Starting phenix.real_space_refine on Thu Feb 22 18:22:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of7_12872/02_2024/7of7_12872_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of7_12872/02_2024/7of7_12872.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of7_12872/02_2024/7of7_12872_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of7_12872/02_2024/7of7_12872_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of7_12872/02_2024/7of7_12872_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of7_12872/02_2024/7of7_12872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of7_12872/02_2024/7of7_12872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of7_12872/02_2024/7of7_12872_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7of7_12872/02_2024/7of7_12872_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1432 5.49 5 Mg 74 5.21 5 S 311 5.16 5 C 58654 2.51 5 N 18329 2.21 5 O 22229 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" Residue "m TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 101032 Number of models: 1 Model: "" Number of chains: 64 Chain: "0" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 880 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "1" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "3" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 831 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "4" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 333 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "5" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3199 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 359} Chain: "6" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2723 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 28, 'TRANS': 295} Chain breaks: 3 Chain: "7" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2334 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 17, 'TRANS': 269} Chain: "8" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 651 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "9" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 107} Chain breaks: 1 Chain: "A" Number of atoms: 29222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1376, 29222 Classifications: {'RNA': 1376} Modifications used: {'rna2p_pur': 147, 'rna2p_pyr': 109, 'rna3p': 3, 'rna3p_pur': 577, 'rna3p_pyr': 540} Link IDs: {'rna2p': 255, 'rna3p': 1120} Chain breaks: 17 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: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1872 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 13, 'TRANS': 226} Chain: "E" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2427 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 24, 'TRANS': 283} Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "G" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1943 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 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: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 971 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "S" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "T" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1368 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 12, 'TRANS': 153} Chain: "U" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1154 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain breaks: 1 Chain: "V" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 395 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "W" Number of atoms: 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: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 937 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 10, 'TRANS': 104} Chain: "a" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 597 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 8, 'TRANS': 62} Chain breaks: 1 Chain: "b" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1178 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "c" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2217 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 258} Chain breaks: 1 Chain: "d" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1653 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 18, 'TRANS': 180} Chain breaks: 4 Chain: "e" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1599 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 9, 'TRANS': 187} Chain breaks: 2 Chain: "f" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 857 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 113} Chain: "h" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 862 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain breaks: 1 Chain: "i" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 827 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "j" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain: "k" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 627 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "m" Number of atoms: 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Unusual residues: {' MG': 71} Classifications: {'undetermined': 71} Link IDs: {None: 70} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 264 SG CYS 0 110 143.465 39.877 127.086 1.00 73.16 S ATOM 286 SG CYS 0 113 146.693 40.570 125.447 1.00 79.58 S ATOM 366 SG CYS 0 123 143.925 43.211 125.090 1.00 64.20 S ATOM 389 SG CYS 0 126 144.101 39.982 123.132 1.00 67.74 S ATOM 2605 SG CYS 4 76 65.331 109.161 169.001 1.00 99.92 S ATOM 2628 SG CYS 4 79 69.049 108.886 168.287 1.00 94.22 S ATOM 2752 SG CYS 4 92 66.659 105.862 167.978 1.00 91.75 S ATOM 55127 SG CYS I 64 91.683 114.186 197.529 1.00 94.10 S ATOM 93725 SG CYS r 70 89.868 110.782 199.040 1.00 87.39 S ATOM 93746 SG CYS r 73 92.106 112.316 199.785 1.00 87.85 S ATOM 94040 SG CYS r 108 88.948 112.529 196.940 1.00 83.92 S Time building chain proxies: 40.18, per 1000 atoms: 0.40 Number of scatterers: 101032 At special positions: 0 Unit cell: (234.15, 237.3, 227.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 311 16.00 P 1432 15.00 Mg 74 11.99 O 22229 8.00 N 18329 7.00 C 58654 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: 37.92 Conformation dependent library (CDL) restraints added in 10.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb=" ZN 4 200 " pdb="ZN ZN 4 200 " - pdb=" ND1 HIS 4 98 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 76 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 92 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 79 " pdb=" ZN r 301 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 73 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 108 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 70 " pdb="ZN ZN r 301 " - pdb=" SG CYS I 64 " Number of angles added : 15 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16296 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 76 sheets defined 43.3% alpha, 13.4% beta 381 base pairs and 707 stacking pairs defined. Time for finding SS restraints: 60.60 Creating SS restraints... Processing helix chain '0' and resid 86 through 95 Processing helix chain '0' and resid 96 through 101 removed outlier: 5.308A 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 72 removed outlier: 4.050A pdb=" N THR 2 72 " --> pdb=" O ARG 2 68 " (cutoff:3.500A) Processing helix chain '2' and resid 73 through 86 Processing helix chain '3' and resid 107 through 114 removed outlier: 3.630A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG 3 113 " --> pdb=" O ALA 3 109 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 3.945A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.522A 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: 3.848A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 4.920A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 182 removed outlier: 4.677A pdb=" N ASP 3 182 " --> pdb=" O GLN 3 178 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 40 removed outlier: 5.084A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 53 removed outlier: 4.252A pdb=" N GLU 5 51 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE 5 52 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) Proline residue: 5 53 - end of helix No H-bonds generated for 'chain '5' and resid 47 through 53' Processing helix chain '5' and resid 116 through 125 Processing helix chain '5' and resid 133 through 142 removed outlier: 4.173A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP 5 141 " --> pdb=" O LEU 5 137 " (cutoff:3.500A) removed outlier: 4.337A 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: 4.129A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.545A 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: 4.108A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 304 removed outlier: 4.977A 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: 3.957A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 49 removed outlier: 5.259A pdb=" N GLU 6 49 " --> pdb=" O LEU 6 45 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 68 removed outlier: 3.748A 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: 3.848A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 99 through 117 removed outlier: 5.312A 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: 4.984A pdb=" N GLY 6 248 " --> pdb=" O ARG 6 244 " (cutoff:3.500A) removed outlier: 5.867A 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: 3.542A pdb=" N HIS 6 307 " --> pdb=" O PHE 6 303 " (cutoff:3.500A) Processing helix chain '6' and resid 324 through 333 removed outlier: 3.526A pdb=" N THR 6 328 " --> pdb=" O ASP 6 324 " (cutoff:3.500A) Processing helix chain '6' and resid 362 through 371 removed outlier: 4.959A pdb=" N LEU 6 366 " --> pdb=" O PRO 6 362 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP 6 367 " --> pdb=" O LEU 6 363 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP 6 371 " --> pdb=" O ASP 6 367 " (cutoff:3.500A) Processing helix chain '6' and resid 157 through 163 removed outlier: 4.079A pdb=" N PHE 6 162 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 60 Proline residue: 7 60 - end of helix Processing helix chain '7' and resid 87 through 96 Processing helix chain '7' and resid 97 through 103 Processing helix chain '7' and resid 135 through 158 removed outlier: 4.046A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 186 through 191 removed outlier: 4.707A 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 322 removed outlier: 3.675A pdb=" N ARG 7 321 " --> pdb=" O LEU 7 317 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 3.510A pdb=" N ILE 7 274 " --> pdb=" O ARG 7 271 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS 7 275 " --> pdb=" O THR 7 272 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 271 through 276' Processing helix chain '8' and resid 107 through 154 removed outlier: 3.503A pdb=" N THR 8 111 " --> pdb=" O THR 8 107 " (cutoff:3.500A) Processing helix chain '8' and resid 155 through 164 removed outlier: 5.138A pdb=" N ALA 8 159 " --> pdb=" O PRO 8 155 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU 8 160 " --> pdb=" O LYS 8 156 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE 8 162 " --> pdb=" O HIS 8 158 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS 8 163 " --> pdb=" O ALA 8 159 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '8' and resid 165 through 170 removed outlier: 3.923A pdb=" N LEU 8 168 " --> pdb=" O ASP 8 165 " (cutoff:3.500A) removed outlier: 4.418A 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 35 removed outlier: 5.685A pdb=" N GLY 9 35 " --> pdb=" O ARG 9 31 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 58 removed outlier: 3.573A 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: 3.658A pdb=" N ASP 9 106 " --> pdb=" O LYS 9 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 57 removed outlier: 3.573A pdb=" N SER C 53 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL C 54 " --> pdb=" O MET C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 removed outlier: 4.756A pdb=" N SER C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 4.808A 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 107 removed outlier: 3.903A pdb=" N GLU C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 103 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N HIS C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 170 removed outlier: 4.024A pdb=" N LEU C 163 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Proline residue: C 165 - end of helix removed outlier: 3.968A pdb=" N GLY C 170 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 195 removed outlier: 3.872A pdb=" N THR C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 220 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 237 through 245 removed outlier: 3.544A pdb=" N TRP C 241 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 5.617A 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 277 through 300 