 0.8919 (t0) REVERT: O 73 MET cc_start: 0.9505 (tpt) cc_final: 0.9277 (mmm) REVERT: P 57 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7705 (tm-30) REVERT: P 58 LEU cc_start: 0.9338 (mt) cc_final: 0.8911 (mt) REVERT: P 81 LEU cc_start: 0.9202 (tp) cc_final: 0.8922 (tm) REVERT: P 100 LYS cc_start: 0.9012 (mtpt) cc_final: 0.8617 (mtmm) REVERT: P 137 LEU cc_start: 0.9441 (mp) cc_final: 0.9075 (mp) REVERT: P 138 GLU cc_start: 0.8509 (pt0) cc_final: 0.8281 (pt0) REVERT: P 147 GLN cc_start: 0.8889 (mt0) cc_final: 0.8605 (mt0) REVERT: P 162 GLN cc_start: 0.9283 (mt0) cc_final: 0.9060 (mt0) REVERT: Q 98 ASP cc_start: 0.8002 (m-30) cc_final: 0.7747 (m-30) REVERT: Q 101 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: Q 123 ASP cc_start: 0.8608 (t0) cc_final: 0.8366 (t0) REVERT: Q 224 MET cc_start: 0.9086 (mmm) cc_final: 0.8355 (mmp) REVERT: Q 239 ASN cc_start: 0.8996 (t0) cc_final: 0.8457 (t0) REVERT: R 40 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8140 (ttm-80) REVERT: R 109 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8163 (mm-30) REVERT: T 119 GLU cc_start: 0.7948 (tp30) cc_final: 0.7615 (tm-30) REVERT: U 23 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8172 (t0) REVERT: U 56 TYR cc_start: 0.9195 (t80) cc_final: 0.8916 (t80) REVERT: U 128 SER cc_start: 0.8831 (p) cc_final: 0.8622 (p) REVERT: V 18 HIS cc_start: 0.8510 (m-70) cc_final: 0.8156 (m170) REVERT: V 75 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8749 (tppp) REVERT: V 82 GLN cc_start: 0.9219 (mp10) cc_final: 0.8578 (mp10) REVERT: V 92 ASN cc_start: 0.9068 (t0) cc_final: 0.8231 (t0) REVERT: V 119 GLN cc_start: 0.9006 (mt0) cc_final: 0.8602 (mp10) REVERT: V 131 THR cc_start: 0.8820 (p) cc_final: 0.8533 (t) REVERT: W 49 ARG cc_start: 0.8261 (mtm180) cc_final: 0.7990 (mpp-170) REVERT: W 57 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: W 122 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8276 (mtpm) REVERT: W 139 GLU cc_start: 0.8570 (pm20) cc_final: 0.8305 (pm20) REVERT: X 98 SER cc_start: 0.8986 (t) cc_final: 0.8595 (p) REVERT: X 175 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8450 (mp10) REVERT: Y 143 ASP cc_start: 0.8377 (t70) cc_final: 0.8041 (t0) REVERT: Y 150 GLU cc_start: 0.8140 (tp30) cc_final: 0.7715 (tp30) REVERT: Z 84 ASP cc_start: 0.8051 (m-30) cc_final: 0.7746 (m-30) REVERT: Z 136 ASN cc_start: 0.8034 (t0) cc_final: 0.7575 (t0) REVERT: a 41 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7518 (t70) REVERT: a 46 ASN cc_start: 0.8768 (m-40) cc_final: 0.8212 (m-40) REVERT: a 56 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8276 (mtp180) REVERT: b 45 GLU cc_start: 0.8251 (tp30) cc_final: 0.7433 (tp30) REVERT: b 49 ARG cc_start: 0.8253 (mtp180) cc_final: 0.7799 (mtm-85) REVERT: c 46 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: c 67 ASP cc_start: 0.8640 (t0) cc_final: 0.8074 (t0) REVERT: c 105 ARG cc_start: 0.7906 (ptm160) cc_final: 0.7245 (tpm170) REVERT: d 53 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7555 (mp0) REVERT: d 196 GLN cc_start: 0.8024 (pt0) cc_final: 0.7319 (pp30) REVERT: e 139 GLU cc_start: 0.5161 (OUTLIER) cc_final: 0.4865 (mm-30) REVERT: f 109 TYR cc_start: 0.8266 (t80) cc_final: 0.7918 (t80) REVERT: f 113 LEU cc_start: 0.9111 (mm) cc_final: 0.8665 (tt) REVERT: f 117 LEU cc_start: 0.9051 (mt) cc_final: 0.8801 (mp) REVERT: g 56 ARG cc_start: 0.8098 (mtp-110) cc_final: 0.7751 (ttm110) REVERT: g 73 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7699 (tm130) REVERT: g 98 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8206 (mtpp) REVERT: h 73 TYR cc_start: 0.9131 (m-80) cc_final: 0.8790 (m-80) REVERT: h 99 ASN cc_start: 0.9474 (m-40) cc_final: 0.9096 (m110) REVERT: h 103 HIS cc_start: 0.8760 (m-70) cc_final: 0.8459 (m170) REVERT: h 116 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7718 (mtp180) REVERT: h 122 ARG cc_start: 0.7482 (mtt-85) cc_final: 0.7077 (ptp90) REVERT: h 153 LYS cc_start: 0.9315 (mmtm) cc_final: 0.9024 (mmmt) REVERT: i 58 ASP cc_start: 0.8610 (m-30) cc_final: 0.8393 (m-30) REVERT: i 84 LYS cc_start: 0.9012 (ttpt) cc_final: 0.8773 (ttpt) REVERT: j 61 LYS cc_start: 0.9111 (mmmm) cc_final: 0.8854 (mttp) REVERT: k 14 LYS cc_start: 0.7393 (mmtp) cc_final: 0.7176 (mptt) REVERT: k 43 ARG cc_start: 0.8625 (mtm180) cc_final: 0.8388 (mtm180) REVERT: k 56 ARG cc_start: 0.6437 (tmt170) cc_final: 0.6195 (tpt-90) REVERT: k 84 LEU cc_start: 0.9135 (mm) cc_final: 0.8763 (tt) REVERT: k 90 PHE cc_start: 0.9052 (t80) cc_final: 0.8698 (t80) REVERT: o 91 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: p 156 ASP cc_start: 0.8507 (m-30) cc_final: 0.8229 (m-30) REVERT: p 179 ARG cc_start: 0.8051 (ttp-110) cc_final: 0.7569 (mtm-85) REVERT: p 183 MET cc_start: 0.8540 (ttt) cc_final: 0.8151 (tmm) REVERT: q 134 ASN cc_start: 0.9238 (m110) cc_final: 0.8980 (m110) REVERT: r 104 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9195 (mp) REVERT: r 113 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7716 (mpt-90) REVERT: s 265 LYS cc_start: 0.8381 (mppt) cc_final: 0.8061 (mmtm) REVERT: u 158 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8563 (ttpt) REVERT: u 160 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7952 (mt-10) REVERT: u 186 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7669 (pp20) REVERT: u 187 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8462 (mm) REVERT: v 12 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8549 (tp) REVERT: v 27 ASP cc_start: 0.8397 (t0) cc_final: 0.8143 (t0) REVERT: v 56 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8391 (tp30) REVERT: x 74 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6665 (p0) REVERT: x 81 CYS cc_start: 0.8471 (t) cc_final: 0.8057 (t) REVERT: x 90 SER cc_start: 0.9065 (t) cc_final: 0.8700 (m) REVERT: x 104 ASP cc_start: 0.8170 (m-30) cc_final: 0.7841 (m-30) REVERT: x 135 PHE cc_start: 0.8974 (m-80) cc_final: 0.8590 (m-80) REVERT: x 180 TYR cc_start: 0.8548 (t80) cc_final: 0.8287 (t80) REVERT: x 220 GLU cc_start: 0.8021 (tp30) cc_final: 0.7748 (tp30) outliers start: 303 outliers final: 163 residues processed: 1755 average time/residue: 1.6921 time to fit residues: 4166.5145 Evaluate side-chains 1714 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1519 time to evaluate : 7.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 140 GLN Chi-restraints excluded: chain 0 residue 155 GLU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 3 residue 146 GLU Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 4 residue 70 THR Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 5 residue 274 LYS Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 6 residue 107 LYS Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 148 LYS Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 229 ASP Chi-restraints excluded: chain 6 residue 353 LYS Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 52 GLN Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 100 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 324 GLU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 99 CYS Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 143 ASN Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain M residue 14 ASP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain N residue 177 ASP Chi-restraints excluded: chain N residue 207 ARG Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 202 VAL Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 276 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 111 GLU Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 23 ASN Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 75 LYS Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 86 ASN Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain W residue 122 LYS Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 175 GLN Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 136 LYS Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 136 CYS Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain d residue 118 SER Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 142 LYS Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain e residue 192 LEU Chi-restraints excluded: chain f residue 162 LEU Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain j residue 97 LYS Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain j residue 100 GLU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 94 ILE Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain r residue 159 VAL Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 266 CYS Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 158 LYS Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain u residue 186 GLU Chi-restraints excluded: chain u residue 187 ILE Chi-restraints excluded: chain v residue 12 LEU Chi-restraints excluded: chain v residue 56 GLU Chi-restraints excluded: chain x residue 74 ASP Chi-restraints excluded: chain x residue 124 SER Chi-restraints excluded: chain x residue 204 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 930 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 549 optimal weight: 0.9980 chunk 704 optimal weight: 8.9990 chunk 545 optimal weight: 10.0000 chunk 812 optimal weight: 8.9990 chunk 538 optimal weight: 7.9990 chunk 960 optimal weight: 20.0000 chunk 601 optimal weight: 30.0000 chunk 585 optimal weight: 6.9990 chunk 443 optimal weight: 6.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 170 GLN ** 1 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 3 185 ASN 5 191 GLN 6 191 ASN ** 6 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS G 137 ASN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 GLN M 289 ASN N 138 HIS N 202 GLN P 176 GLN Q 261 ASN R 89 ASN R 147 GLN T 109 ASN T 202 GLN ** V 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 GLN Y 92 ASN Z 61 GLN b 135 ASN c 249 ASN d 149 HIS ** d 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 220 GLN d 274 GLN d 286 GLN ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 130 ASN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 108062 Z= 0.419 Angle : 0.696 14.102 152990 Z= 0.354 Chirality : 0.043 0.260 17868 Planarity : 0.005 0.121 14284 Dihedral : 20.677 179.672 31398 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.74 % Favored : 96.25 % Rotamer: Outliers : 3.89 % Allowed : 22.47 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.09), residues: 8666 helix: 1.30 (0.09), residues: 3076 sheet: -0.38 (0.15), residues: 1163 loop : 0.31 (0.10), residues: 4427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP 8 121 HIS 0.010 0.001 HIS 2 92 PHE 0.030 0.002 PHE G 316 TYR 0.036 0.002 TYR C 376 ARG 0.013 0.001 ARG L 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1860 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1557 time to evaluate : 7.227 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: 0.8225 (tm-30) cc_final: 0.7381 (tm-30) REVERT: 0 132 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8432 (mttp) REVERT: 0 144 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8510 (tm-30) REVERT: 1 20 MET cc_start: 0.8774 (mmm) cc_final: 0.8417 (mmm) REVERT: 3 146 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: 4 73 LYS cc_start: 0.8837 (ttmm) cc_final: 0.8404 (mttp) REVERT: 4 74 LYS cc_start: 0.9295 (mtpt) cc_final: 0.9060 (mtpm) REVERT: 6 107 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9060 (tmmt) REVERT: 6 148 LYS cc_start: 0.9073 (mmmm) cc_final: 0.8740 (mmmm) REVERT: 7 50 LYS cc_start: 0.9413 (mmtm) cc_final: 0.9100 (mmtm) REVERT: 7 143 TRP cc_start: 0.9042 (OUTLIER) cc_final: 0.8075 (m-90) REVERT: 7 181 TYR cc_start: 0.8928 (t80) cc_final: 0.8285 (t80) REVERT: 7 235 TYR cc_start: 0.8369 (m-80) cc_final: 0.8042 (m-80) REVERT: 9 94 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7327 (mt-10) REVERT: C 243 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8066 (pp20) REVERT: C 255 ASP cc_start: 0.8452 (t0) cc_final: 0.7645 (t70) REVERT: C 308 SER cc_start: 0.8451 (t) cc_final: 0.7079 (p) REVERT: C 349 MET cc_start: 0.8671 (tpp) cc_final: 0.8398 (tpp) REVERT: D 78 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8390 (tppt) REVERT: D 161 ASP cc_start: 0.8375 (m-30) cc_final: 0.7895 (m-30) REVERT: D 197 GLU cc_start: 0.8372 (pt0) cc_final: 0.7965 (pt0) REVERT: D 199 GLU cc_start: 0.8054 (mp0) cc_final: 0.7665 (mp0) REVERT: F 103 GLN cc_start: 0.8980 (mt0) cc_final: 0.8678 (mt0) REVERT: F 201 GLN cc_start: 0.8548 (tp40) cc_final: 0.8068 (tp-100) REVERT: G 123 GLN cc_start: 0.8569 (tp40) cc_final: 0.8310 (pt0) REVERT: G 232 TYR cc_start: 0.8813 (t80) cc_final: 0.8127 (t80) REVERT: H 89 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7820 (mtm-85) REVERT: I 108 ASP cc_start: 0.8942 (m-30) cc_final: 0.8697 (m-30) REVERT: I 119 HIS cc_start: 0.8597 (t70) cc_final: 0.8265 (t70) REVERT: I 144 LEU cc_start: 0.9027 (mm) cc_final: 0.8555 (mm) REVERT: J 52 GLU cc_start: 0.8881 (tp30) cc_final: 0.8583 (tp30) REVERT: J 102 ARG cc_start: 0.8048 (tpt170) cc_final: 0.7740 (mpt180) REVERT: J 154 ARG cc_start: 0.8377 (ptp90) cc_final: 0.7771 (ptp90) REVERT: K 98 ARG cc_start: 0.8660 (ttm170) cc_final: 0.8355 (ttm170) REVERT: K 160 GLN cc_start: 0.8280 (tp-100) cc_final: 0.7966 (tp-100) REVERT: K 164 ASP cc_start: 0.8493 (m-30) cc_final: 0.7741 (m-30) REVERT: L 96 MET cc_start: 0.9258 (mmm) cc_final: 0.8823 (mmm) REVERT: L 135 SER cc_start: 0.9136 (m) cc_final: 0.8897 (m) REVERT: M 99 ASN cc_start: 0.9127 (m110) cc_final: 0.8763 (m110) REVERT: M 218 LYS cc_start: 0.8963 (ptpp) cc_final: 0.8560 (ptpp) REVERT: M 280 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8860 (mmmm) REVERT: N 65 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: N 173 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7999 (mm-40) REVERT: N 200 LYS cc_start: 0.9241 (mptt) cc_final: 0.8888 (mmtm) REVERT: N 207 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7457 (ptp-110) REVERT: O 40 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8129 (mt-10) REVERT: O 50 ASP cc_start: 0.8329 (t70) cc_final: 0.8108 (t70) REVERT: O 69 ASN cc_start: 0.9289 (t0) cc_final: 0.8975 (t0) REVERT: O 73 MET cc_start: 0.9516 (tpt) cc_final: 0.9285 (mmm) REVERT: P 57 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7743 (tm-30) REVERT: P 58 LEU cc_start: 0.9358 (mt) cc_final: 0.9092 (mt) REVERT: P 81 LEU cc_start: 0.9305 (tp) cc_final: 0.8983 (tm) REVERT: P 100 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8635 (mtmm) REVERT: P 138 GLU cc_start: 0.8626 (pt0) cc_final: 0.8287 (pt0) REVERT: P 147 GLN cc_start: 0.8986 (mt0) cc_final: 0.8692 (mt0) REVERT: P 158 MET cc_start: 0.9285 (mmp) cc_final: 0.8751 (mmt) REVERT: P 162 GLN cc_start: 0.9263 (mt0) cc_final: 0.9043 (mt0) REVERT: Q 98 ASP cc_start: 0.8059 (m-30) cc_final: 0.7821 (m-30) REVERT: Q 101 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: Q 123 ASP cc_start: 0.8629 (t0) cc_final: 0.8382 (t0) REVERT: Q 239 ASN cc_start: 0.9004 (t0) cc_final: 0.8477 (t0) REVERT: R 40 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.8175 (ttm-80) REVERT: R 109 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8273 (mm-30) REVERT: T 119 GLU cc_start: 0.7993 (tp30) cc_final: 0.7594 (tm-30) REVERT: U 23 ASN cc_start: 0.8701 (t0) cc_final: 0.8330 (t0) REVERT: U 56 TYR cc_start: 0.9284 (t80) cc_final: 0.8928 (t80) REVERT: U 128 SER cc_start: 0.8863 (p) cc_final: 0.8612 (p) REVERT: V 18 HIS cc_start: 0.8584 (m-70) cc_final: 0.8173 (m170) REVERT: V 75 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8712 (tppp) REVERT: V 82 GLN cc_start: 0.9222 (mp10) cc_final: 0.8594 (mp10) REVERT: V 92 ASN cc_start: 0.9112 (t0) cc_final: 0.8265 (t0) REVERT: V 119 GLN cc_start: 0.9012 (mt0) cc_final: 0.8584 (mp10) REVERT: V 131 THR cc_start: 0.8900 (p) cc_final: 0.8616 (t) REVERT: W 57 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: W 99 TYR cc_start: 0.8972 (m-80) cc_final: 0.8736 (m-80) REVERT: X 98 SER cc_start: 0.8995 (t) cc_final: 0.8565 (p) REVERT: X 175 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8446 (mp10) REVERT: Y 143 ASP cc_start: 0.8380 (t70) cc_final: 0.8027 (t0) REVERT: Y 150 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7844 (tp30) REVERT: Z 84 ASP cc_start: 0.8067 (m-30) cc_final: 0.7767 (m-30) REVERT: Z 136 ASN cc_start: 0.8167 (t0) cc_final: 0.7650 (t0) REVERT: a 41 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7565 (t70) REVERT: a 46 ASN cc_start: 0.8774 (m-40) cc_final: 0.8241 (m-40) REVERT: a 56 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8311 (mtp180) REVERT: b 45 GLU cc_start: 0.8299 (tp30) cc_final: 0.7441 (tp30) REVERT: b 49 ARG cc_start: 0.8341 (mtp180) cc_final: 0.7775 (mtm-85) REVERT: c 46 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: c 67 ASP cc_start: 0.8674 (t0) cc_final: 0.8148 (t0) REVERT: c 105 ARG