Proline residue: C 285 - end of helix removed outlier: 5.765A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 331 removed outlier: 3.821A pdb=" N TYR C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL C 320 " --> pdb=" O GLN C 316 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 349 Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.810A 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: 3.755A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 294 removed outlier: 4.489A pdb=" N SER D 294 " --> pdb=" O PRO D 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 3.651A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 3.908A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.728A pdb=" N ASN E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.357A pdb=" N LYS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 6.144A 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: 4.567A pdb=" N PHE E 198 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 through 199' Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 108 removed outlier: 4.623A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 6.277A 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: 3.643A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 3.788A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 5.050A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 3.727A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG F 279 " --> pdb=" O TRP F 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 103 removed outlier: 3.673A pdb=" N MET G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 4.613A 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 removed outlier: 3.595A pdb=" N GLY G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) 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: 4.314A pdb=" N LYS G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG G 178 " --> pdb=" O GLY G 174 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL G 179 " --> pdb=" O LYS G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 190 removed outlier: 5.781A pdb=" N ARG G 190 " --> pdb=" O ILE G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 203 Processing helix chain 'G' and resid 208 through 219 Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.906A pdb=" N ARG G 224 " --> pdb=" O PRO G 220 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP G 226 " --> pdb=" O VAL G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 239 removed outlier: 5.724A pdb=" N GLU G 231 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 252 Processing helix chain 'G' and resid 257 through 272 removed outlier: 3.568A pdb=" N TYR G 267 " --> pdb=" O GLN G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 294 Processing helix chain 'G' and resid 297 through 304 Processing helix chain 'G' and resid 309 through 328 Processing helix chain 'H' and resid 74 through 79 removed outlier: 3.760A pdb=" N ARG H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.423A 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: 3.992A 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: 3.740A 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: 3.754A pdb=" N GLN I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 120 removed outlier: 3.962A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.386A 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: 3.719A pdb=" N GLU I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 148 removed outlier: 3.803A pdb=" N PHE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 143 through 148' Processing helix chain 'I' and resid 160 through 172 removed outlier: 3.669A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) Proline residue: I 172 - end of helix Processing helix chain 'I' and resid 187 through 197 Processing helix chain 'J' and resid 36 through 41 removed outlier: 3.729A pdb=" N GLN J 41 " --> pdb=" O PRO J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 4.349A pdb=" N LYS J 61 " --> pdb=" O THR J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 96 removed outlier: 3.931A pdb=" N PHE J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 125 removed outlier: 4.241A pdb=" N ILE J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA J 125 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 152 removed outlier: 4.082A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 4.057A 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: 4.902A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU K 125 " --> pdb=" O MET K 121 " (cutoff:3.500A) removed outlier: 5.484A 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: 5.414A 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: 4.801A pdb=" N LYS L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLU L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 125 through 131' Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'M' and resid 10 through 20 removed outlier: 3.626A 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: 3.518A 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: 3.634A 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: 3.630A 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: 3.892A pdb=" N PHE M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Proline residue: M 230 - end of helix Processing helix chain 'M' and resid 246 through 251 removed outlier: 3.951A pdb=" N ASP M 250 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 5.371A 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: 4.703A pdb=" N ILE N 72 " --> pdb=" O ASN N 68 " (cutoff:3.500A) removed outlier: 4.987A 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: 3.792A pdb=" N VAL N 172 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.773A 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: 4.366A pdb=" N VAL N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 4.471A 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: 4.371A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 81 removed outlier: 5.050A pdb=" N THR O 81 " --> pdb=" O ASP O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 98 removed outlier: 4.331A pdb=" N ILE O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 87 - end of helix removed outlier: 3.847A pdb=" N LEU O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA O 94 " --> pdb=" O PHE O 90 " (cutoff:3.500A) Proline residue: O 95 - end of helix Processing helix chain 'O' and resid 143 through 160 Processing helix chain 'P' and resid 54 through 60 Processing helix chain 'P' and resid 109 through 117 removed outlier: 5.082A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU P 116 " --> pdb=" O ILE P 112 " (cutoff:3.500A) removed outlier: 5.760A 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: 4.162A 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 106 removed outlier: 3.799A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 193 removed outlier: 4.736A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASP Q 192 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 199 removed outlier: 4.041A pdb=" N SER Q 198 " --> pdb=" O LEU Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 removed outlier: 3.927A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 262 removed outlier: 3.736A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 268 removed outlier: 4.386A 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: 3.770A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA R 28 " --> pdb=" O VAL R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 38 removed outlier: 4.477A pdb=" N ARG R 37 " --> pdb=" O GLY R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 64 removed outlier: 3.906A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS R 61 " --> pdb=" O ARG R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 79 removed outlier: 3.695A pdb=" N HIS R 79 " --> pdb=" O ALA R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 Processing helix chain 'R' and resid 98 through 108 Processing helix chain 'R' and resid 109 through 125 Processing helix chain 'S' and resid 68 through 90 Processing helix chain 'S' and resid 150 through 155 removed outlier: 3.559A pdb=" N VAL S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 5.011A 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: 3.775A pdb=" N LYS T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN T 55 " --> pdb=" O TRP T 51 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE T 57 " --> pdb=" O LYS T 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 95 removed outlier: 3.995A pdb=" N TYR T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 109 removed outlier: 3.708A pdb=" N PHE T 108 " --> pdb=" O ALA T 104 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN T 109 " --> pdb=" O GLN T 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 131 removed outlier: 4.207A pdb=" N LYS T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 206 removed outlier: 3.699A 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 178 through 184 Processing helix chain 'V' and resid 193 through 203 Processing helix chain 'W' and resid 110 through 121 removed outlier: 3.566A 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: 3.706A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) removed outlier: 4.885A 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: 5.446A pdb=" N GLU X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 79 removed outlier: 4.079A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG X 77 " --> pdb=" O PRO X 73 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 4.528A 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: 4.546A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) removed outlier: 3.638A 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: 3.622A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 69 removed outlier: 4.721A pdb=" N PHE Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 5.141A 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 86 through 94 removed outlier: 3.802A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS Y 93 " --> pdb=" O GLN Y 89 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 removed outlier: 3.651A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 129 through 158 removed outlier: 3.813A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 192 removed outlier: 5.377A pdb=" N LYS Y 192 " --> pdb=" O TRP Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 198 removed outlier: 5.249A pdb=" N ARG Y 198 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 238 removed outlier: 4.440A pdb=" N ASP Y 206 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 48 removed outlier: 4.404A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) removed outlier: 5.843A 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: 4.064A pdb=" N THR a 72 " --> pdb=" O PRO a 68 " (cutoff:3.500A) removed outlier: 5.510A 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: 4.666A pdb=" N TRP a 123 " --> pdb=" O THR a 119 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR a 124 " --> pdb=" O LYS a 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 119 through 124' Processing helix chain 'a' and resid 127 through 135 removed outlier: 5.662A pdb=" N ASN a 135 " --> pdb=" O ARG a 131 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.608A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 4.722A 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: 3.604A pdb=" N ARG b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.275A 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: 5.499A 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: 3.802A 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: 3.531A pdb=" N VAL c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASN c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 107 removed outlier: 3.593A 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: 3.618A pdb=" N ILE c 220 " --> pdb=" O ARG c 216 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N MET c 223 " --> pdb=" O LEU c 219 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR c 224 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 4.255A 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: 4.283A pdb=" N THR d 52 " --> pdb=" O PRO d 48 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS d 54 " --> pdb=" O PHE d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 118 through 130 removed outlier: 4.202A 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 removed outlier: 3.682A pdb=" N ASN d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 164 removed outlier: 3.946A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 174 Proline residue: d 170 - end of helix Processing helix chain 'e' and resid 64 through 82 Processing helix chain 'e' and resid 116 through 132 removed outlier: 3.798A pdb=" N LEU e 120 " --> pdb=" O LEU e 116 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE e 131 " --> pdb=" O LYS e 127 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 143 removed outlier: 4.826A pdb=" N GLU e 142 " --> pdb=" O THR e 138 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS e 143 " --> pdb=" O GLU e 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 138 through 143' Processing helix chain 'e' and resid 183 through 194 removed outlier: 3.964A pdb=" N ALA e 193 " --> pdb=" O GLU e 189 " (cutoff:3.500A) Processing helix chain 'e' and resid 256 through 264 removed outlier: 6.391A pdb=" N LEU e 260 " --> pdb=" O THR e 256 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY e 261 " --> pdb=" O LYS e 257 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 277 removed outlier: 3.696A pdb=" N GLN e 271 " --> pdb=" O LYS e 267 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL e 272 " --> pdb=" O TYR e 268 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG e 273 " --> pdb=" O LEU e 269 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N SER e 277 " --> pdb=" O ARG e 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 64 removed outlier: 4.669A pdb=" N LYS f 64 " --> pdb=" O LYS f 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 99 through 118 Processing helix chain 'f' and resid 163 through 178 removed outlier: 3.588A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU f 178 " --> pdb=" O ILE f 174 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 53 removed outlier: 4.406A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) Proline residue: g 53 - end of helix Processing helix chain 'g' and resid 116 through 132 Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 153 through 165 Processing helix chain 'h' and resid 65 through 78 Processing helix chain 'h' and resid 93 through 109 Processing helix chain 'h' and resid 113 through 121 removed outlier: 4.320A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET h 120 " --> pdb=" O ARG h 116 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N CYS h 121 " --> pdb=" O LEU h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 132 removed outlier: 3.633A pdb=" N VAL h 132 " --> pdb=" O ASP h 128 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 147 removed outlier: 4.261A pdb=" N SER h 146 " --> pdb=" O GLU h 142 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASN h 147 " --> pdb=" O LEU h 143 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 54 Processing helix chain 'i' and resid 59 through 64 Processing helix chain 'i' and resid 69 through 74 removed outlier: 4.089A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE i 74 " --> pdb=" O PRO i 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 69 through 74' Processing helix chain 'i' and resid 86 through 98 Processing helix chain 'i' and resid 103 through 123 Processing helix chain 'j' and resid 24 through 32 removed outlier: 3.735A pdb=" N ARG j 28 " --> pdb=" O GLY j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 36 through 41 removed outlier: 4.981A pdb=" N TYR j 40 " --> pdb=" O ASN j 36 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLY j 41 " --> pdb=" O PRO j 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 36 through 41' Processing helix chain 'j' and resid 60 through 105 Processing helix chain 'k' and resid 27 through 37 removed outlier: 3.693A pdb=" N ARG k 31 " --> pdb=" O VAL k 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 47 removed outlier: 5.143A 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: 4.208A pdb=" N MET o 51 " --> pdb=" O TYR o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 63 through 81 removed outlier: 3.906A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 removed outlier: 3.503A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS o 99 " --> pdb=" O LEU o 95 " (cutoff:3.500A) removed outlier: 5.848A 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: 4.056A pdb=" N ALA p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TRP p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 72 through 77 removed outlier: 5.068A 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: 3.764A pdb=" N ILE p 178 " --> pdb=" O LYS p 174 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLN p 190 " --> pdb=" O GLU p 186 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 53 removed outlier: 3.954A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 3.746A 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: 4.317A pdb=" N LEU q 75 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 4.596A 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: 4.181A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 5.651A 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: 4.216A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 5.070A 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 167 through 193 removed outlier: 4.250A 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: 4.163A 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: 4.464A pdb=" N ILE s 320 " --> pdb=" O CYS s 316 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU s 321 " --> pdb=" O ALA s 317 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 387 removed outlier: 5.396A pdb=" N ASN s 386 " --> pdb=" O GLN s 382 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASN s 387 " --> pdb=" O ALA s 383 " (cutoff:3.500A) Processing helix chain 's' and resid 414 through 427 removed outlier: 3.871A 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 24 removed outlier: 4.059A pdb=" N VAL v 9 " --> pdb=" O SER v 5 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU v 10 " --> pdb=" O ARG v 6 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU v 23 " --> pdb=" O GLN v 19 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG v 24 " --> pdb=" O GLY v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 41 Processing helix chain 'v' and resid 47 through 64 removed outlier: 3.839A pdb=" N ARG v 51 " --> pdb=" O ASP v 47 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU v 52 " --> pdb=" O ALA v 48 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG v 53 " --> pdb=" O GLU v 49 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 90 removed outlier: 3.566A pdb=" N TYR w 90 " --> pdb=" O VAL w 86 " (cutoff:3.500A) Processing helix chain 'w' and resid 111 through 126 removed outlier: 5.130A pdb=" N GLU w 125 " --> pdb=" O ALA w 121 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 139 removed outlier: 4.347A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) removed outlier: 4.747A 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 197 removed outlier: 4.039A pdb=" N PHE x 195 " --> pdb=" O GLY x 191 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU x 196 " --> pdb=" O ASN x 192 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ALA x 197 " --> pdb=" O ARG x 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 191 through 197' 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 16 through 22 removed outlier: 6.142A 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: 6.042A 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 removed outlier: 5.630A pdb=" N TRP 3 122 " --> pdb=" O CYS 3 150 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '4' and resid 66 through 69 removed outlier: 6.937A 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: 5.317A 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: 8.698A 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: 5.802A pdb=" N SER 5 207 " --> pdb=" O GLY 5 226 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLY 5 226 " --> pdb=" O SER 5 207 " (cutoff:3.500A) removed outlier: 5.045A 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: 8.510A 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: 3.683A pdb=" N ASP 6 183 " --> pdb=" O VAL 6 179 " (cutoff:3.500A) removed outlier: 4.464A 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: 4.607A pdb=" N ARG 6 322 " --> pdb=" O VAL 6 193 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG 6 267 " --> pdb=" O LEU 6 221 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) removed outlier: 3.854A 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: 4.040A 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: 6.613A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) removed outlier: 8.727A 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: 4.346A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE 7 127 " --> pdb=" O VAL 7 70 " (cutoff:3.500A) removed outlier: 3.683A 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: 6.906A pdb=" N ASP 7 182 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLN 7 298 " --> pdb=" O SER 7 281 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '7' and resid 217 through 220 removed outlier: 5.018A pdb=" N LYS 7 253 " --> pdb=" O SER 7 264 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '7' and resid 282 through 286 removed outlier: 5.355A 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: 3.749A pdb=" N ARG 9 49 " --> pdb=" O THR 9 45 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'C' and resid 74 through 78 removed outlier: 6.966A 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: 4.002A pdb=" N TRP C 236 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP C 255 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ASP C 250 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY C 303 " --> pdb=" O ARG C 382 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS C 379 " --> pdb=" O GLU C 339 " (cutoff:3.500A) removed outlier: 6.390A 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: 6.630A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.343A 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: 3.790A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 138 through 144 removed outlier: 5.277A pdb=" N ASP D 138 " --> pdb=" O ALA D 153 " (cutoff:3.500A) 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: 3.765A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASN E 281 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLU E 330 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'E' and resid 176 through 181 removed outlier: 6.458A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR E 191 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'E' and resid 202 through 205 removed outlier: 4.401A pdb=" N GLN E 202 " --> pdb=" O VAL E 273 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'F' and resid 46 through 50 Processing sheet with id= 30, first strand: chain 'F' and resid 186 through 189 Processing sheet with id= 31, first strand: chain 'H' and resid 55 through 58 removed outlier: 6.964A pdb=" N ILE H 55 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'H' and resid 94 through 97 Processing sheet with id= 33, first strand: chain 'I' and resid 94 through 100 removed outlier: 4.231A pdb=" N ALA I 97 " --> pdb=" O LEU I 154 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'J' and resid 18 through 25 removed outlier: 3.611A pdb=" N ILE J 70 " --> pdb=" O ILE J 20 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA J 22 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL J 24 " --> pdb=" O LEU J 66 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS J 81 " --> pdb=" O LYS J 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU J 71 " --> pdb=" O GLU J 79 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU J 79 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'K' and resid 55 through 60 removed outlier: 5.202A pdb=" N ASP K 22 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'L' and resid 38 through 41 Processing sheet with id= 37, first strand: chain 'L' and resid 72 through 76 Processing sheet with id= 38, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 39, first strand: chain 'M' and resid 273 through 277 Processing sheet with id= 40, first strand: chain 'N' and resid 118 through 123 removed outlier: 5.234A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE N 87 " --> pdb=" O MET N 163 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ALA N 186 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'N' and resid 128 through 131 No H-bonds generated for sheet with id= 41 Processing sheet with id= 42, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.138A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N TYR O 104 " --> pdb=" O LYS O 126 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'P' and resid 80 through 85 removed outlier: 6.592A pdb=" N VAL P 90 " --> pdb=" O THR P 107 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Q' and resid 129 through 135 removed outlier: 4.487A pdb=" N LYS Q 129 " --> pdb=" O ASP Q 123 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Q' and resid 139 through 142 removed outlier: 7.860A pdb=" N ALA Q 147 " --> pdb=" O LEU Q 166 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'S' and resid 105 through 109 Processing sheet with id= 47, first