cc_start: 0.7952 (ptm160) cc_final: 0.7191 (tpm170) REVERT: c 217 ASP cc_start: 0.8570 (m-30) cc_final: 0.8332 (m-30) REVERT: d 53 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7606 (mp0) REVERT: d 196 GLN cc_start: 0.8169 (pt0) cc_final: 0.7415 (pp30) REVERT: f 60 LYS cc_start: 0.9221 (mtpp) cc_final: 0.8957 (mtpp) REVERT: f 109 TYR cc_start: 0.8318 (t80) cc_final: 0.7978 (t80) REVERT: f 113 LEU cc_start: 0.9116 (mm) cc_final: 0.8705 (tt) REVERT: f 117 LEU cc_start: 0.9043 (mt) cc_final: 0.8820 (mp) REVERT: g 98 LYS cc_start: 0.8616 (mtmm) cc_final: 0.8248 (mtpp) REVERT: g 116 ASP cc_start: 0.8366 (t0) cc_final: 0.8108 (t70) REVERT: h 73 TYR cc_start: 0.9076 (m-80) cc_final: 0.8827 (m-80) REVERT: h 99 ASN cc_start: 0.9472 (m-40) cc_final: 0.9107 (m110) REVERT: h 103 HIS cc_start: 0.8760 (m-70) cc_final: 0.8470 (m170) REVERT: h 116 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7779 (mtp180) REVERT: h 122 ARG cc_start: 0.7596 (mtt-85) cc_final: 0.7176 (ptp90) REVERT: h 153 LYS cc_start: 0.9318 (mmtm) cc_final: 0.9089 (mmmt) REVERT: i 58 ASP cc_start: 0.8648 (m-30) cc_final: 0.8426 (m-30) REVERT: i 84 LYS cc_start: 0.9049 (ttpt) cc_final: 0.8798 (ttpt) REVERT: j 61 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8909 (mttp) REVERT: k 43 ARG cc_start: 0.8616 (mtm180) cc_final: 0.7949 (mtm180) REVERT: k 56 ARG cc_start: 0.6445 (tmt170) cc_final: 0.5936 (tmt90) REVERT: k 84 LEU cc_start: 0.9168 (mm) cc_final: 0.8773 (tt) REVERT: k 90 PHE cc_start: 0.9066 (t80) cc_final: 0.8735 (t80) REVERT: o 91 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: p 124 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8892 (ptpp) REVERT: p 136 THR cc_start: 0.9116 (p) cc_final: 0.8914 (p) REVERT: p 156 ASP cc_start: 0.8536 (m-30) cc_final: 0.8297 (m-30) REVERT: p 179 ARG cc_start: 0.8061 (ttp-110) cc_final: 0.7828 (mtm110) REVERT: p 183 MET cc_start: 0.8564 (ttt) cc_final: 0.8211 (tmm) REVERT: q 134 ASN cc_start: 0.9227 (m110) cc_final: 0.8955 (m110) REVERT: r 59 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8335 (tp30) REVERT: r 104 ILE cc_start: 0.9470 (OUTLIER) cc_final: 0.9209 (mp) REVERT: r 113 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7746 (mpt-90) REVERT: r 117 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7931 (mm-30) REVERT: s 265 LYS cc_start: 0.8456 (mppt) cc_final: 0.8176 (mmtm) REVERT: u 160 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7894 (mt-10) REVERT: u 183 GLU cc_start: 0.8281 (pm20) cc_final: 0.7984 (pm20) REVERT: u 186 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7620 (pp20) REVERT: v 12 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8552 (tp) REVERT: v 27 ASP cc_start: 0.8459 (t0) cc_final: 0.8144 (t0) REVERT: v 56 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8393 (tp30) REVERT: w 103 HIS cc_start: 0.6451 (t70) cc_final: 0.6202 (t-90) REVERT: x 74 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6783 (p0) REVERT: x 81 CYS cc_start: 0.8518 (t) cc_final: 0.8092 (t) REVERT: x 90 SER cc_start: 0.9090 (t) cc_final: 0.8737 (m) REVERT: x 104 ASP cc_start: 0.8160 (m-30) cc_final: 0.7845 (m-30) REVERT: x 164 LYS cc_start: 0.8798 (ptpt) cc_final: 0.8188 (mptt) outliers start: 303 outliers final: 185 residues processed: 1716 average time/residue: 1.7439 time to fit residues: 4219.2789 Evaluate side-chains 1720 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1506 time to evaluate : 7.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 140 GLN Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 3 residue 146 GLU Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 4 residue 70 THR Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 5 residue 148 GLU Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 6 residue 107 LYS Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 52 GLN Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 100 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 324 GLU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain L residue 43 ASN Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 143 ASN Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain M residue 14 ASP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain N residue 207 ARG Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 156 ASP Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 202 VAL Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 276 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 111 GLU Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 75 LYS Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 175 GLN Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 150 GLU Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 136 LYS Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 136 CYS Chi-restraints excluded: chain d residue 118 SER Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 142 LYS Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain e residue 192 LEU Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 162 LEU Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain j residue 97 LYS Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 94 ILE Chi-restraints excluded: chain o residue 51 MET Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 124 LYS Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain r residue 117 GLU Chi-restraints excluded: chain r residue 159 VAL Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 254 ASP Chi-restraints excluded: chain s residue 266 CYS Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain u residue 186 GLU Chi-restraints excluded: chain v residue 12 LEU Chi-restraints excluded: chain v residue 29 ASP Chi-restraints excluded: chain v residue 42 ASN Chi-restraints excluded: chain v residue 56 GLU Chi-restraints excluded: chain x residue 74 ASP Chi-restraints excluded: chain x residue 124 SER Chi-restraints excluded: chain x residue 153 LEU Chi-restraints excluded: chain x residue 204 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 594 optimal weight: 4.9990 chunk 383 optimal weight: 0.8980 chunk 573 optimal weight: 10.0000 chunk 289 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 610 optimal weight: 4.9990 chunk 654 optimal weight: 10.0000 chunk 475 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 755 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 15 ASN ** 2 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 3 185 ASN 6 191 ASN ** 6 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS E 336 ASN F 184 GLN G 137 ASN G 195 ASN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 289 ASN N 138 HIS N 202 GLN Q 261 ASN R 77 GLN R 89 ASN R 147 GLN T 109 ASN T 133 ASN T 202 GLN ** V 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 GLN Y 92 ASN b 25 GLN d 149 HIS d 161 HIS ** d 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 286 GLN e 67 GLN ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 182 ASN r 130 ASN s 152 GLN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 108062 Z= 0.264 Angle : 0.663 14.309 152990 Z= 0.337 Chirality : 0.040 0.392 17868 Planarity : 0.005 0.116 14284 Dihedral : 20.702 179.782 31398 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 3.21 % Allowed : 23.87 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.09), residues: 8666 helix: 1.25 (0.09), residues: 3093 sheet: -0.36 (0.15), residues: 1133 loop : 0.32 (0.10), residues: 4440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP 6 214 HIS 0.009 0.001 HIS 2 92 PHE 0.042 0.001 PHE G 316 TYR 0.044 0.002 TYR f 106 ARG 0.015 0.000 ARG g 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1828 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1578 time to evaluate : 7.239 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: 0 127 TYR cc_start: 0.8879 (t80) cc_final: 0.8623 (t80) REVERT: 0 128 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7424 (tm-30) REVERT: 0 132 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8437 (mttp) REVERT: 0 143 LYS cc_start: 0.8846 (mtpp) cc_final: 0.8552 (mtmm) REVERT: 0 144 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8454 (tm-30) REVERT: 1 20 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8380 (mmm) REVERT: 3 146 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: 4 73 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8346 (mttp) REVERT: 6 107 LYS cc_start: 0.9488 (ttpt) cc_final: 0.8975 (tmmt) REVERT: 