strand: chain 'S' and resid 112 through 117 removed outlier: 3.738A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU S 126 " --> pdb=" O VAL S 160 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'S' and resid 162 through 165 Processing sheet with id= 49, first strand: chain 'S' and resid 168 through 175 removed outlier: 3.975A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'T' and resid 71 through 78 removed outlier: 4.923A pdb=" N ALA T 71 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS T 177 " --> pdb=" O ALA T 143 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN T 139 " --> pdb=" O GLY T 181 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'T' and resid 152 through 159 No H-bonds generated for sheet with id= 51 Processing sheet with id= 52, first strand: chain 'U' and resid 26 through 29 removed outlier: 4.299A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP U 38 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY U 75 " --> pdb=" O PRO U 90 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'W' and resid 97 through 101 Processing sheet with id= 54, first strand: chain 'X' and resid 49 through 52 removed outlier: 5.181A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'X' and resid 85 through 92 removed outlier: 5.060A pdb=" N LYS X 99 " --> pdb=" O ALA X 92 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 57, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.159A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'a' and resid 47 through 52 removed outlier: 5.887A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'b' and resid 61 through 67 removed outlier: 6.004A pdb=" N VAL b 33 " --> pdb=" O ASN b 66 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'c' and resid 254 through 258 removed outlier: 6.731A pdb=" N PHE c 271 " --> pdb=" O THR c 258 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'd' and resid 212 through 219 removed outlier: 4.076A pdb=" N TYR d 245 " --> pdb=" O ILE d 265 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'e' and resid 175 through 178 removed outlier: 3.768A pdb=" N TRP e 178 " --> pdb=" O LEU e 47 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU e 47 " --> pdb=" O TRP e 178 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N LEU e 51 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL e 161 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU e 159 " --> pdb=" O LEU e 53 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG e 162 " --> pdb=" O HIS e 251 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N HIS e 251 " --> pdb=" O ARG e 162 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'e' and resid 201 through 204 removed outlier: 7.026A pdb=" N GLU e 201 " --> pdb=" O LEU e 239 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'f' and resid 123 through 127 removed outlier: 4.842A pdb=" N GLU f 123 " --> pdb=" O GLN f 158 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR f 125 " --> pdb=" O VAL f 156 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET f 127 " --> pdb=" O GLU f 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLU f 154 " --> pdb=" O MET f 127 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'g' and resid 95 through 101 removed outlier: 5.477A pdb=" N VAL g 137 " --> pdb=" O LYS g 150 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'k' and resid 49 through 56 removed outlier: 4.243A pdb=" N PHE k 20 " --> pdb=" O ASP k 54 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS k 72 " --> pdb=" O PHE k 68 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'm' and resid 63 through 67 removed outlier: 5.416A pdb=" N ARG m 73 " --> pdb=" O PRO m 53 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU m 55 " --> pdb=" O ARG m 73 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'p' and resid 78 through 82 Processing sheet with id= 69, first strand: chain 'r' and resid 35 through 41 removed outlier: 4.184A pdb=" N PHE r 35 " --> pdb=" O THR r 54 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 's' and resid 90 through 93 removed outlier: 4.230A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 's' and resid 112 through 116 removed outlier: 6.430A pdb=" N ASN s 391 " --> pdb=" O ASN s 375 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN s 375 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N CYS s 393 " --> pdb=" O GLN s 373 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLN s 373 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLY s 395 " --> pdb=" O CYS s 371 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N CYS s 371 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLN s 397 " --> pdb=" O PHE s 369 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE s 369 " --> pdb=" O GLN s 397 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N LYS s 365 " --> pdb=" O LEU s 401 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR s 297 " --> pdb=" O ILE s 241 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 's' and resid 241 through 244 removed outlier: 6.638A pdb=" N ILE s 241 " --> pdb=" O HIS s 296 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'u' and resid 107 through 114 removed outlier: 3.904A pdb=" N ASP u 108 " --> pdb=" O SER u 128 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASP u 122 " --> pdb=" O VAL u 114 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'x' and resid 74 through 85 Processing sheet with id= 75, first strand: chain 'x' and resid 146 through 150 removed outlier: 6.786A pdb=" N VAL x 114 " --> pdb=" O ALA x 182 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASP x 178 " --> pdb=" O VAL x 118 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'x' and resid 107 through 111 No H-bonds generated for sheet with id= 76 2774 hydrogen bonds defined for protein. 8235 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 930 hydrogen bonds 1598 hydrogen bond angles 0 basepair planarities 381 basepair parallelities 707 stacking parallelities Total time for adding SS restraints: 62.22 Time building geometry restraints manager: 41.23 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: 19355 1.33 - 1.45: 32275 1.45 - 1.57: 51266 1.57 - 1.69: 2841 1.69 - 1.81: 486 Bond restraints: 106223 Sorted by residual: bond pdb=" C2 OMU A3039 " pdb=" N3 OMU A3039 " ideal model delta sigma weight residual 1.489 1.327 0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" N3 OMG A3040 " pdb=" C4 OMG A3040 " ideal model delta sigma weight residual 1.492 1.345 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" N3 OMG A2815 " pdb=" C4 OMG A2815 " ideal model delta sigma weight residual 1.492 1.349 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" N3 OMU A3039 " pdb=" C4 OMU A3039 " ideal model delta sigma weight residual 1.455 1.327 0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" N1 OMG A3040 " pdb=" C2 OMG A3040 " ideal model delta sigma weight residual 1.462 1.337 0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 106218 not shown) Histogram of bond angle deviations from ideal: 98.84 - 106.41: 10798 106.41 - 113.98: 62569 113.98 - 121.55: 52425 121.55 - 129.12: 22647 129.12 - 136.69: 1966 Bond angle restraints: 150405 Sorted by residual: angle pdb=" C1' OMG A3040 " pdb=" N9 OMG A3040 " pdb=" C4 OMG A3040 " ideal model delta sigma weight residual 108.29 125.32 -17.03 3.00e+00 1.11e-01 3.22e+01 angle pdb=" C1' OMG A3040 " pdb=" N9 OMG A3040 " pdb=" C8 OMG A3040 " ideal model delta sigma weight residual 142.82 126.03 16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" C1' OMG A2815 " pdb=" N9 OMG A2815 " pdb=" C8 OMG A2815 " ideal model delta sigma weight residual 142.82 127.38 15.44 3.00e+00 1.11e-01 2.65e+01 angle pdb=" C1' OMG A2815 " pdb=" N9 OMG A2815 " pdb=" C4 OMG A2815 " ideal model delta sigma weight residual 108.29 123.68 -15.39 3.00e+00 1.11e-01 2.63e+01 angle pdb=" C3' OMG A2815 " pdb=" C2' OMG A2815 " pdb=" C1' OMG A2815 " ideal model delta sigma weight residual 101.30 105.90 -4.60 1.00e+00 1.00e+00 2.12e+01 ... (remaining 150400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 61638 35.80 - 71.60: 3350 71.60 - 107.40: 458 107.40 - 143.20: 25 143.20 - 179.00: 30 Dihedral angle restraints: 65501 sinusoidal: 40320 harmonic: 25181 Sorted by residual: dihedral pdb=" O4' C A2379 " pdb=" C1' C A2379 " pdb=" N1 C A2379 " pdb=" C2 C A2379 " ideal model delta sinusoidal sigma weight residual 200.00 21.00 179.00 1 1.50e+01 4.44e-03 8.53e+01 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 16.34 -176.34 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C A3170 " pdb=" C1' C A3170 " pdb=" N1 C A3170 " pdb=" C2 C A3170 " ideal model delta sinusoidal sigma weight residual -160.00 15.58 -175.58 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 65498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 16369 0.076 - 0.152: 1186 0.152 - 0.229: 29 0.229 - 0.305: 3 0.305 - 0.381: 1 Chirality restraints: 17588 Sorted by residual: chirality pdb=" C1' A A2163 " pdb=" O4' A A2163 " pdb=" C2' A A2163 " pdb=" N9 A A2163 " both_signs ideal model delta sigma weight residual False 2.46 2.08 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C3' A A2457 " pdb=" C4' A A2457 " pdb=" O3' A A2457 " pdb=" C2' A A2457 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C3' C A2186 " pdb=" C4' C A2186 " pdb=" O3' C A2186 " pdb=" C2' C A2186 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 17585 not shown) Planarity restraints: 14010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A3040 " -0.033 2.00e-02 2.50e+03 5.47e-01 6.74e+03 pdb=" C4' OMG A3040 " 0.412 2.00e-02 2.50e+03 pdb=" O4' OMG A3040 " 0.633 2.00e-02 2.50e+03 pdb=" C3' OMG A3040 " -0.615 2.00e-02 2.50e+03 pdb=" O3' OMG A3040 " -0.465 2.00e-02 2.50e+03 pdb=" C2' OMG A3040 " -0.240 2.00e-02 2.50e+03 pdb=" O2' OMG A3040 " 0.854 2.00e-02 2.50e+03 pdb=" C1' OMG A3040 " 0.273 2.00e-02 2.50e+03 pdb=" N9 OMG A3040 " -0.818 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMU A3039 " -0.003 2.00e-02 2.50e+03 5.36e-01 6.47e+03 pdb=" C4' OMU A3039 " 0.418 2.00e-02 2.50e+03 pdb=" O4' OMU A3039 " 0.608 2.00e-02 2.50e+03 pdb=" C3' OMU A3039 " -0.591 2.00e-02 2.50e+03 pdb=" O3' OMU A3039 " -0.450 2.00e-02 2.50e+03 pdb=" C2' OMU A3039 " -0.235 2.00e-02 2.50e+03 pdb=" O2' OMU A3039 " 0.819 2.00e-02 2.50e+03 pdb=" C1' OMU A3039 " 0.267 2.00e-02 2.50e+03 pdb=" N1 OMU A3039 " -0.833 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2815 " -0.179 2.00e-02 2.50e+03 4.50e-01 4.55e+03 pdb=" C4' OMG A2815 " 0.401 2.00e-02 2.50e+03 pdb=" O4' OMG A2815 " 0.597 2.00e-02 2.50e+03 pdb=" C3' OMG A2815 " -0.541 2.00e-02 2.50e+03 pdb=" O3' OMG A2815 " -0.176 2.00e-02 2.50e+03 pdb=" C2' OMG A2815 " -0.334 2.00e-02 2.50e+03 pdb=" O2' OMG A2815 " 0.551 2.00e-02 2.50e+03 pdb=" C1' OMG A2815 " 0.332 2.00e-02 2.50e+03 pdb=" N9 OMG A2815 " -0.650 2.00e-02 2.50e+03 ... (remaining 14007 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 416 2.41 - 3.03: 61419 3.03 - 3.65: 171566 3.65 - 4.28: 271602 4.28 - 4.90: 407236 Nonbonded interactions: 912239 Sorted by model distance: nonbonded pdb=" OP1 A A1961 " pdb="MG MG A3313 " model vdw 1.785 2.170 nonbonded pdb=" OP2 G A2692 " pdb="MG MG A3351 " model vdw 1.787 2.170 nonbonded pdb=" O4 U A2475 " pdb="MG MG A3326 " model vdw 1.807 2.170 nonbonded pdb=" OP2 U A2660 " pdb="MG MG A3344 " model vdw 1.823 2.170 nonbonded pdb=" OP1 U A3037 " pdb="MG MG A3326 " model vdw 1.833 2.170 ... (remaining 912234 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: 2.320 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: 0.090 Extract box with map and model: 13.020 Check model and map are aligned: 1.180 Set scattering table: 0.700 Process input model: 298.600 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 328.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.162 106223 Z= 0.398 Angle : 0.592 17.032 150405 Z= 0.309 Chirality : 0.042 0.381 17588 Planarity : 0.009 0.547 14010 Dihedral : 19.003 179.005 49205 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.85 (0.09), residues: 8496 helix: 1.56 (0.10), residues: 3044 sheet: -0.32 (0.15), residues: 1084 loop : 0.20 (0.10), residues: 4368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP 6 235 HIS 0.010 0.001 HIS S 76 PHE 0.028 0.002 PHE c 140 TYR 0.033 0.002 TYR E 284 ARG 0.013 0.001 ARG 8 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1991 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1991 time to evaluate : 7.066 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: 0 132 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8375 (mtpp) REVERT: 0 144 GLN cc_start: 0.8614 (tt0) cc_final: 0.8362 (tm-30) REVERT: 4 77 LYS cc_start: 0.9113 (tttt) cc_final: 0.8908 (mttt) REVERT: 5 64 MET cc_start: 0.8466 (mtm) cc_final: 0.8170 (ttm) REVERT: 5 183 ASN cc_start: 0.9153 (m-40) cc_final: 0.8916 (m-40) REVERT: 5 384 GLN cc_start: 0.7026 (pp30) cc_final: 0.6795 (tm-30) REVERT: 6 263 SER cc_start: 0.9016 (t) cc_final: 0.8768 (t) REVERT: 6 330 ILE cc_start: 0.9054 (mt) cc_final: 0.8755 (mp) REVERT: 7 43 MET cc_start: 0.9167 (ppp) cc_final: 0.8892 (pp-130) REVERT: 8 109 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7994 (tp30) REVERT: 9 59 GLU cc_start: 0.7983 (tt0) cc_final: 0.7750 (tt0) REVERT: 9 83 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7488 (mm-30) REVERT: C 140 SER cc_start: 0.8841 (m) cc_final: 0.8580 (p) REVERT: C 158 MET cc_start: 0.8536 (ppp) cc_final: 0.8204 (ppp) REVERT: C 215 LYS cc_start: 0.9028 (tttp) cc_final: 0.8721 (tppt) REVERT: C 267 GLU cc_start: 0.7998 (tp30) cc_final: 0.7703 (pp20) REVERT: C 349 MET cc_start: 0.8550 (tpp) cc_final: 0.8316 (tpp) REVERT: C 376 TYR cc_start: 0.9013 (t80) cc_final: 0.8766 (t80) REVERT: C 378 CYS cc_start: 0.7410 (t) cc_final: 0.6369 (p) REVERT: D 161 ASP cc_start: 0.8534 (m-30) cc_final: 0.8217 (m-30) REVERT: D 234 MET cc_start: 0.8915 (ttt) cc_final: 0.8678 (ttt) REVERT: F 201 GLN cc_start: 0.8145 (tp40) cc_final: 0.7571 (tp40) REVERT: G 126 ASP cc_start: 0.8024 (m-30) cc_final: 0.7802 (m-30) REVERT: G 157 MET cc_start: 0.8435 (mmp) cc_final: 0.8184 (mmm) REVERT: G 161 LYS cc_start: 0.9338 (ttmm) cc_final: 0.9095 (tptt) REVERT: G 210 GLN cc_start: 0.7982 (tp-100) cc_final: 0.7706 (tp-100) REVERT: G 226 ASP cc_start: 0.8465 (p0) cc_final: 0.7788 (p0) REVERT: H 112 VAL cc_start: 0.9415 (m) cc_final: 0.9073 (m) REVERT: H 126 GLN cc_start: 0.8611 (mt0) cc_final: 0.8402 (mt0) REVERT: J 92 LYS cc_start: 0.1791 (mmtt) cc_final: 0.0509 (mttp) REVERT: K 94 GLN cc_start: 0.8889 (mt0) cc_final: 0.8606 (mt0) REVERT: K 164 ASP cc_start: 0.8600 (m-30) cc_final: 0.8334 (m-30) REVERT: L 48 ASN cc_start: 0.8452 (m-40) cc_final: 0.8250 (m-40) REVERT: L 68 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8742 (mmtt) REVERT: L 71 ASP cc_start: 0.8276 (m-30) cc_final: 0.7975 (m-30) REVERT: L 82 LYS cc_start: 0.9101 (tppt) cc_final: 0.8870 (tppt) REVERT: L 109 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8234 (mm-30) REVERT: L 135 SER cc_start: 0.9228 (m) cc_final: 0.8898 (m) REVERT: M 114 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8219 (mm110) REVERT: M 219 ASN cc_start: 0.9131 (m110) cc_final: 0.8886 (m110) REVERT: M 228 LYS cc_start: 0.8958 (mttm) cc_final: 0.8754 (mtpp) REVERT: M 276 ASN cc_start: 0.8716 (t0) cc_final: 0.8363 (t0) REVERT: M 289 ASN cc_start: 0.8913 (m-40) cc_final: 0.8494 (m-40) REVERT: N 80 THR cc_start: 0.9201 (m) cc_final: 0.8991 (t) REVERT: N 86 ASN cc_start: 0.7527 (p0) cc_final: 0.7226 (p0) REVERT: N 117 ASN cc_start: 0.8333 (m-40) cc_final: 0.7608 (m110) REVERT: N 197 LYS cc_start: 0.8972 (ttpt) cc_final: 0.8703 (tmmm) REVERT: N 201 ASP cc_start: 0.8211 (m-30) cc_final: 0.7941 (m-30) REVERT: O 100 GLN cc_start: 0.8236 (mt0) cc_final: 0.8010 (mt0) REVERT: P 113 LYS cc_start: 0.8300 (ptmm) cc_final: 0.8002 (ptmt) REVERT: P 132 LEU cc_start: 0.8889 (tp) cc_final: 0.8685 (tp) REVERT: Q 224 MET cc_start: 0.8733 (mmm) cc_final: 0.8453 (mmp) REVERT: Q 239 ASN cc_start: 0.8806 (t0) cc_final: 0.8576 (t0) REVERT: R 64 MET cc_start: 0.8478 (mmp) cc_final: 0.8213 (mmp) REVERT: U 129 MET cc_start: -0.6285 (ttt) cc_final: -0.6496 (ttp) REVERT: W 56 MET cc_start: 0.9041 (mmt) cc_final: 0.8161 (mmt) REVERT: W 94 GLU cc_start: 0.8082 (tt0) cc_final: 0.7809 (tt0) REVERT: W 110 ASN cc_start: 0.8847 (t0) cc_final: 0.8301 (t0) REVERT: X 53 ASN cc_start: 0.7994 (p0) cc_final: 0.7710 (p0) REVERT: Y 70 ASP cc_start: 0.8061 (t70) cc_final: 0.7861 (t0) REVERT: Y 88 GLN cc_start: 0.8966 (tp40) cc_final: 0.8531 (tp40) REVERT: Y 157 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8665 (mm-40) REVERT: Z 62 ASN cc_start: 0.8458 (t0) cc_final: 0.8211 (t0) REVERT: Z 131 GLU cc_start: 0.8546 (tp30) cc_final: 0.8337 (tp30) REVERT: b 22 TYR cc_start: 0.9346 (t80) cc_final: 0.9136 (t80) REVERT: c 283 GLU cc_start: 0.8106 (pt0) cc_final: 0.7901 (pt0) REVERT: d 143 ASP cc_start: 0.6590 (m-30) cc_final: 0.6022 (p0) REVERT: d 172 MET cc_start: 0.5607 (mmm) cc_final: 0.4997 (mpm) REVERT: e 48 LEU cc_start: 0.4241 (mt) cc_final: 0.3614 (tp) REVERT: e 78 GLU cc_start: 0.6185 (tm-30) cc_final: 0.5471 (tt0) REVERT: e 177 GLU cc_start: 0.5086 (pm20) cc_final: 0.4537 (mm-30) REVERT: e 185 ARG cc_start: 0.2872 (mmp-170) cc_final: 0.2538 (mmt180) REVERT: e 203 LYS cc_start: 0.5078 (tptt) cc_final: 0.4639 (tttt) REVERT: h 86 TRP cc_start: 0.8515 (p-90) cc_final: 0.8140 (p-90) REVERT: h 156 TRP cc_start: 0.6540 (m100) cc_final: 0.6288 (m100) REVERT: j 55 ARG cc_start: 0.8757 (mtp180) cc_final: 0.8555 (mtp180) REVERT: p 47 LYS cc_start: 0.9248 (mttp) cc_final: 0.8977 (mttm) REVERT: p 118 LYS cc_start: 0.8650 (mttt) cc_final: 0.8426 (ttmm) REVERT: p 125 ASN cc_start: 0.9214 (m-40) cc_final: 0.8964 (m-40) REVERT: p 152 GLN cc_start: 0.9040 (tp40) cc_final: 0.7792 (tp40) REVERT: p 156 ASP cc_start: 0.8287 (m-30) cc_final: 0.7453 (m-30) REVERT: r 110 GLU cc_start: 0.7273 (pm20) cc_final: 0.7058 (pm20) REVERT: s 341 MET cc_start: 0.8866 (mtp) cc_final: 0.8559 (mtt) REVERT: u 134 HIS cc_start: 0.8683 (t-90) cc_final: 0.8283 (t-170) REVERT: v 14 ARG cc_start: 0.8084 (ttm-80) cc_final: 0.7559 (ttm-80) REVERT: v 51 ARG cc_start: 0.8246 (mmt90) cc_final: 0.7763 (mmt-90) REVERT: v 60 VAL cc_start: 0.9471 (t) cc_final: 0.8962 (t) REVERT: x 115 ILE cc_start: 0.5983 (mt) cc_final: 0.5778 (mm) REVERT: x 138 GLU cc_start: 0.7794 (mp0) cc_final: 0.7460 (mp0) REVERT: x 148 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.8250 (ttp80) outliers start: 0 outliers final: 3 residues processed: 1991 average time/residue: 1.9178 time to fit residues: 5141.9395 Evaluate side-chains 1437 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1434 time to evaluate : 7.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain u residue 187 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 825 optimal weight: 5.9990 chunk 740 optimal weight: 0.8980 chunk 410 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 499 optimal weight: 1.9990 chunk 395 optimal weight: 6.9990 chunk 765 optimal weight: 7.9990 chunk 296 optimal weight: 8.9990 chunk 465 optimal weight: 7.9990 chunk 569 optimal weight: 0.3980 chunk 887 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 165 GLN 6 37 ASN 7 82 ASN ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN C 85 HIS C 282 GLN C 316 GLN C 367 ASN D 249 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 GLN F 228 GLN F 257 GLN G 158 GLN G 167 GLN G 287 ASN H 93 ASN H 121 ASN ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN L 43 ASN L 80 GLN L 142 GLN N 178 GLN P 147 GLN R 79 HIS ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 109 ASN T 133 ASN T 201 GLN X 27 HIS ** X 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 147 GLN Y 183 GLN Z 126 GLN b 66 ASN c 172 ASN c 315 ASN e 156 ASN ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN h 99 ASN h 119 GLN o 33 GLN p 117 GLN p 128 ASN q 81 GLN q 136 GLN q 147 GLN r 76 ASN s 319 GLN s 397 GLN s 408 ASN u 103 GLN ** v 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 93 HIS Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 106223 Z= 0.244 Angle : 0.618 22.166 150405 Z= 0.319 Chirality : 0.040 0.442 17588 Planarity : 0.005 0.128 14010 Dihedral : 20.862 179.447 30996 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.21 % Allowed : 11.79 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.99 (0.09), residues: 8496 helix: 1.58 (0.10), residues: 3050 sheet: -0.14 (0.15), residues: 1105 loop : 0.33 (0.10), residues: 4341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Z 81 HIS 0.018 0.001 HIS C 266 PHE 0.041 0.002 PHE e 215 TYR 0.029 0.001 TYR v 13 ARG 0.010 0.001 ARG s 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1696 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1527 time to evaluate : 7.589 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: 0 144 GLN cc_start: 0.8551 (tt0) cc_final: 0.8325 (tm-30) REVERT: 4 77 LYS cc_start: 0.9074 (tttt) cc_final: 0.8852 (mttt) REVERT: 4 78 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8362 (m-30) REVERT: 5 64 MET cc_start: 0.8390 (mtm) cc_final: 0.8128 (ttm) REVERT: 5 183 ASN cc_start: 0.9130 (m-40) cc_final: 0.8865 (m-40) REVERT: 6 50 LYS cc_start: 0.8465 (mmtm) cc_final: 0.8223 (mmtm) REVERT: 6 263 SER cc_start: 0.9021 (t) cc_final: 0.8774 (t) REVERT: 6 320 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7183 (mm110) REVERT: 6 330 ILE cc_start: 0.9074 (mt) cc_final: 0.8822 (mp) REVERT: 8 109 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7956 (tp30) REVERT: 9 59 GLU cc_start: 0.7971 (tt0) cc_final: 0.7745 (tt0) REVERT: C 140 SER cc_start: 0.8810 (m) cc_final: 0.8605 (p) REVERT: C 215 LYS cc_start: 0.8992 (tttp) cc_final: 0.8640 (tppt) REVERT: C 220 TYR cc_start: 0.7992 (m-10) cc_final: 0.7782 (m-10) REVERT: C 314 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7062 (t70) REVERT: C 349 MET cc_start: 0.8576 (tpp) cc_final: 0.8307 (tpp) REVERT: C 376 TYR cc_start: 0.8934 (t80) cc_final: 0.8704 (t80) REVERT: D 161 ASP cc_start: 0.8500 (m-30) cc_final: 0.8196 (m-30) REVERT: D 234 MET cc_start: 0.8913 (ttt) cc_final: 0.8682 (ttt) REVERT: F 201 GLN cc_start: 0.8087 (tp40) cc_final: 0.7516 (tp40) REVERT: F 241 ASN cc_start: 0.8604 (m110) cc_final: 0.8363 (m110) REVERT: G 126 ASP cc_start: 0.8088 (m-30) cc_final: 0.7827 (m-30) REVERT: G 142 CYS cc_start: 0.8197 (t) cc_final: 0.7318 (p) REVERT: G 161 LYS cc_start: 0.9338 (ttmm) cc_final: 0.9089 (tptt) REVERT: G 196 ASP cc_start: 0.8419 (p0) cc_final: 0.8212 (p0) REVERT: H 84 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: H 89 ARG cc_start: 0.8308 (mtt90) cc_final: 0.8054 (ttm-80) REVERT: H 126 GLN cc_start: 0.8698 (mt0) cc_final: 0.8485 (mt0) REVERT: J 92 LYS cc_start: 0.1573 (mmtt) cc_final: 0.0279 (mttp) REVERT: K 94 GLN cc_start: 0.8798 (mt0) cc_final: 0.8522 (mt0) REVERT: K 160 GLN cc_start: 0.8725 (tp-100) cc_final: 0.8447 (tp-100) REVERT: K 164 ASP cc_start: 0.8460 (m-30) cc_final: 0.8216 (m-30) REVERT: L 48 ASN cc_start: 0.8491 (m-40) cc_final: 0.8260 (m-40) REVERT: L 71 ASP cc_start: 0.8194 (m-30) cc_final: 0.7982 (m-30) REVERT: L 82 LYS cc_start: 0.9078 (tppt) cc_final: 0.8838 (tppt) REVERT: L 109 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8212 (mm-30) REVERT: L 135 SER cc_start: 0.9264 (m) cc_final: 0.9061 (m) REVERT: M 219 ASN cc_start: 0.9018 (m110) cc_final: 0.8775 (m110) REVERT: N 80 THR cc_start: 0.9290 (m) cc_final: 0.9014 (t) REVERT: N 86 ASN cc_start: 0.7702 (p0) cc_final: 0.7197 (p0) REVERT: N 178 GLN cc_start: 0.8307 (mt0) cc_final: 0.8095 (mt0) REVERT: N 197 LYS cc_start: 0.8967 (ttpt) cc_final: 0.8679 (tmmm) REVERT: N 201 ASP cc_start: 0.8172 (m-30) cc_final: 0.7901 (m-30) REVERT: N 223 MET cc_start: 0.8101 (mmm) cc_final: 0.7736 (mtt) REVERT: N 247 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.7590 (mpt) REVERT: P 84 ILE cc_start: 0.9138 (mp) cc_final: 0.8895 (pt) REVERT: P 114 LYS cc_start: 0.9206 (ptmt) cc_final: 0.8897 (ptpp) REVERT: Q 239 ASN cc_start: 0.8771 (t0) cc_final: 0.8506 (t0) REVERT: T 163 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7304 (mtp180) REVERT: V 181 ASP cc_start: 0.8557 (m-30) cc_final: 0.8025 (m-30) REVERT: W 56 MET cc_start: 0.9022 (mmt) cc_final: 0.8190 (mmt) REVERT: W 110 ASN cc_start: 0.8887 (t0) cc_final: 0.8421 (t0) REVERT: W 118 THR cc_start: 0.9079 (m) cc_final: 0.8835 (p) REVERT: X 53 ASN cc_start: 0.7799 (p0) cc_final: 0.7362 (p0) REVERT: Y 143 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: Z 131 GLU cc_start: 0.8548 (tp30) cc_final: 0.8322 (tp30) REVERT: c 231 MET cc_start: 0.8897 (mtm) cc_final: 0.8597 (mtm) REVERT: d 158 ASP cc_start: 0.6972 (p0) cc_final: 0.6676 (p0) REVERT: d 172 MET cc_start: 0.6098 (mmm) cc_final: 0.5561 (mpm) REVERT: d 227 ARG cc_start: 0.8850 (mtm110) cc_final: 0.8633 (mtm110) REVERT: d 231 LEU cc_start: 0.8829 (tp) cc_final: 0.8420 (tm) REVERT: d 261 MET cc_start: 0.7059 (mpt) cc_final: 0.6622 (mmt) REVERT: e 48 LEU cc_start: 0.3956 (mt) cc_final: 0.3481 (tp) REVERT: e 55 ARG cc_start: 0.5180 (tmt170) cc_final: 0.4709 (tmt170) REVERT: e 78 GLU cc_start: 0.6134 (tm-30) cc_final: 0.5654 (tt0) REVERT: e 177 GLU cc_start: 0.5134 (pm20) cc_final: 0.4608 (tp30) REVERT: e 234 PHE cc_start: 0.3827 (m-10) cc_final: 0.3524 (t80) REVERT: h 70 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9171 (tm) REVERT: h 86 TRP cc_start: 0.8437 (p-90) cc_final: 0.8046 (p-90) REVERT: h 118 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.8058 (p-80) REVERT: k 19 GLN cc_start: 0.6142 (pp30) cc_final: 0.5796 (pp30) REVERT: k 31 ARG cc_start: 0.8209 (ttt180) cc_final: 0.7689 (mtp180) REVERT: k 76 MET cc_start: 0.6870 (mmm) cc_final: 0.6666 (mmm) REVERT: p 47 LYS cc_start: 0.9319 (mttp) cc_final: 0.9045 (mttm) REVERT: p 59 TRP cc_start: 0.9183 (OUTLIER) cc_final: 0.8727 (m100) REVERT: p 118 LYS cc_start: 0.8620 (mttt) cc_final: 0.8368 (ttmm) REVERT: p 152 GLN cc_start: 0.8991 (tp40) cc_final: 0.7771 (tp40) REVERT: p 156 ASP cc_start: 0.8262 (m-30) cc_final: 0.7338 (m-30) REVERT: q 125 MET cc_start: 0.8535 (mmp) cc_final: 0.8200 (mmm) REVERT: q 128 MET cc_start: 0.6317 (tpt) cc_final: 0.5431 (tpt) REVERT: q 131 MET cc_start: 0.7513 (ptt) cc_final: 0.7246 (ppp) REVERT: r 72 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9210 (mp) REVERT: s 341 MET cc_start: 0.8985 (mtp) cc_final: 0.8623 (mtt) REVERT: u 96 MET cc_start: 0.8781 (mmm) cc_final: 0.8521 (mmm) REVERT: u 153 ARG cc_start: 0.8311 (pmm-80) cc_final: 0.7923 (ptp90) REVERT: u 160 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8185 (mt-10) REVERT: v 56 GLU cc_start: 0.9025 (tp30) cc_final: 0.8734 (tp30) REVERT: v 60 VAL cc_start: 0.9386 (t) cc_final: 0.9100 (t) outliers start: 169 outliers final: 60 residues processed: 1601 average time/residue: 1.8091 time to fit residues: 3966.8937 Evaluate side-chains 1482 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1411 time to evaluate : 7.