6 148 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8700 (mmmm) REVERT: 6 214 TRP cc_start: 0.7733 (m100) cc_final: 0.7251 (m100) REVERT: 7 50 LYS cc_start: 0.9411 (mmtm) cc_final: 0.9110 (mmtm) REVERT: 7 143 TRP cc_start: 0.8980 (OUTLIER) cc_final: 0.8106 (m-90) REVERT: 7 181 TYR cc_start: 0.8887 (t80) cc_final: 0.8288 (t80) REVERT: 7 235 TYR cc_start: 0.8314 (m-80) cc_final: 0.8053 (m-80) REVERT: C 243 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8063 (pp20) REVERT: C 255 ASP cc_start: 0.8338 (t0) cc_final: 0.7476 (t70) REVERT: C 308 SER cc_start: 0.8311 (t) cc_final: 0.7100 (p) REVERT: C 349 MET cc_start: 0.8656 (tpp) cc_final: 0.8378 (tpp) REVERT: D 78 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8413 (tppt) REVERT: D 161 ASP cc_start: 0.8363 (m-30) cc_final: 0.7893 (m-30) REVERT: D 197 GLU cc_start: 0.8404 (pt0) cc_final: 0.8001 (pt0) REVERT: D 199 GLU cc_start: 0.8057 (mp0) cc_final: 0.7851 (mp0) REVERT: D 246 ARG cc_start: 0.8703 (ptp-110) cc_final: 0.8457 (ptm160) REVERT: F 201 GLN cc_start: 0.8501 (tp40) cc_final: 0.7999 (tp-100) REVERT: G 123 GLN cc_start: 0.8572 (tp40) cc_final: 0.8333 (pt0) REVERT: G 158 GLN cc_start: 0.8003 (mp10) cc_final: 0.7720 (mp10) REVERT: H 93 ASN cc_start: 0.8852 (m-40) cc_final: 0.8650 (t0) REVERT: I 95 MET cc_start: 0.7830 (ppp) cc_final: 0.7538 (ppp) REVERT: I 100 GLN cc_start: 0.6239 (mt0) cc_final: 0.5357 (mt0) REVERT: I 108 ASP cc_start: 0.9062 (m-30) cc_final: 0.8738 (m-30) REVERT: I 114 HIS cc_start: 0.8945 (t70) cc_final: 0.8636 (t-170) REVERT: I 119 HIS cc_start: 0.8602 (t70) cc_final: 0.8296 (t70) REVERT: I 144 LEU cc_start: 0.9031 (mm) cc_final: 0.8565 (mm) REVERT: I 152 MET cc_start: 0.6884 (mpt) cc_final: 0.6427 (pmm) REVERT: J 54 ASN cc_start: 0.8572 (m-40) cc_final: 0.8055 (m110) REVERT: J 102 ARG cc_start: 0.8019 (tpt170) cc_final: 0.7764 (mpt180) REVERT: J 142 ARG cc_start: 0.8694 (mtt90) cc_final: 0.8401 (mtt90) REVERT: J 154 ARG cc_start: 0.8367 (ptp90) cc_final: 0.7755 (ptp90) REVERT: K 98 ARG cc_start: 0.8644 (ttm170) cc_final: 0.8349 (ttm170) REVERT: K 135 GLU cc_start: 0.7581 (tp30) cc_final: 0.7333 (tp30) REVERT: K 139 LYS cc_start: 0.9184 (mmmm) cc_final: 0.8966 (mmtp) REVERT: K 160 GLN cc_start: 0.8318 (tp-100) cc_final: 0.8001 (tp-100) REVERT: K 164 ASP cc_start: 0.8574 (m-30) cc_final: 0.7809 (m-30) REVERT: L 135 SER cc_start: 0.9128 (m) cc_final: 0.8887 (m) REVERT: M 99 ASN cc_start: 0.9084 (m110) cc_final: 0.8739 (m110) REVERT: M 218 LYS cc_start: 0.8931 (ptpp) cc_final: 0.8530 (ptpp) REVERT: M 238 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7802 (mtt90) REVERT: M 280 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8882 (mmmm) REVERT: M 292 LYS cc_start: 0.8771 (ttpp) cc_final: 0.8564 (pttm) REVERT: N 65 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8042 (pt0) REVERT: N 148 ASP cc_start: 0.7871 (t0) cc_final: 0.7639 (t0) REVERT: N 173 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8253 (mm-40) REVERT: O 40 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8085 (mt-10) REVERT: O 69 ASN cc_start: 0.9275 (t0) cc_final: 0.8969 (t0) REVERT: O 73 MET cc_start: 0.9508 (tpt) cc_final: 0.9295 (mmm) REVERT: P 57 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7720 (tm-30) REVERT: P 58 LEU cc_start: 0.9350 (mt) cc_final: 0.8913 (mt) REVERT: P 81 LEU cc_start: 0.9220 (tp) cc_final: 0.8970 (tm) REVERT: P 100 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8605 (mtmm) REVERT: P 113 LYS cc_start: 0.9224 (ptmt) cc_final: 0.8783 (ptpt) REVERT: P 137 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9013 (mp) REVERT: P 138 GLU cc_start: 0.8592 (pt0) cc_final: 0.8308 (pt0) REVERT: P 147 GLN cc_start: 0.8995 (mt0) cc_final: 0.8714 (mt0) REVERT: P 158 MET cc_start: 0.9259 (mmp) cc_final: 0.8714 (mmt) REVERT: P 162 GLN cc_start: 0.9211 (mt0) cc_final: 0.8991 (mt0) REVERT: Q 98 ASP cc_start: 0.7988 (m-30) cc_final: 0.7717 (m-30) REVERT: Q 101 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: Q 123 ASP cc_start: 0.8587 (t0) cc_final: 0.8338 (t0) REVERT: Q 224 MET cc_start: 0.9093 (mmm) cc_final: 0.8504 (mmp) REVERT: Q 239 ASN cc_start: 0.8983 (t0) cc_final: 0.8428 (t0) REVERT: R 40 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.8145 (ttm-80) REVERT: R 141 ILE cc_start: 0.9491 (mm) cc_final: 0.9282 (tp) REVERT: T 119 GLU cc_start: 0.7963 (tp30) cc_final: 0.7610 (tm-30) REVERT: U 22 THR cc_start: 0.9181 (m) cc_final: 0.8877 (m) REVERT: U 23 ASN cc_start: 0.8595 (t0) cc_final: 0.8282 (t0) REVERT: U 56 TYR cc_start: 0.9203 (t80) cc_final: 0.8944 (t80) REVERT: V 18 HIS cc_start: 0.8487 (m-70) cc_final: 0.8276 (m-70) REVERT: V 75 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8729 (tppp) REVERT: V 82 GLN cc_start: 0.9212 (mp10) cc_final: 0.8593 (mp10) REVERT: V 92 ASN cc_start: 0.9103 (t0) cc_final: 0.8245 (t0) REVERT: V 119 GLN cc_start: 0.8957 (mt0) cc_final: 0.8579 (mt0) REVERT: V 131 THR cc_start: 0.8868 (p) cc_final: 0.8570 (t) REVERT: W 57 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: X 36 ARG cc_start: 0.7205 (ptm-80) cc_final: 0.6787 (ptm-80) REVERT: X 98 SER cc_start: 0.8989 (t) cc_final: 0.8616 (p) REVERT: X 175 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8422 (mp10) REVERT: Y 143 ASP cc_start: 0.8365 (t70) cc_final: 0.8015 (t0) REVERT: Y 150 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7720 (tp30) REVERT: Z 84 ASP cc_start: 0.8036 (m-30) cc_final: 0.7750 (m-30) REVERT: Z 136 ASN cc_start: 0.8221 (t0) cc_final: 0.7711 (t0) REVERT: a 41 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7546 (t70) REVERT: a 46 ASN cc_start: 0.8755 (m-40) cc_final: 0.8229 (m-40) REVERT: a 56 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8273 (mtp180) REVERT: b 45 GLU cc_start: 0.8227 (tp30) cc_final: 0.7827 (tp30) REVERT: b 49 ARG cc_start: 0.8331 (mtp180) cc_final: 0.7774 (mtm-85) REVERT: c 46 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: c 67 ASP cc_start: 0.8632 (t0) cc_final: 0.8089 (t0) REVERT: c 105 ARG cc_start: 0.7965 (ptm160) cc_final: 0.7155 (tpm170) REVERT: c 217 ASP cc_start: 0.8571 (m-30) cc_final: 0.8332 (m-30) REVERT: d 53 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7611 (mp0) REVERT: d 196 GLN cc_start: 0.8238 (pt0) cc_final: 0.7573 (pp30) REVERT: d 216 MET cc_start: 0.7073 (mmm) cc_final: 0.6481 (mmm) REVERT: f 109 TYR cc_start: 0.8255 (t80) cc_final: 0.7964 (t80) REVERT: f 113 LEU cc_start: 0.9116 (mm) cc_final: 0.8679 (tt) REVERT: f 117 LEU cc_start: 0.9044 (mt) cc_final: 0.8792 (mp) REVERT: g 56 ARG cc_start: 0.8106 (mtp-110) cc_final: 0.7802 (ttm110) REVERT: g 98 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8212 (mtpp) REVERT: g 116 ASP cc_start: 0.8280 (t0) cc_final: 0.8047 (t70) REVERT: h 73 TYR cc_start: 0.9116 (m-80) cc_final: 0.8882 (m-80) REVERT: h 103 HIS cc_start: 0.8731 (m-70) cc_final: 0.8455 (m170) REVERT: h 116 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7726 (mtp180) REVERT: h 122 ARG cc_start: 0.7513 (mtt-85) cc_final: 0.7000 (ptp-110) REVERT: h 153 LYS cc_start: 0.9309 (mmtm) cc_final: 0.9075 (mmmt) REVERT: i 84 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8790 (ttpt) REVERT: j 61 LYS cc_start: 0.9076 (mmmm) cc_final: 0.8836 (mttp) REVERT: k 43 ARG cc_start: 0.8628 (mtm180) cc_final: 0.7972 (mtm180) REVERT: k 56 ARG cc_start: 0.6943 (tmt170) cc_final: 0.6521 (tmt90) REVERT: k 84 LEU cc_start: 0.9192 (mm) cc_final: 0.8807 (tt) REVERT: k 90 PHE cc_start: 0.9031 (t80) cc_final: 0.8700 (t80) REVERT: o 91 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8132 (tt0) REVERT: p 118 LYS cc_start: 0.9247 (ttmm) cc_final: 0.9038 (ttpt) REVERT: p 136 THR cc_start: 0.9091 (p) cc_final: 0.8891 (p) REVERT: p 156 ASP cc_start: 0.8598 (m-30) cc_final: 0.8324 (m-30) REVERT: p 179 ARG cc_start: 0.8095 (ttp-110) cc_final: 0.7866 (mtm110) REVERT: p 183 MET cc_start: 0.8563 (ttt) cc_final: 0.8230 (tmm) REVERT: q 134 ASN cc_start: 0.9219 (m110) cc_final: 0.8950 (m110) REVERT: q 143 TRP cc_start: 0.7844 (m100) cc_final: 0.7375 (t60) REVERT: r 59 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8384 (tp30) REVERT: r 104 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9192 (mp) REVERT: r 113 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7730 (mpt-90) REVERT: s 265 LYS cc_start: 0.8360 (mppt) cc_final: 0.8116 (mmtm) REVERT: u 160 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7892 (mt-10) REVERT: u 183 GLU cc_start: 0.8324 (pm20) cc_final: 0.8075 (pm20) REVERT: u 186 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7583 (pp20) REVERT: v 12 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8530 (tp) REVERT: v 27 ASP cc_start: 0.8483 (t0) cc_final: 0.8167 (t0) REVERT: v 56 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8361 (tp30) REVERT: w 87 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7857 (mm) REVERT: x 74 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6756 (p0) REVERT: x 81 CYS cc_start: 0.8490 (t) cc_final: 0.8064 (t) REVERT: x 90 SER cc_start: 0.9073 (t) cc_final: 0.8713 (m) REVERT: x 104 ASP cc_start: 0.8133 (m-30) cc_final: 0.7853 (m-30) REVERT: x 119 ASP cc_start: 0.8460 (m-30) cc_final: 0.8079 (m-30) outliers start: 250 outliers final: 156 residues processed: 1703 average time/residue: 1.6805 time to fit residues: 4025.4631 Evaluate side-chains 1684 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1501 time to evaluate : 7.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 140 GLN Chi-restraints excluded: chain 0 residue 155 GLU Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 20 MET Chi-restraints excluded: chain 1 residue 29 CYS Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 3 residue 146 GLU Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 4 residue 70 THR Chi-restraints excluded: chain 5 residue 274 LYS Chi-restraints excluded: chain 5 residue 364 LEU Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 325 ASP Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 353 LYS Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 52 GLN Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 100 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 324 GLU Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain L residue 43 ASN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 143 ASN Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain M residue 14 ASP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 202 VAL Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 111 GLU Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 75 LYS Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 175 GLN Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 150 GLU Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 136 LYS Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 136 CYS Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 142 LYS Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain e residue 192 LEU Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain g residue 57 ILE Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 134 LYS Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 94 ILE Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain r residue 159 VAL Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 266 CYS Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain u residue 186 GLU Chi-restraints excluded: chain v residue 12 LEU Chi-restraints excluded: chain v residue 29 ASP Chi-restraints excluded: chain v residue 56 GLU Chi-restraints excluded: chain w residue 87 LEU Chi-restraints excluded: chain x residue 74 ASP Chi-restraints excluded: chain x residue 124 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 874 optimal weight: 6.9990 chunk 920 optimal weight: 5.9990 chunk 839 optimal weight: 0.9990 chunk 895 optimal weight: 4.9990 chunk 538 optimal weight: 8.9990 chunk 390 optimal weight: 0.9990 chunk 703 optimal weight: 8.9990 chunk 274 optimal weight: 10.0000 chunk 809 optimal weight: 40.0000 chunk 846 optimal weight: 6.9990 chunk 892 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 3 178 GLN 3 185 ASN 6 191 ASN ** 6 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS G 137 ASN G 158 GLN ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 GLN ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 GLN M 289 ASN N 86 ASN N 138 HIS N 202 GLN R 89 ASN R 147 GLN T 109 ASN T 202 GLN V 35 ASN W 70 GLN Y 92 ASN b 25 GLN b 135 ASN c 249 ASN d 149 HIS d 161 HIS ** d 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 274 GLN d 286 GLN ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 152 GLN r 130 ASN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 ASN x 199 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 108062 Z= 0.313 Angle : 0.684 14.713 152990 Z= 0.348 Chirality : 0.041 0.422 17868 Planarity : 0.005 0.117 14284 Dihedral : 20.665 179.803 31398 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 2.97 % Allowed : 24.47 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.09), residues: 8666 helix: 1.17 (0.09), residues: 3105 sheet: -0.42 (0.15), residues: 1158 loop : 0.31 (0.10), residues: 4403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP 6 214 HIS 0.011 0.001 HIS 2 92 PHE 0.040 0.002 PHE G 316 TYR 0.034 0.002 TYR C 376 ARG 0.014 0.001 ARG j 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1773 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1542 time to evaluate : 6.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 128 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7445 (tm-30) REVERT: 0 132 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8466 (mttp) REVERT: 0 143 LYS cc_start: 0.8866 (mtpp) cc_final: 0.8557 (mtmm) REVERT: 0 144 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8634 (tm-30) REVERT: 1 20 MET cc_start: 0.8727 (mmm) cc_final: 0.8390 (mmm) REVERT: 3 146 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: 4 73 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8349 (mttp) REVERT: 6 107 LYS cc_start: 0.9378 (ttpt) cc_final: 0.8983 (tmmt) REVERT: 6 148 LYS cc_start: 0.9060 (mmmm) cc_final: 0.8708 (mmmm) REVERT: 7 50 LYS cc_start: 0.9425 (mmtm) cc_final: 0.9114 (mmtm) REVERT: 7 143 TRP cc_start: 0.9031 (OUTLIER) cc_final: 0.8105 (m-90) REVERT: 7 163 MET cc_start: 0.7447 (tpp) cc_final: 0.7190 (tpt) REVERT: 7 181 TYR cc_start: 0.8932 (t80) cc_final: 0.8292 (t80) REVERT: 7 235 TYR cc_start: 0.8338 (m-80) cc_final: 0.8069 (m-80) REVERT: 9 115 GLU cc_start: 0.8668 (mp0) cc_final: 0.8452 (mp0) REVERT: C 243 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8074 (pp20) REVERT: C 255 ASP cc_start: 0.8444 (t0) cc_final: 0.7827 (t70) REVERT: C 308 SER cc_start: 0.8460 (t) cc_final: 0.7292 (p) REVERT: C 349 MET cc_start: 0.8658 (tpp) cc_final: 0.8385 (tpp) REVERT: D 78 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8416 (tppt) REVERT: D 161 ASP cc_start: 0.8368 (m-30) cc_final: 0.7901 (m-30) REVERT: D 197 GLU cc_start: 0.8502 (pt0) cc_final: 0.8073 (pt0) REVERT: D 246 ARG cc_start: 0.8707 (ptp-110) cc_final: 0.8476 (ptm160) REVERT: F 103 GLN cc_start: 0.8920 (mt0) cc_final: 0.8637 (mt0) REVERT: F 201 GLN cc_start: 0.8523 (tp40) cc_final: 0.8016 (tp-100) REVERT: G 123 GLN cc_start: 0.8574 (tp40) cc_final: 0.8335 (pt0) REVERT: H 89 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7894 (mtm-85) REVERT: H 116 LYS cc_start: 0.9093 (mttm) cc_final: 0.8779 (mttp) REVERT: I 95 MET cc_start: 0.7905 (ppp) cc_final: 0.7552 (ppp) REVERT: I 108 ASP cc_start: 0.9068 (m-30) cc_final: 0.8789 (m-30) REVERT: I 119 HIS cc_start: 0.8605 (t70) cc_final: 0.8302 (t70) REVERT: I 144 LEU cc_start: 0.9061 (mm) cc_final: 0.8588 (mm) REVERT: I 152 MET cc_start: 0.6855 (mpt) cc_final: 0.6503 (pmm) REVERT: J 54 ASN cc_start: 0.8624 (m-40) cc_final: 0.8297 (m110) REVERT: J 154 ARG cc_start: 0.8371 (ptp90) cc_final: 0.7802 (ptp90) REVERT: K 98 ARG cc_start: 0.8648 (ttm170) cc_final: 0.8354 (ttm170) REVERT: K 135 GLU cc_start: 0.7666 (tp30) cc_final: 0.7432 (tp30) REVERT: K 136 ASP cc_start: 0.8146 (p0) cc_final: 0.7831 (p0) REVERT: K 160 GLN cc_start: 0.8370 (tp-100) cc_final: 0.8041 (tp-100) REVERT: K 164 ASP cc_start: 0.8561 (m-30) cc_final: 0.7795 (m-30) REVERT: L 96 MET cc_start: 0.9241 (mmm) cc_final: 0.8784 (mmm) REVERT: L 128 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.6641 (ttm170) REVERT: L 135 SER cc_start: 0.9138 (m) cc_final: 0.8888 (m) REVERT: M 99 ASN cc_start: 0.9086 (m110) cc_final: 0.8760 (m110) REVERT: M 218 LYS cc_start: 0.8944 (ptpp) cc_final: 0.8546 (ptpp) REVERT: M 238 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7702 (mtt90) REVERT: M 280 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8881 (mmmm) REVERT: M 292 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8535 (pttm) REVERT: N 65 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8041 (pt0) REVERT: N 173 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7958 (mm-40) REVERT: N 197 LYS cc_start: 0.9346 (tmtp) cc_final: 0.8967 (tptm) REVERT: N 201 ASP cc_start: 0.8562 (m-30) cc_final: 0.8271 (m-30) REVERT: O 40 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8090 (mt-10) REVERT: O 69 ASN cc_start: 0.9285 (t0) cc_final: 0.8954 (t0) REVERT: O 73 MET cc_start: 0.9511 (tpt) cc_final: 0.9296 (mmm) REVERT: P 57 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7661 (tm-30) REVERT: P 58 LEU cc_start: 0.9356 (mt) cc_final: 0.8918 (mt) REVERT: P 81 LEU cc_start: 0.9302 (tp) cc_final: 0.9009 (tm) REVERT: P 100 LYS cc_start: 0.9014 (mtpt) cc_final: 0.8594 (mtmm) REVERT: P 108 ARG cc_start: 0.3862 (tmt170) cc_final: 0.3154 (tmt170) REVERT: P 113 LYS cc_start: 0.9240 (ptmt) cc_final: 0.8834 (ptpt) REVERT: P 137 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9009 (mp) REVERT: P 138 GLU cc_start: 0.8585 (pt0) cc_final: 0.8314 (pt0) REVERT: P 147 GLN cc_start: 0.9003 (mt0) cc_final: 0.8718 (mt0) REVERT: P 158 MET cc_start: 0.9270 (mmp) cc_final: 0.8708 (mmt) REVERT: P 162 GLN cc_start: 0.9197 (mt0) cc_final: 0.8986 (mt0) REVERT: Q 101 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: Q 123 ASP cc_start: 0.8597 (t0) cc_final: 0.8352 (t0) REVERT: Q 239 ASN cc_start: 0.8981 (t0) cc_final: 0.8420 (t0) REVERT: R 40 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.8158 (ttm-80) REVERT: R 141 ILE cc_start: 0.9487 (mm) cc_final: 0.9270 (tp) REVERT: T 119 GLU cc_start: 0.7967 (tp30) cc_final: 0.7588 (tm-30) REVERT: U 22 THR cc_start: 0.9117 (m) cc_final: 0.8859 (m) REVERT: U 23 ASN cc_start: 0.8608 (t0) cc_final: 0.8305 (t0) REVERT: U 56 TYR cc_start: 0.9201 (t80) cc_final: 0.8917 (t80) REVERT: V 18 HIS cc_start: 0.8499 (m-70) cc_final: 0.8067 (m170) REVERT: V 75 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8728 (tppp) REVERT: V 82 GLN cc_start: 0.9224 (mp10) cc_final: 0.8610 (mp10) REVERT: V 92 ASN cc_start: 0.9100 (t0) cc_final: 0.8224 (t0) REVERT: V 119 GLN cc_start: 0.8900 (mt0) cc_final: 0.8537 (mp10) REVERT: V 131 THR cc_start: 0.8855 (p) cc_final: 0.8594 (t) REVERT: W 57 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7368 (tt0) REVERT: W 139 GLU cc_start: 0.8400 (pm20) cc_final: 0.8177 (pt0) REVERT: X 36 ARG cc_start: 0.7218 (ptm-80) cc_final: 0.6793 (ptm-80) REVERT: X 98 SER cc_start: 0.8998 (t) cc_final: 0.8630 (p) REVERT: X 175 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8437 (mp10) REVERT: Y 111 MET cc_start: 0.8543 (tmt) cc_final: 0.8245 (tmm) REVERT: Y 150 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7802 (tp30) REVERT: Z 84 ASP cc_start: 0.8043 (m-30) cc_final: 0.7774 (m-30) REVERT: Z 136 ASN cc_start: 0.8201 (t0) cc_final: 0.7708 (t0) REVERT: a 41 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7631 (t70) REVERT: a 56 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8274 (mtp180) REVERT: b 45 GLU cc_start: 0.8221 (tp30) cc_final: 0.7945 (tp30) REVERT: b 49 ARG cc_start: 0.8354 (mtp180) cc_final: 0.7826 (mtm-85) REVERT: c 46 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: c 67 ASP cc_start: 0.8653 (t0) cc_final: 0.8117 (t0) REVERT: c 105 ARG cc_start: 0.7958 (ptm160) cc_final: 0.7169 (tpm170) REVERT: c 217 ASP cc_start: 0.8574 (m-30) cc_final: 0.8327 (m-30) REVERT: d 53 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7661 (mp0) REVERT: d 196 GLN cc_start: 0.8260 (pt0) cc_final: 0.7585 (pp30) REVERT: d 216 MET cc_start: 0.7158 (mmm) cc_final: 0.6565 (mmm) REVERT: f 109 TYR cc_start: 0.8409 (t80) cc_final: 0.8101 (t80) REVERT: f 113 LEU cc_start: 0.9123 (mm) cc_final: 0.8673 (tt) REVERT: f 117 LEU cc_start: 0.8951 (mt) cc_final: 0.8740 (mp) REVERT: g 49 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8285 (mm-30) REVERT: g 56 ARG cc_start: 0.8112 (mtp-110) cc_final: 0.7768 (ttm110) REVERT: g 98 LYS cc_start: 0.8606 (mtmm) cc_final: 0.8226 (mtpp) REVERT: h 103 HIS cc_start: 0.8734 (m-70) cc_final: 0.8481 (m170) REVERT: h 122 ARG cc_start: 0.7480 (mtt-85) cc_final: 0.7004 (ptp-110) REVERT: h 153 LYS cc_start: 0.9310 (mmtm) cc_final: 0.9070 (mmmt) REVERT: i 84 LYS cc_start: 0.9052 (ttpt) cc_final: 0.8800 (ttpt) REVERT: j 61 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8848 (mttp) REVERT: k 43 ARG cc_start: 0.8630 (mtm180) cc_final: 0.7988 (mtm180) REVERT: k 56 ARG cc_start: 0.6958 (tmt170) cc_final: 0.6502 (tmt90) REVERT: k 84 LEU cc_start: 0.9170 (mm) cc_final: 0.8783 (tt) REVERT: k 90 PHE cc_start: 0.9013 (t80) cc_final: 0.8690 (t80) REVERT: o 91 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: p 118 LYS cc_start: 0.9246 (ttmm) cc_final: 0.9014 (ttpt) REVERT: p 136 THR cc_start: 0.9101 (p) cc_final: 0.8893 (p) REVERT: p 156 ASP cc_start: 0.8594 (m-30) cc_final: 0.8326 (m-30) REVERT: p 179 ARG cc_start: 0.8110 (ttp-110) cc_final: 0.7881 (mtm110) REVERT: p 183 MET cc_start: 0.8567 (ttt) cc_final: 0.8232 (tmm) REVERT: q 134 ASN cc_start: 0.9224 (m110) cc_final: 0.8959 (m110) REVERT: r 59 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8429 (tp30) REVERT: r 104 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9202 (mp) REVERT: r 113 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7733 (mpt-90) REVERT: s 265 LYS cc_start: 0.8413 (mppt) cc_final: 0.8174 (mmtm) REVERT: u 160 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7795 (mt-10) REVERT: u 183 GLU cc_start: 0.8307 (pm20) cc_final: 0.8075 (pm20) REVERT: u 186 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7605 (pp20) REVERT: v 12 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8542 (tp) REVERT: v 27 ASP cc_start: 0.8508 (t0) cc_final: 0.8200 (t0) REVERT: v 56 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8348 (tp30) REVERT: x 74 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6704 (p0) REVERT: x 81 CYS cc_start: 0.8430 (t) cc_final: 0.7992 (t) REVERT: x 90 SER cc_start: 0.9073 (t) cc_final: 0.8717 (m) REVERT: x 104 ASP cc_start: 0.8162 (m-30) cc_final: 0.7882 (m-30) REVERT: x 119 ASP cc_start: 0.8368 (m-30) cc_final: 0.8164 (m-30) outliers start: 231 outliers final: 161 residues processed: 1667 average time/residue: 1.6334 time to fit residues: 3827.4457 Evaluate side-chains 1686 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1499 time to evaluate : 6.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 155 GLU Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 3 residue 146 GLU Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 4 residue 70 THR Chi-restraints excluded: chain 4 residue 94 THR Chi-restraints excluded: chain 5 residue 148 GLU Chi-restraints excluded: chain 5 residue 274 LYS Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 6 residue 62 GLU Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 353 LYS Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 52 GLN Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 100 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 308 THR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 324 GLU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 43 ASN Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 128 ARG Chi-restraints excluded: chain L residue 143 ASN Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain M residue 14 ASP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 202 VAL Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 276 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 111 GLU Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain V residue 75 LYS Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 175 GLN Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 150 GLU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 136 CYS Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 142 LYS Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain e residue 192 LEU Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 162 LEU Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 134 LYS Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 94 ILE Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 108 LEU Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain r residue 159 VAL Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 266 CYS Chi-restraints excluded: chain s residue 269 ASP Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain u residue 186 GLU Chi-restraints excluded: chain v residue 12 LEU Chi-restraints excluded: chain v residue 29 ASP Chi-restraints excluded: chain v residue 42 ASN Chi-restraints excluded: chain v residue 56 GLU Chi-restraints excluded: chain x residue 74 ASP Chi-restraints excluded: chain x residue 124 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 588 optimal weight: 7.9990 chunk 946 optimal weight: 1.9990 chunk 577 optimal weight: 1.9990 chunk 449 optimal weight: 20.0000 chunk 658 optimal weight: 4.9990 chunk 993 optimal weight: 30.0000 chunk 914 optimal weight: 0.4980 chunk 790 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 610 optimal weight: 7.9990 chunk 484 optimal weight: 8.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 170 GLN ** 2 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 3 185 ASN 6 191 ASN ** 6 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 285 ASN C 218 HIS D 235 GLN G 137 ASN G 195 ASN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 GLN M 289 ASN N 138 HIS N 202 GLN R 77 GLN R 89 ASN R 147 GLN T 202 GLN U 138 GLN W 70 GLN Y 92 ASN b 25 GLN d 149 HIS d 161 HIS d 274 GLN d 286 GLN ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 130 ASN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 ASN x 144 ASN x 199 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 108062 Z= 0.276 Angle : 0.688 14.834 152990 Z= 0.349 Chirality : 0.041 0.362 17868 Planarity : 0.005 0.116 14284 Dihedral : 20.663 179.875 31398 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 2.58 % Allowed : 25.13 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.09), residues: 8666 helix: 1.15 (0.09), residues: 3095 sheet: -0.41 (0.15), residues: 1149 loop : 0.30 (0.10), residues: 4422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.001 TRP 6 214 HIS 0.016 0.001 HIS V 117 PHE 0.043 0.001 PHE G 316 TYR 0.039 0.002 TYR f 106 ARG 0.025 0.000 ARG j 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17332 Ramachandran restraints generated. 8666 Oldfield, 0 Emsley, 8666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1747 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1546 time to evaluate : 7.069 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: 0 128 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7432 (tm-30) REVERT: 0 132 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8478 (mttp) REVERT: 0 143 LYS cc_start: 0.8845 (mtpp) cc_final: 0.8554 (mtmm) REVERT: 0 144 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8640 (tm-30) REVERT: 3 146 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: 4 73 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8336 (mttp) REVERT: 4 74 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8968 (mtpm) REVERT: 6 107 LYS cc_start: 0.9306 (ttpt) cc_final: 0.8964 (tmmt) REVERT: 6 148 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8668 (mmmm) REVERT: 6 274 LYS cc_start: 0.8302 (tppp) cc_final: 0.8016 (mmtm) REVERT: 7 50 LYS cc_start: 0.9427 (mmtm) cc_final: 0.9110 (mmtm) REVERT: 7 143 TRP cc_start: 0.9015 (OUTLIER) cc_final: 0.8083 (m-90) REVERT: 7 163 MET cc_start: 0.7445 (tpp) cc_final: 0.7188 (tpt) REVERT: 7 181 TYR cc_start: 0.8917 (t80) cc_final: 0.8317 (t80) REVERT: 7 235 TYR cc_start: 0.8342 (m-80) cc_final: 0.8069 (m-80) REVERT: 9 59 GLU cc_start: 0.8185 (tp30) cc_final: 0.7961 (tm-30) REVERT: 9 115 GLU cc_start: 0.8646 (mp0) cc_final: 0.8423 (mp0) REVERT: C 243 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8086 (pp20) REVERT: C 255 ASP cc_start: 0.8347 (t0) cc_final: 0.7534 (t70) REVERT: C 308 SER cc_start: 0.8325 (t) cc_final: 0.7154 (p) REVERT: C 349 MET cc_start: 0.8653 (tpp) cc_final: 0.8383 (tpp) REVERT: D 161 ASP cc_start: 0.8355 (m-30) cc_final: 0.7888 (m-30) REVERT: D 197 GLU cc_start: 0.8523 (pt0) cc_final: 0.8096 (pt0) REVERT: D 199 GLU cc_start: 0.8160 (mp0) cc_final: 0.7805 (mp0) REVERT: D 246 ARG cc_start: 0.8745 (ptp-110) cc_final: 0.8545 (ptm160) REVERT: F 201 GLN cc_start: 0.8509 (tp40) cc_final: 0.8004 (tp-100) REVERT: G 92 LEU cc_start: 0.8835 (mt) cc_final: 0.8626 (tm) REVERT: H 116 LYS cc_start: 0.9086 (mttm) cc_final: 0.8784 (mttp) REVERT: H 141 GLU cc_start: 0.8050 (pp20) cc_final: 0.7809 (pp20) REVERT: I 95 MET cc_start: 0.7912 (ppp) cc_final: 0.7552 (ppp) REVERT: I 108 ASP cc_start: 0.8909 (m-30) cc_final: 0.8519 (m-30) REVERT: I 114 HIS cc_start: 0.8795 (t70) cc_final: 0.8543 (t-170) REVERT: I 119 HIS cc_start: 0.8618 (t70) cc_final: 0.8327 (t70) REVERT: I 144 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8518 (mm) REVERT: I 152 MET cc_start: 0.6930 (mpt) cc_final: 0.6647 (pmm) REVERT: J 54 ASN cc_start: 0.8663 (m-40) cc_final: 0.8312 (m110) REVERT: J 142 ARG cc_start: 0.8634 (mtt90) cc_final: 0.8397 (mtt90) REVERT: J 154 ARG cc_start: 0.8380 (ptp90) cc_final: 0.7808 (ptp90) REVERT: K 98 ARG cc_start: 0.8644 (ttm170) cc_final: 0.8349 (ttm170) REVERT: K 136 ASP cc_start: 0.8120 (p0) cc_final: 0.7875 (p0) REVERT: K 160 GLN cc_start: 0.8383 (tp-100) cc_final: 0.8054 (tp-100) REVERT: K 164 ASP cc_start: 0.8537 (m-30) cc_final: 0.7756 (m-30) REVERT: L 96 MET cc_start: 0.9204 (mmm) cc_final: 0.8726 (mmm) REVERT: L 135 SER cc_start: 0.9133 (m) cc_final: 0.8893 (m) REVERT: M 99 ASN cc_start: 0.9079 (m110) cc_final: 0.8747 (m110) REVERT: M 218 LYS cc_start: 0.8939 (ptpp) cc_final: 0.8538 (ptpp) REVERT: M 280 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8853 (mmmm) REVERT: M 292 LYS cc_start: 0.8776 (ttpp) cc_final: 0.8528 (pttm) REVERT: N 65 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8045 (pt0) REVERT: N 140 MET cc_start: 0.7058 (mpm) cc_final: 0.6335 (pp-130) REVERT: O 40 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8087 (mt-10) REVERT: O 69 ASN cc_start: 0.9281 (t0) cc_final: 0.8954 (t0) REVERT: O 73 MET cc_start: 0.9497 (tpt) cc_final: 0.9259 (mmm) REVERT: P 58 LEU cc_start: 0.9360 (mt) cc_final: 0.9115 (mt) REVERT: P 81 LEU cc_start: 0.9238 (tp) cc_final: 0.8996 (tm) REVERT: P 100 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8608 (mtmm) REVERT: P 108 ARG cc_start: 0.3850 (tmt170) cc_final: 0.3104 (tmt170) REVERT: P 113 LYS cc_start: 0.9257 (ptmt) cc_final: 0.8884 (ptpt) REVERT: P 138 GLU cc_start: 0.8587 (pt0) cc_final: 0.8272 (pt0) REVERT: P 147 GLN cc_start: 0.8940 (mt0) cc_final: 0.8662 (mt0) REVERT: P 158 MET cc_start: 0.9265 (mmp) cc_final: 0.8708 (mmt) REVERT: P 162 GLN cc_start: 0.9201 (mt0) cc_final: 0.8992 (mt0) REVERT: Q 123 ASP cc_start: 0.8586 (t0) cc_final: 0.8339 (t0) REVERT: Q 224 MET cc_start: 0.9090 (mmm) cc_final: 0.8460 (mmp) REVERT: Q 239 ASN cc_start: 0.8972 (t0) cc_final: 0.8406 (t0) REVERT: R 40 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.8124 (ttm-80) REVERT: T 119 GLU cc_start: 0.7961 (tp30) cc_final: 0.7601 (tm-30) REVERT: U 22 THR cc_start: 0.9119 (m) cc_final: 0.8866 (m) REVERT: U 23 ASN cc_start: 0.8588 (t0) cc_final: 0.8276 (t0) REVERT: U 56 TYR cc_start: 0.9147 (t80) cc_final: 0.8869 (t80) REVERT: U 131 GLU cc_start: 0.7965 (pp20) cc_final: 0.6175 (pm20) REVERT: V 75 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8731 (tppp) REVERT: V 82 GLN cc_start: 0.9223 (mp10) cc_final: 0.8618 (mp10) REVERT: V 92 ASN cc_start: 0.9111 (t0) cc_final: 0.8280 (t0) REVERT: V 119 GLN cc_start: 0.8867 (mt0) cc_final: 0.8498 (mp10) REVERT: V 131 THR cc_start: 0.8862 (p) cc_final: 0.8599 (t) REVERT: W 57 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: X 36 ARG cc_start: 0.7223 (ptm-80) cc_final: 0.6766 (ptm-80) REVERT: X 98 SER cc_start: 0.8986 (t) cc_final: 0.8627 (p) REVERT: X 175 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8431 (mp10) REVERT: Y 111 MET cc_start: 0.8513 (tmt) cc_final: 0.8181 (tmm) REVERT: Y 150 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7795 (tp30) REVERT: Z 84 ASP cc_start: 0.8019 (m-30) cc_final: 0.7754 (m-30) REVERT: Z 136 ASN cc_start: 0.8226 (t0) cc_final: 0.7686 (t0) REVERT: a 41 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7630 (t70) REVERT: a 56 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8268 (mtp180) REVERT: b 45 GLU cc_start: 0.8184 (tp30) cc_final: 0.7620 (tp30) REVERT: b 49 ARG cc_start: 0.8340 (mtp180) cc_final: 0.7681 (mtm-85) REVERT: b 92 LYS cc_start: 0.9184 (mttm) cc_final: 0.8913 (mttp) REVERT: c 46 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: c 67 ASP cc_start: 0.8642 (t0) cc_final: 0.8101 (t0) REVERT: c 105 ARG cc_start: 0.7949 (ptm160) cc_final: 0.7107 (tpm170) REVERT: c 217 ASP cc_start: 0.8574 (m-30) cc_final: 0.8329 (m-30) REVERT: c 249 ASN cc_start: 0.8612 (t0) cc_final: 0.8394 (t0) REVERT: d 53 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7658 (mp0) REVERT: d 196 GLN cc_start: 0.8263 (pt0) cc_final: 0.7628 (pp30) REVERT: d 216 MET cc_start: 0.7226 (mmm) cc_final: 0.6633 (mmm) REVERT: f 109 TYR cc_start: 0.8388 (t80) cc_final: 0.8125 (t80) REVERT: f 113 LEU cc_start: 0.9110 (mm) cc_final: 0.8658 (tt) REVERT: f 117 LEU cc_start: 0.8950 (mt) cc_final: 0.8722 (mp) REVERT: g 56 ARG cc_start: 0.8134 (mtp-110) cc_final: 0.7802 (ttm110) REVERT: g 73 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7700 (tm130) REVERT: g 98 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8221 (mtpp) REVERT: g 116 ASP cc_start: 0.8326 (t0) cc_final: 0.8090 (t70) REVERT: g 142 GLU cc_start: 0.8549 (tt0) cc_final: 0.8282 (pt0) REVERT: h 73 TYR cc_start: 0.9100 (m-80) cc_final: 0.8856 (m-80) REVERT: h 103 HIS cc_start: 0.8720 (m-70) cc_final: 0.8449 (m170) REVERT: h 122 ARG cc_start: 0.7469 (mtt-85) cc_final: 0.6998 (ptp-110) REVERT: h 153 LYS cc_start: 0.9306 (mmtm) cc_final: 0.9062 (mmmt) REVERT: i 84 LYS cc_start: 0.9042 (ttpt) cc_final: 0.8784 (ttpt) REVERT: j 61 LYS cc_start: 0.9049 (mmmm) cc_final: 0.8821 (mttp) REVERT: k 43 ARG cc_start: 0.8611 (mtm180) cc_final: 0.7958 (mtm180) REVERT: k 56 ARG cc_start: 0.6960 (tmt170) cc_final: 0.6548 (tmt90) REVERT: k 84 LEU cc_start: 0.9173 (mm) cc_final: 0.8784 (tt) REVERT: k 90 PHE cc_start: 0.8988 (t80) cc_final: 0.8724 (t80) REVERT: o 91 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: p 118 LYS cc_start: 0.9255 (ttmm) cc_final: 0.9036 (ttpt) REVERT: p 124 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8822 (ptpp) REVERT: p 136 THR cc_start: 0.9089 (p) cc_final: 0.8870 (p) REVERT: p 156 ASP cc_start: 0.8552 (m-30) cc_final: 0.8280 (m-30) REVERT: p 179 ARG cc_start: 0.8108 (ttp-110) cc_final: 0.7893 (mtm110) REVERT: p 183 MET cc_start: 0.8552 (ttt) cc_final: 0.8187 (tmm) REVERT: q 134 ASN cc_start: 0.9223 (m110) cc_final: 0.8961 (m110) REVERT: q 143 TRP cc_start: 0.7896 (m100) cc_final: 0.7414 (t60) REVERT: r 59 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8480 (tp30) REVERT: r 104 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9195 (mp) REVERT: r 113 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7697 (mpt-90) REVERT: r 117 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7878 (mm-30) REVERT: s 265 LYS cc_start: 0.8386 (mppt) cc_final: 0.8132 (mmtm) REVERT: u 138 MET cc_start: 0.8877 (ptm) cc_final: 0.8312 (mtp) REVERT: u 160 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7930 (mt-10) REVERT: u 186 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7597 (pp20) REVERT: v 12 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8527 (tp) REVERT: v 27 ASP cc_start: 0.8530 (t0) cc_final: 0.8235 (t0) REVERT: v 56 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8340 (tp30) REVERT: x 74 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6655 (p0) REVERT: x 81 CYS cc_start: 0.8492 (t) cc_final: 0.8154 (t) REVERT: x 90 SER cc_start: 0.9063 (t) cc_final: 0.8710 (m) REVERT: x 104 ASP cc_start: 0.8162 (m-30) cc_final: 0.7901 (m-30) outliers start: 201 outliers final: 158 residues processed: 1650 average time/residue: 1.6617 time to fit residues: 3858.8777 Evaluate side-chains 1675 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1494 time to evaluate : 6.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 86 THR Chi-restraints excluded: chain 0 residue 155 GLU Chi-restraints excluded: chain 0 residue 172 LYS Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 3 residue 146 GLU Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 4 residue 70 THR Chi-restraints excluded: chain 5 residue 274 LYS Chi-restraints excluded: chain 5 residue 404 VAL Chi-restraints excluded: chain 6 residue 133 ASP Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 7 residue 38 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain 7 residue 166 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 7 residue 293 LEU Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 140 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 52 GLN Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 100 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 324 GLU Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 90 PHE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 43 ASN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 143 ASN Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain M residue 14 ASP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 156 ASP 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 150 ILE Chi-restraints excluded: chain Q residue 198 SER Chi-restraints excluded: chain Q residue 202 VAL Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 276 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 111 GLU Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 138 GLN Chi-restraints excluded: chain V residue 75 LYS Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 183 LEU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain X residue 175 GLN Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 70 ASP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 150 GLU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain b residue 6 THR Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 136 CYS Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 142 LYS Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain e residue 191 THR Chi-restraints excluded: chain e residue 192 LEU Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 162 LEU Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 134 LYS Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 94 ILE Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 124 LYS Chi-restraints excluded: chain p residue 135 LEU Chi-restraints excluded: chain q residue 41 ASP Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 104 ILE Chi-restraints excluded: chain r residue 113 ARG Chi-restraints excluded: chain r residue 159 VAL Chi-restraints excluded: chain r residue 190 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 266 CYS Chi-restraints excluded: chain u residue 126 ILE Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain u residue 186 GLU Chi-restraints excluded: chain v residue 12 LEU Chi-restraints excluded: chain v residue 29 ASP Chi-restraints excluded: chain v residue 42 ASN Chi-restraints excluded: chain v residue 56 GLU Chi-restraints excluded: chain x residue 74 ASP Chi-restraints excluded: chain x residue 124 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 628 optimal weight: 6.9990 chunk 842 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 729 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 792 optimal weight: 20.0000 chunk 331 optimal weight: 0.9990 chunk 813 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 154 GLN 3 185 ASN 6 191 ASN ** 6 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN G 137 ASN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 GLN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 HIS L 72 GLN M 289 ASN N 138 HIS N 202 GLN R 89 ASN R 147 GLN T 202 GLN U 138 GLN V 35 ASN W 70 GLN Y 92 ASN b 25 GLN b 135 ASN d 149 HIS ** d 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 274 GLN ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 182 ASN r 130 ASN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 ASN x 144 ASN x 199 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.080836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.057601 restraints weight = 278957.795| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.96 r_work: 0.2740 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.235 108062 Z= 0.374 Angle : 0.748 59.200 152990 Z= 0.384 Chirality : 0.043 0.700 17868 Planarity : 0.005 0.121 14284 Dihedral : 20.656 179.893 31398 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 2.73 % Allowed : 25.28 % Favored : 71.99 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.09), residues: 8666 helix: 1.12 (0.09), residues: 3095 sheet: -0.39 (0.15), residues: 1151 loop : 0.30 (0.10), residues: 4420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP Q 264 HIS 0.018 0.001 HIS V 117 PHE 0.038 0.002 PHE G 316 TYR 0.031 0.002 TYR C 376 ARG 0.023 0.001 ARG c 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 55348.36 seconds wall clock time: 954 minutes 8.91 seconds (57248.91 seconds total)