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 164 THR Chi-restraints excluded: chain 4 residue 78 ASP Chi-restraints excluded: chain 5 residue 47 ASP Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 320 GLN Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain N residue 167 CYS Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 74 GLU Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 143 ASP Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain e residue 151 ARG Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain j residue 53 ASP Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain p residue 59 TRP Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain r residue 72 ILE Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 173 SER Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain u residue 131 SER Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain x residue 81 CYS Chi-restraints excluded: chain x residue 142 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 493 optimal weight: 3.9990 chunk 275 optimal weight: 30.0000 chunk 738 optimal weight: 10.0000 chunk 604 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 888 optimal weight: 20.0000 chunk 960 optimal weight: 30.0000 chunk 791 optimal weight: 50.0000 chunk 881 optimal weight: 2.9990 chunk 303 optimal weight: 0.9990 chunk 713 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 GLN ** 5 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 384 GLN 6 63 GLN 6 191 ASN ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN C 85 HIS C 304 HIS D 271 ASN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN F 257 GLN G 137 ASN G 210 GLN H 93 ASN ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN L 80 GLN L 142 GLN M 114 GLN P 147 GLN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 133 ASN X 240 GLN X 241 GLN Y 88 GLN Y 92 ASN Y 147 GLN Y 183 GLN Z 126 GLN a 126 HIS c 172 ASN d 47 GLN e 156 ASN e 212 HIS ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 158 GLN h 67 GLN o 33 GLN ** q 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 76 ASN s 408 ASN u 103 GLN x 84 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 106223 Z= 0.268 Angle : 0.608 14.826 150405 Z= 0.315 Chirality : 0.040 0.430 17588 Planarity : 0.005 0.122 14010 Dihedral : 20.732 179.094 30990 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.79 % Allowed : 13.83 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.09), residues: 8496 helix: 1.54 (0.09), residues: 3055 sheet: -0.09 (0.15), residues: 1129 loop : 0.33 (0.10), residues: 4312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 110 HIS 0.011 0.001 HIS P 115 PHE 0.044 0.002 PHE G 316 TYR 0.030 0.001 TYR v 13 ARG 0.011 0.001 ARG s 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1656 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1443 time to evaluate : 7.383 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: 0 144 GLN cc_start: 0.8612 (tt0) cc_final: 0.8384 (tm-30) REVERT: 4 77 LYS cc_start: 0.9089 (tttt) cc_final: 0.8856 (mttt) REVERT: 4 78 ASP cc_start: 0.8572 (m-30) cc_final: 0.8345 (m-30) REVERT: 5 64 MET cc_start: 0.8385 (mtm) cc_final: 0.8130 (ttm) REVERT: 5 183 ASN cc_start: 0.9127 (m-40) cc_final: 0.8867 (m-40) REVERT: 5 384 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6818 (tp40) REVERT: 6 320 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7114 (mm110) REVERT: 6 330 ILE cc_start: 0.9041 (mt) cc_final: 0.8795 (mp) REVERT: 6 355 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8693 (mtpp) REVERT: 8 109 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7905 (tp30) REVERT: 8 145 GLU cc_start: 0.5598 (OUTLIER) cc_final: 0.5238 (pm20) REVERT: 9 41 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8541 (tp) REVERT: 9 59 GLU cc_start: 0.7967 (tt0) cc_final: 0.7722 (tt0) REVERT: 9 69 LYS cc_start: 0.8383 (ptmm) cc_final: 0.8182 (ptmm) REVERT: C 140 SER cc_start: 0.8804 (m) cc_final: 0.8589 (p) REVERT: C 215 LYS cc_start: 0.8967 (tttp) cc_final: 0.8575 (tppt) REVERT: C 314 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.6996 (t70) REVERT: C 349 MET cc_start: 0.8557 (tpp) cc_final: 0.8314 (tpp) REVERT: D 161 ASP cc_start: 0.8511 (m-30) cc_final: 0.8209 (m-30) REVERT: D 234 MET cc_start: 0.8908 (ttt) cc_final: 0.8704 (ttt) REVERT: F 63 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8334 (mt0) REVERT: F 241 ASN cc_start: 0.8588 (m110) cc_final: 0.8288 (m110) REVERT: G 125 LEU cc_start: 0.9104 (tp) cc_final: 0.8889 (pp) REVERT: G 126 ASP cc_start: 0.8138 (m-30) cc_final: 0.7409 (m-30) REVERT: G 142 CYS cc_start: 0.8036 (t) cc_final: 0.7833 (p) REVERT: G 161 LYS cc_start: 0.9316 (ttmm) cc_final: 0.9050 (tptt) REVERT: G 225 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7387 (tp30) REVERT: H 84 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: H 89 ARG cc_start: 0.8308 (mtt90) cc_final: 0.8026 (ttm-80) REVERT: H 126 GLN cc_start: 0.8689 (mt0) cc_final: 0.8465 (mt0) REVERT: H 141 GLU cc_start: 0.7739 (pp20) cc_final: 0.6615 (pp20) REVERT: K 94 GLN cc_start: 0.8804 (mt0) cc_final: 0.8532 (mt0) REVERT: K 160 GLN cc_start: 0.8709 (tp-100) cc_final: 0.8430 (tp-100) REVERT: K 164 ASP cc_start: 0.8494 (m-30) cc_final: 0.8231 (m-30) REVERT: L 71 ASP cc_start: 0.8220 (m-30) cc_final: 0.8013 (m-30) REVERT: L 120 LYS cc_start: 0.8769 (tptm) cc_final: 0.8546 (tppp) REVERT: N 68 ASN cc_start: 0.8092 (p0) cc_final: 0.7867 (p0) REVERT: N 80 THR cc_start: 0.9284 (m) cc_final: 0.8965 (t) REVERT: N 86 ASN cc_start: 0.7745 (p0) cc_final: 0.7189 (p0) REVERT: N 178 GLN cc_start: 0.8260 (mt0) cc_final: 0.8009 (mt0) REVERT: N 197 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8718 (tmmm) REVERT: N 201 ASP cc_start: 0.8168 (m-30) cc_final: 0.7948 (m-30) REVERT: N 223 MET cc_start: 0.8109 (mmm) cc_final: 0.7796 (mtt) REVERT: N 247 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7587 (mpt) REVERT: P 89 HIS cc_start: 0.7303 (m-70) cc_final: 0.6419 (m-70) REVERT: P 132 LEU cc_start: 0.8938 (tp) cc_final: 0.8722 (tp) REVERT: P 158 MET cc_start: 0.9194 (mmm) cc_final: 0.8933 (tpp) REVERT: P 159 LYS cc_start: 0.8923 (mttp) cc_final: 0.8438 (mttp) REVERT: Q 123 ASP cc_start: 0.7480 (t0) cc_final: 0.7270 (t0) REVERT: Q 239 ASN cc_start: 0.8803 (t0) cc_final: 0.8521 (t0) REVERT: S 121 ASP cc_start: 0.7839 (t0) cc_final: 0.7633 (t0) REVERT: T 163 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7396 (mtp180) REVERT: V 181 ASP cc_start: 0.8473 (m-30) cc_final: 0.8159 (m-30) REVERT: W 56 MET cc_start: 0.9046 (mmt) cc_final: 0.8153 (mmt) REVERT: W 85 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8747 (mtpp) REVERT: W 94 GLU cc_start: 0.8298 (tt0) cc_final: 0.8087 (tt0) REVERT: W 109 ARG cc_start: 0.8508 (ptp90) cc_final: 0.8050 (ptp90) REVERT: W 110 ASN cc_start: 0.8880 (t0) cc_final: 0.8537 (t0) REVERT: W 118 THR cc_start: 0.9092 (m) cc_final: 0.8856 (p) REVERT: W 122 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8015 (mmmm) REVERT: X 60 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7409 (pm20) REVERT: Z 43 GLU cc_start: 0.7356 (pm20) cc_final: 0.7071 (pm20) REVERT: Z 62 ASN cc_start: 0.8398 (t0) cc_final: 0.8182 (t0) REVERT: Z 131 GLU cc_start: 0.8565 (tp30) cc_final: 0.8341 (tp30) REVERT: b 36 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7451 (m-30) REVERT: c 231 MET cc_start: 0.8901 (mtm) cc_final: 0.8602 (mtm) REVERT: d 136 ASP cc_start: 0.6163 (m-30) cc_final: 0.5556 (t0) REVERT: d 143 ASP cc_start: 0.6717 (m-30) cc_final: 0.6455 (p0) REVERT: d 190 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.5550 (pp20) REVERT: d 227 ARG cc_start: 0.8783 (mtm110) cc_final: 0.8553 (mtm110) REVERT: d 231 LEU cc_start: 0.8858 (tp) cc_final: 0.8510 (tm) REVERT: d 261 MET cc_start: 0.7155 (mpt) cc_final: 0.6694 (mmp) REVERT: e 73 LEU cc_start: 0.8525 (pp) cc_final: 0.7783 (tm) REVERT: h 70 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9222 (tm) REVERT: h 86 TRP cc_start: 0.8438 (p-90) cc_final: 0.8141 (p-90) REVERT: h 116 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7655 (mtp85) REVERT: h 118 HIS cc_start: 0.8531 (OUTLIER) cc_final: 0.8078 (p-80) REVERT: h 119 GLN cc_start: 0.8552 (pt0) cc_final: 0.8156 (pt0) REVERT: k 19 GLN cc_start: 0.6221 (pp30) cc_final: 0.5812 (pp30) REVERT: k 31 ARG cc_start: 0.8203 (ttt180) cc_final: 0.7687 (mtp180) REVERT: k 76 MET cc_start: 0.6994 (mmm) cc_final: 0.6672 (mmm) REVERT: o 99 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8760 (ttpt) REVERT: p 47 LYS cc_start: 0.9350 (mttp) cc_final: 0.9076 (mttm) REVERT: p 118 LYS cc_start: 0.8627 (mttt) cc_final: 0.8367 (ttmm) REVERT: p 152 GLN cc_start: 0.8981 (tp40) cc_final: 0.7786 (tp40) REVERT: p 156 ASP cc_start: 0.8253 (m-30) cc_final: 0.7336 (m-30) REVERT: r 72 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9235 (mp) REVERT: s 160 ARG cc_start: 0.6873 (mmm160) cc_final: 0.6671 (mtp85) REVERT: s 341 MET cc_start: 0.8997 (mtp) cc_final: 0.8636 (mtt) REVERT: u 96 MET cc_start: 0.8871 (mmm) cc_final: 0.8532 (tpt) REVERT: u 100 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8666 (mp) REVERT: u 151 CYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6853 (t) REVERT: u 153 ARG cc_start: 0.8214 (pmm-80) cc_final: 0.8012 (ptp90) REVERT: v 56 GLU cc_start: 0.9111 (tp30) cc_final: 0.8837 (tp30) REVERT: v 63 ASN cc_start: 0.9330 (m-40) cc_final: 0.9074 (m110) REVERT: x 125 LEU cc_start: 0.1991 (OUTLIER) cc_final: 0.1667 (tp) outliers start: 213 outliers final: 98 residues processed: 1547 average time/residue: 1.7815 time to fit residues: 3798.0883 Evaluate side-chains 1482 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1362 time to evaluate : 7.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 164 THR Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 47 ASP Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 366 CYS Chi-restraints excluded: chain 5 residue 384 GLN Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 320 GLN Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 8 residue 131 MET Chi-restraints excluded: chain 8 residue 145 GLU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 167 CYS Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 195 HIS Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 85 LYS Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 60 GLU Chi-restraints excluded: chain X residue 74 GLU Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain d residue 190 GLU Chi-restraints excluded: chain e residue 151 ARG Chi-restraints excluded: chain e residue 152 LYS Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain f residue 171 LEU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain h residue 135 GLN Chi-restraints excluded: chain j residue 67 LYS Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain r residue 72 ILE Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 111 GLU Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 173 SER Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 257 VAL Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain u residue 100 LEU Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 151 CYS Chi-restraints excluded: chain u residue 177 ILE Chi-restraints excluded: chain u residue 200 ASP Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain x residue 81 CYS Chi-restraints excluded: chain x residue 95 GLU Chi-restraints excluded: chain x residue 125 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 878 optimal weight: 4.9990 chunk 668 optimal weight: 1.9990 chunk 461 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 424 optimal weight: 10.0000 chunk 596 optimal weight: 5.9990 chunk 892 optimal weight: 0.8980 chunk 944 optimal weight: 6.9990 chunk 466 optimal weight: 0.7980 chunk 845 optimal weight: 20.0000 chunk 254 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 GLN 5 308 GLN 5 384 GLN 6 63 GLN 6 191 ASN 6 277 GLN 7 165 ASN 9 90 GLN C 85 HIS C 304 HIS ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN F 228 GLN F 257 GLN H 93 ASN ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN L 80 GLN L 142 GLN O 69 ASN P 147 GLN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 133 ASN X 15 GLN Y 88 GLN Y 89 GLN Y 147 GLN Y 183 GLN Z 126 GLN c 172 ASN ** c 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 217 HIS ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN h 99 ASN ** q 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 148 HIS v 19 GLN x 84 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 106223 Z= 0.248 Angle : 0.601 13.733 150405 Z= 0.311 Chirality : 0.039 0.424 17588 Planarity : 0.005 0.120 14010 Dihedral : 20.700 179.602 30990 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.83 % Allowed : 15.08 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.97 (0.09), residues: 8496 helix: 1.56 (0.09), residues: 3039 sheet: -0.07 (0.15), residues: 1132 loop : 0.31 (0.10), residues: 4325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 110 HIS 0.013 0.001 HIS C 266 PHE 0.035 0.001 PHE e 215 TYR 0.035 0.001 TYR v 13 ARG 0.014 0.000 ARG 1 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1640 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1424 time to evaluate : 7.352 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: 1 20 MET cc_start: 0.6484 (mmp) cc_final: 0.6192 (mmm) REVERT: 1 30 PHE cc_start: 0.8536 (p90) cc_final: 0.8331 (p90) REVERT: 1 45 HIS cc_start: 0.7851 (t70) cc_final: 0.7524 (t70) REVERT: 4 77 LYS cc_start: 0.9081 (tttt) cc_final: 0.8847 (mttt) REVERT: 4 78 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8310 (m-30) REVERT: 5 64 MET cc_start: 0.8384 (mtm) cc_final: 0.8110 (ttm) REVERT: 5 183 ASN cc_start: 0.9122 (m-40) cc_final: 0.8859 (m-40) REVERT: 6 50 LYS cc_start: 0.8546 (mmtm) cc_final: 0.8309 (mmtm) REVERT: 6 277 GLN cc_start: 0.6699 (OUTLIER) cc_final: 0.6120 (pp30) REVERT: 6 320 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7203 (mm110) REVERT: 6 330 ILE cc_start: 0.9076 (mt) cc_final: 0.8807 (mp) REVERT: 6 355 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8684 (mtpp) REVERT: 7 165 ASN cc_start: 0.8617 (m-40) cc_final: 0.8389 (m110) REVERT: 8 109 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7938 (tm-30) REVERT: 8 145 GLU cc_start: 0.5542 (OUTLIER) cc_final: 0.5193 (pm20) REVERT: 9 41 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8524 (tp) REVERT: 9 59 GLU cc_start: 0.7976 (tt0) cc_final: 0.7744 (tt0) REVERT: 9 69 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8148 (ptmm) REVERT: C 215 LYS cc_start: 0.8963 (tttp) cc_final: 0.8585 (tppt) REVERT: C 314 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.7007 (t70) REVERT: C 349 MET cc_start: 0.8536 (tpp) cc_final: 0.8287 (tpp) REVERT: D 86 ASP cc_start: 0.7787 (m-30) cc_final: 0.7478 (m-30) REVERT: D 161 ASP cc_start: 0.8472 (m-30) cc_final: 0.8177 (m-30) REVERT: D 234 MET cc_start: 0.8912 (ttt) cc_final: 0.8711 (ttt) REVERT: F 63 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8383 (mt0) REVERT: F 241 ASN cc_start: 0.8603 (m110) cc_final: 0.8303 (m110) REVERT: G 126 ASP cc_start: 0.8074 (m-30) cc_final: 0.7803 (m-30) REVERT: G 161 LYS cc_start: 0.9329 (ttmm) cc_final: 0.9059 (tptt) REVERT: H 84 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: H 89 ARG cc_start: 0.8312 (mtt90) cc_final: 0.8031 (ttm-80) REVERT: H 93 ASN cc_start: 0.9023 (m-40) cc_final: 0.8769 (m-40) REVERT: H 126 GLN cc_start: 0.8694 (mt0) cc_final: 0.8484 (mt0) REVERT: I 161 VAL cc_start: 0.4817 (OUTLIER) cc_final: 0.4575 (p) REVERT: K 94 GLN cc_start: 0.8788 (mt0) cc_final: 0.8483 (mt0) REVERT: K 160 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8414 (tp-100) REVERT: K 164 ASP cc_start: 0.8495 (m-30) cc_final: 0.8232 (m-30) REVERT: L 71 ASP cc_start: 0.8221 (m-30) cc_final: 0.8003 (m-30) REVERT: M 289 ASN cc_start: 0.8731 (m-40) cc_final: 0.8475 (m110) REVERT: N 80 THR cc_start: 0.9175 (m) cc_final: 0.8846 (t) REVERT: N 86 ASN cc_start: 0.7608 (p0) cc_final: 0.7175 (p0) REVERT: N 104 MET cc_start: 0.9021 (tmt) cc_final: 0.8678 (tmm) REVERT: N 166 ARG cc_start: 0.7189 (ptt-90) cc_final: 0.6853 (ptt-90) REVERT: N 178 GLN cc_start: 0.8226 (mt0) cc_final: 0.8007 (mt0) REVERT: N 197 LYS cc_start: 0.9014 (ttpt) cc_final: 0.8686 (tmmm) REVERT: N 201 ASP cc_start: 0.8169 (m-30) cc_final: 0.7936 (m-30) REVERT: N 247 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.7560 (mpt) REVERT: P 89 HIS cc_start: 0.7372 (m-70) cc_final: 0.6525 (m-70) REVERT: P 132 LEU cc_start: 0.9029 (tp) cc_final: 0.8753 (tp) REVERT: Q 239 ASN cc_start: 0.8807 (t0) cc_final: 0.8525 (t0) REVERT: S 121 ASP cc_start: 0.7966 (t0) cc_final: 0.7755 (t0) REVERT: V 181 ASP cc_start: 0.8544 (m-30) cc_final: 0.8023 (m-30) REVERT: W 56 MET cc_start: 0.9055 (mmt) cc_final: 0.8170 (mmt) REVERT: W 85 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8709 (mtpp) REVERT: W 110 ASN cc_start: 0.8890 (t0) cc_final: 0.8457 (t0) REVERT: W 111 THR cc_start: 0.9222 (p) cc_final: 0.8981 (m) REVERT: W 118 THR cc_start: 0.9108 (m) cc_final: 0.8875 (p) REVERT: Y 88 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.9016 (mm-40) REVERT: Y 143 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: Z 62 ASN cc_start: 0.8457 (t0) cc_final: 0.8183 (t0) REVERT: Z 92 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.5982 (pp20) REVERT: Z 131 GLU cc_start: 0.8546 (tp30) cc_final: 0.8305 (tp30) REVERT: b 36 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: b 86 GLU cc_start: 0.7909 (tt0) cc_final: 0.7645 (tt0) REVERT: d 136 ASP cc_start: 0.6130 (m-30) cc_final: 0.5547 (t0) REVERT: d 143 ASP cc_start: 0.6565 (m-30) cc_final: 0.6329 (p0) REVERT: d 156 ASP cc_start: 0.3265 (OUTLIER) cc_final: 0.2997 (p0) REVERT: d 172 MET cc_start: 0.5892 (OUTLIER) cc_final: 0.5421 (mpm) REVERT: d 176 ILE cc_start: 0.8561 (tp) cc_final: 0.8276 (pp) REVERT: d 227 ARG cc_start: 0.8772 (mtm110) cc_final: 0.8550 (mtm110) REVERT: d 231 LEU cc_start: 0.8880 (tp) cc_final: 0.8557 (tm) REVERT: e 73 LEU cc_start: 0.8464 (pp) cc_final: 0.7872 (tm) REVERT: e 260 LEU cc_start: 0.2927 (OUTLIER) cc_final: 0.2246 (pt) REVERT: g 76 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8375 (ptp-170) REVERT: h 70 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9083 (tm) REVERT: h 86 TRP cc_start: 0.8343 (p-90) cc_final: 0.7686 (p-90) REVERT: h 116 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7648 (mtp85) REVERT: h 118 HIS cc_start: 0.8531 (OUTLIER) cc_final: 0.8061 (p-80) REVERT: h 119 GLN cc_start: 0.8552 (pt0) cc_final: 0.8199 (pt0) REVERT: j 55 ARG cc_start: 0.8836 (mtp180) cc_final: 0.8620 (mtp180) REVERT: k 19 GLN cc_start: 0.6236 (pp30) cc_final: 0.5890 (pp30) REVERT: k 31 ARG cc_start: 0.8199 (ttt180) cc_final: 0.7598 (mtp180) REVERT: k 76 MET cc_start: 0.7018 (mmm) cc_final: 0.6737 (mmm) REVERT: p 47 LYS cc_start: 0.9339 (mttp) cc_final: 0.9079 (mttm) REVERT: p 59 TRP cc_start: 0.9177 (OUTLIER) cc_final: 0.8880 (m100) REVERT: p 118 LYS cc_start: 0.8588 (mttt) cc_final: 0.8306 (ttmm) REVERT: p 152 GLN cc_start: 0.8979 (tp40) cc_final: 0.7800 (tp40) REVERT: p 156 ASP cc_start: 0.8235 (m-30) cc_final: 0.7309 (m-30) REVERT: q 125 MET cc_start: 0.8407 (mmm) cc_final: 0.7983 (mmt) REVERT: r 72 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9233 (mp) REVERT: s 341 MET cc_start: 0.9008 (mtp) cc_final: 0.8654 (mtt) REVERT: u 96 MET cc_start: 0.8805 (mmm) cc_final: 0.8523 (mmm) REVERT: u 100 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8499 (mp) REVERT: u 151 CYS cc_start: 0.7047 (m) cc_final: 0.6807 (t) REVERT: u 154 ASP cc_start: 0.7190 (p0) cc_final: 0.6587 (p0) REVERT: v 39 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: v 56 GLU cc_start: 0.9151 (tp30) cc_final: 0.8873 (tp30) REVERT: x 118 VAL cc_start: 0.0747 (OUTLIER) cc_final: 0.0283 (p) REVERT: x 125 LEU cc_start: 0.1791 (OUTLIER) cc_final: 0.1534 (tp) REVERT: x 173 LEU cc_start: 0.8421 (mm) cc_final: 0.8017 (tp) outliers start: 216 outliers final: 106 residues processed: 1526 average time/residue: 1.7736 time to fit residues: 3756.0044 Evaluate side-chains 1503 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1367 time to evaluate : 7.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 164 THR Chi-restraints excluded: chain 4 residue 78 ASP Chi-restraints excluded: chain 5 residue 47 ASP Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 366 CYS Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 277 GLN Chi-restraints excluded: chain 6 residue 320 GLN Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 8 residue 145 GLU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 69 LYS Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 195 HIS Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain V residue 198 VAL Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 85 LYS Chi-restraints excluded: chain X residue 15 GLN Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 88 GLN Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 143 ASP Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain d residue 156 ASP Chi-restraints excluded: chain d residue 172 MET Chi-restraints excluded: chain e residue 151 ARG Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 260 LEU Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 171 LEU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain h residue 135 GLN Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain j residue 67 LYS Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain p residue 59 TRP Chi-restraints excluded: chain p residue 100 GLU Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain q residue 131 MET Chi-restraints excluded: chain r residue 72 ILE Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 111 GLU Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 173 SER Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain u residue 100 LEU Chi-restraints excluded: chain u residue 131 SER Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 200 ASP Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 39 PHE Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain x residue 81 CYS Chi-restraints excluded: chain x residue 118 VAL Chi-restraints excluded: chain x residue 125 LEU Chi-restraints excluded: chain x residue 142 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 786 optimal weight: 20.0000 chunk 536 optimal weight: 2.9990 chunk 13 optimal weight: 0.0060 chunk 703 optimal weight: 6.9990 chunk 389 optimal weight: 0.9990 chunk 805 optimal weight: 20.0000 chunk 652 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 482 optimal weight: 0.9990 chunk 847 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 GLN 6 37 ASN 6 108 GLN 6 191 ASN 9 90 GLN C 85 HIS C 304 HIS ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN F 228 GLN F 257 GLN H 136 ASN ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN L 80 GLN O 69 ASN P 147 GLN P 176 GLN ** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 133 ASN Y 88 GLN Y 147 GLN Y 183 GLN Z 126 GLN c 172 ASN ** e 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN ** q 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 106223 Z= 0.203 Angle : 0.589 15.638 150405 Z= 0.304 Chirality : 0.038 0.413 17588 Planarity : 0.005 0.117 14010 Dihedral : 20.663 179.889 30990 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.84 % Allowed : 15.90 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.99 (0.09), residues: 8496 helix: 1.57 (0.09), residues: 3048 sheet: -0.03 (0.15), residues: 1128 loop : 0.30 (0.10), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP 6 235 HIS 0.018 0.001 HIS u 148 PHE 0.035 0.001 PHE e 215 TYR 0.037 0.001 TYR v 13 ARG 0.013 0.000 ARG 1 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1640 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1423 time to evaluate : 7.233 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: 1 45 HIS cc_start: 0.7839 (t70) cc_final: 0.7406 (t70) REVERT: 4 77 LYS cc_start: 0.9086 (tttt) cc_final: 0.8852 (mttt) REVERT: 5 64 MET cc_start: 0.8374 (mtm) cc_final: 0.8071 (ttm) REVERT: 5 183 ASN cc_start: 0.9138 (m-40) cc_final: 0.8879 (m-40) REVERT: 6 50 LYS cc_start: 0.8577 (mmtm) cc_final: 0.8347 (mmtm) REVERT: 6 320 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7211 (mm110) REVERT: 6 330 ILE cc_start: 0.9067 (mt) cc_final: 0.8803 (mp) REVERT: 7 165 ASN cc_start: 0.8605 (m-40) cc_final: 0.8380 (m110) REVERT: 8 109 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7889 (tm-30) REVERT: 8 145 GLU cc_start: 0.5580 (OUTLIER) cc_final: 0.5128 (pm20) REVERT: 8 147 LEU cc_start: 0.5678 (OUTLIER) cc_final: 0.5221 (pt) REVERT: 9 41 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8537 (tp) REVERT: 9 59 GLU cc_start: 0.7968 (tt0) cc_final: 0.7734 (tt0) REVERT: 9 69 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8072 (ptmm) REVERT: 9 120 GLU cc_start: 0.8081 (pm20) cc_final: 0.7431 (pm20) REVERT: C 215 LYS cc_start: 0.8955 (tttp) cc_final: 0.8576 (tppt) REVERT: C 314 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.6922 (t70) REVERT: C 349 MET cc_start: 0.8561 (tpp) cc_final: 0.8294 (tpp) REVERT: C 369 MET cc_start: 0.7999 (mmm) cc_final: 0.7736 (mmm) REVERT: D 158 GLN cc_start: 0.7933 (mt0) cc_final: 0.7604 (mt0) REVERT: D 161 ASP cc_start: 0.8459 (m-30) cc_final: 0.8156 (m-30) REVERT: D 234 MET cc_start: 0.8876 (ttt) cc_final: 0.8629 (ttt) REVERT: F 63 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8383 (mt0) REVERT: F 241 ASN cc_start: 0.8575 (m110) cc_final: 0.8275 (m110) REVERT: G 125 LEU cc_start: 0.9093 (tp) cc_final: 0.8876 (pp) REVERT: G 126 ASP cc_start: 0.8052 (m-30) cc_final: 0.7296 (m-30) REVERT: G 161 LYS cc_start: 0.9312 (ttmm) cc_final: 0.9034 (tptt) REVERT: G 225 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: H 84 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7187 (tt0) REVERT: H 89 ARG cc_start: 0.8299 (mtt90) cc_final: 0.8012 (ttm-80) REVERT: H 93 ASN cc_start: 0.9044 (m-40) cc_final: 0.8786 (m-40) REVERT: H 126 GLN cc_start: 0.8696 (mt0) cc_final: 0.8492 (mt0) REVERT: I 161 VAL cc_start: 0.4741 (OUTLIER) cc_final: 0.4494 (p) REVERT: K 94 GLN cc_start: 0.8756 (mt0) cc_final: 0.8450 (mt0) REVERT: K 160 GLN cc_start: 0.8604 (tp-100) cc_final: 0.8309 (tp-100) REVERT: K 164 ASP cc_start: 0.8524 (m-30) cc_final: 0.8216 (m-30) REVERT: L 85 LEU cc_start: 0.9528 (tp) cc_final: 0.9240 (tp) REVERT: M 228 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8609 (mtmt) REVERT: N 80 THR cc_start: 0.9176 (m) cc_final: 0.8822 (t) REVERT: N 86 ASN cc_start: 0.7676 (p0) cc_final: 0.7147 (p0) REVERT: N 178 GLN cc_start: 0.8269 (mt0) cc_final: 0.8029 (mt0) REVERT: N 197 LYS cc_start: 0.9004 (ttpt) cc_final: 0.8673 (tmmm) REVERT: N 201 ASP cc_start: 0.8157 (m-30) cc_final: 0.7923 (m-30) REVERT: N 223 MET cc_start: 0.8093 (mmm) cc_final: 0.7855 (mtt) REVERT: P 89 HIS cc_start: 0.7341 (m-70) cc_final: 0.6500 (m-70) REVERT: P 134 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8197 (tm-30) REVERT: Q 239 ASN cc_start: 0.8796 (t0) cc_final: 0.8514 (t0) REVERT: U 129 MET cc_start: -0.6249 (ttt) cc_final: -0.6691 (tmm) REVERT: V 175 LYS cc_start: 0.8804 (mttt) cc_final: 0.8530 (mtpt) REVERT: V 181 ASP cc_start: 0.8537 (m-30) cc_final: 0.8133 (m-30) REVERT: W 56 MET cc_start: 0.9044 (mmt) cc_final: 0.8155 (mmt) REVERT: W 85 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8691 (mtpp) REVERT: W 110 ASN cc_start: 0.8840 (t0) cc_final: 0.8548 (t0) REVERT: W 118 THR cc_start: 0.9099 (m) cc_final: 0.8860 (p) REVERT: X 60 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: X 113 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: Y 143 ASP cc_start: 0.8221 (t0) cc_final: 0.7862 (m-30) REVERT: Y 157 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8205 (mm-40) REVERT: Z 62 ASN cc_start: 0.8528 (t0) cc_final: 0.8251 (t0) REVERT: b 85 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7421 (mtp180) REVERT: c 67 ASP cc_start: 0.8601 (t0) cc_final: 0.8400 (t0) REVERT: d 136 ASP cc_start: 0.6171 (m-30) cc_final: 0.5535 (t0) REVERT: d 143 ASP cc_start: 0.6805 (m-30) cc_final: 0.6314 (p0) REVERT: d 156 ASP cc_start: 0.3251 (OUTLIER) cc_final: 0.2957 (p0) REVERT: d 166 GLU cc_start: 0.6458 (pm20) cc_final: 0.6237 (pp20) REVERT: d 172 MET cc_start: 0.5674 (OUTLIER) cc_final: 0.5281 (mpm) REVERT: d 190 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5961 (pp20) REVERT: d 231 LEU cc_start: 0.8864 (tp) cc_final: 0.8569 (tm) REVERT: d 242 VAL cc_start: 0.8676 (m) cc_final: 0.8413 (p) REVERT: d 261 MET cc_start: 0.7116 (mpt) cc_final: 0.6725 (mmt) REVERT: e 73 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8120 (mm) REVERT: e 260 LEU cc_start: 0.2974 (OUTLIER) cc_final: 0.2416 (tp) REVERT: h 70 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9197 (tm) REVERT: h 118 HIS cc_start: 0.8503 (OUTLIER) cc_final: 0.8063 (p-80) REVERT: h 153 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8361 (mmmm) REVERT: k 19 GLN cc_start: 0.6265 (pp30) cc_final: 0.5935 (pp30) REVERT: k 31 ARG cc_start: 0.8234 (ttt180) cc_final: 0.7561 (mtp180) REVERT: k 76 MET cc_start: 0.7094 (mmm) cc_final: 0.6827 (mmm) REVERT: p 47 LYS cc_start: 0.9348 (mttp) cc_final: 0.9069 (mttm) REVERT: p 118 LYS cc_start: 0.8543 (mttt) cc_final: 0.8222 (ttmm) REVERT: p 152 GLN cc_start: 0.8973 (tp40) cc_final: 0.7824 (tp40) REVERT: p 156 ASP cc_start: 0.8274 (m-30) cc_final: 0.7362 (m-30) REVERT: q 125 MET cc_start: 0.8425 (mmm) cc_final: 0.8022 (mmt) REVERT: r 72 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9226 (mp) REVERT: s 341 MET cc_start: 0.9014 (mtp) cc_final: 0.8659 (mtt) REVERT: u 96 MET cc_start: 0.8729 (mmm) cc_final: 0.8346 (tpt) REVERT: u 151 CYS cc_start: 0.7025 (m) cc_final: 0.6698 (t) REVERT: u 153 ARG cc_start: 0.8482 (pmm-80) cc_final: 0.8118 (ptp90) REVERT: u 154 ASP cc_start: 0.7083 (p0) cc_final: 0.6417 (p0) REVERT: v 39 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: v 56 GLU cc_start: 0.9150 (tp30) cc_final: 0.8860 (tp30) REVERT: w 145 VAL cc_start: 0.5123 (t) cc_final: 0.4910 (p) REVERT: x 118 VAL cc_start: 0.0756 (OUTLIER) cc_final: 0.0232 (p) REVERT: x 173 LEU cc_start: 0.8409 (mm) cc_final: 0.8082 (tp) outliers start: 217 outliers final: 114 residues processed: 1534 average time/residue: 1.7689 time to fit residues: 3747.2605 Evaluate side-chains 1505 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1367 time to evaluate : 7.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 366 CYS Chi-restraints excluded: chain 6 residue 179 VAL Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 291 TYR Chi-restraints excluded: chain 6 residue 320 GLN Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 7 residue 269 ILE Chi-restraints excluded: chain 8 residue 145 GLU Chi-restraints excluded: chain 8 residue 147 LEU Chi-restraints excluded: chain 9 residue 20 LYS Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 69 LYS Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 195 HIS Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain V residue 198 VAL Chi-restraints excluded: chain W residue 85 LYS Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 60 GLU Chi-restraints excluded: chain X residue 113 GLU Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 148 THR Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 235 LEU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain d residue 156 ASP Chi-restraints excluded: chain d residue 172 MET Chi-restraints excluded: chain d residue 190 GLU Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain e residue 151 ARG Chi-restraints excluded: chain e residue 152 LYS Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 260 LEU Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain h residue 135 GLN Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain j residue 67 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain p residue 100 GLU Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain q residue 131 MET Chi-restraints excluded: chain r residue 72 ILE Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 111 GLU Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 173 SER Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 131 SER Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 177 ILE Chi-restraints excluded: chain v residue 39 PHE Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain x residue 81 CYS Chi-restraints excluded: chain x residue 118 VAL Chi-restraints excluded: chain x residue 142 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 317 optimal weight: 6.9990 chunk 850 optimal weight: 50.0000 chunk 186 optimal weight: 8.9990 chunk 554 optimal weight: 20.0000 chunk 233 optimal weight: 7.9990 chunk 945 optimal weight: 8.9990 chunk 784 optimal weight: 40.0000 chunk 437 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 312 optimal weight: 6.9990 chunk 496 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 109 HIS 5 165 GLN 6 191 ASN 7 84 ASN 9 90 GLN C 55 GLN C 85 HIS C 304 HIS ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN F 257 GLN G 167 GLN H 100 GLN ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN L 80 GLN O 69 ASN O 150 GLN P 147 GLN P 176 GLN S 118 ASN T 101 GLN T 133 ASN T 201 GLN X 15 GLN Y 88 GLN Y 147 GLN Z 47 GLN Z 126 GLN b 58 ASN ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN h 99 ASN ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 147 GLN ** r 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 113 GLN ** u 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 ASN x 133 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.127 106223 Z= 0.494 Angle : 0.691 14.620 150405 Z= 0.355 Chirality : 0.045 0.414 17588 Planarity : 0.006 0.126 14010 Dihedral : 20.676 179.407 30990 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.42 % Allowed : 16.13 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.86 (0.09), residues: 8496 helix: 1.42 (0.09), residues: 3050 sheet: -0.03 (0.15), residues: 1108 loop : 0.24 (0.10), residues: 4338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP 6 235 HIS 0.012 0.001 HIS C 85 PHE 0.034 0.002 PHE e 215 TYR 0.040 0.002 TYR 6 291 ARG 0.017 0.001 ARG 1 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1622 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1361 time to evaluate : 7.187 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: 0 127 TYR cc_start: 0.8754 (t80) cc_final: 0.8510 (t80) REVERT: 4 74 LYS cc_start: 0.9240 (mttt) cc_final: 0.9029 (mttp) REVERT: 4 77 LYS cc_start: 0.9102 (tttt) cc_final: 0.8886 (mttt) REVERT: 5 64 MET cc_start: 0.8493 (mtm) cc_final: 0.8125 (mtp) REVERT: 5 183 ASN cc_start: 0.9136 (m-40) cc_final: 0.8875 (m-40) REVERT: 6 50 LYS cc_start: 0.8592 (mmtm) cc_final: 0.8370 (mmtm) REVERT: 6 320 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7150 (mm110) REVERT: 6 324 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8141 (m-30) REVERT: 6 355 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8731 (mtpp) REVERT: 8 109 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7881 (tm-30) REVERT: 8 145 GLU cc_start: 0.5849 (OUTLIER) cc_final: 0.5351 (pm20) REVERT: 9 41 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8497 (tp) REVERT: 9 59 GLU cc_start: 0.8044 (tt0) cc_final: 0.7815 (tt0) REVERT: C 158 MET cc_start: 0.8507 (ppp) cc_final: 0.8123 (ppp) REVERT: C 215 LYS cc_start: 0.8940 (tttp) cc_final: 0.8709 (tppt) REVERT: C 314 HIS cc_start: 0.7666 (OUTLIER) cc_final: 0.6918 (t70) REVERT: C 349 MET cc_start: 0.8527 (tpp) cc_final: 0.8283 (tpp) REVERT: C 369 MET cc_start: 0.7969 (mmm) cc_final: 0.7723 (mmm) REVERT: D 161 ASP cc_start: 0.8522 (m-30) cc_final: 0.8291 (m-30) REVERT: F 63 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8412 (mt0) REVERT: G 125 LEU cc_start: 0.9100 (tp) cc_final: 0.8896 (pp) REVERT: G 126 ASP cc_start: 0.8136 (m-30) cc_final: 0.7390 (m-30) REVERT: G 161 LYS cc_start: 0.9308 (ttmm) cc_final: 0.9023 (tptt) REVERT: G 225 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: H 84 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: H 89 ARG cc_start: 0.8404 (mtt90) cc_final: 0.8063 (mtm-85) REVERT: H 126 GLN cc_start: 0.8727 (mt0) cc_final: 0.8493 (mt0) REVERT: I 161 VAL cc_start: 0.4752 (OUTLIER) cc_final: 0.4508 (p) REVERT: K 94 GLN cc_start: 0.8895 (mt0) cc_final: 0.8685 (mt0) REVERT: K 111 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8112 (mtt) REVERT: K 164 ASP cc_start: 0.8552 (m-30) cc_final: 0.8315 (m-30) REVERT: N 80 THR cc_start: 0.9165 (m) cc_final: 0.8759 (t) REVERT: N 86 ASN cc_start: 0.7654 (p0) cc_final: 0.7325 (p0) REVERT: N 178 GLN cc_start: 0.8266 (mt0) cc_final: 0.8011 (mt0) REVERT: N 197 LYS cc_start: 0.9068 (ttpt) cc_final: 0.8796 (tmmm) REVERT: N 201 ASP cc_start: 0.8251 (m-30) cc_final: 0.7996 (m-30) REVERT: N 202 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8122 (tp-100) REVERT: N 247 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.7329 (mpt) REVERT: P 89 HIS cc_start: 0.7574 (m-70) cc_final: 0.6668 (m-70) REVERT: Q 239 ASN cc_start: 0.8837 (t0) cc_final: 0.8556 (t0) REVERT: S 68 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7816 (t70) REVERT: U 129 MET cc_start: -0.6225 (ttt) cc_final: -0.6602 (tmm) REVERT: V 175 LYS cc_start: 0.8835 (mttt) cc_final: 0.8610 (mtpt) REVERT: V 181 ASP cc_start: 0.8572 (m-30) cc_final: 0.8046 (m-30) REVERT: W 110 ASN cc_start: 0.9005 (t0) cc_final: 0.8499 (t0) REVERT: W 118 THR cc_start: 0.9198 (m) cc_final: 0.8964 (p) REVERT: X 60 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7335 (pm20) REVERT: Y 143 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: Z 62 ASN cc_start: 0.8518 (t0) cc_final: 0.8228 (t0) REVERT: Z 92 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6123 (pp20) REVERT: b 36 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7524 (m-30) REVERT: b 85 ARG cc_start: 0.7709 (mtp85) cc_final: 0.7464 (mtp180) REVERT: c 47 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7955 (ttp80) REVERT: d 136 ASP cc_start: 0.6204 (m-30) cc_final: 0.5462 (t0) REVERT: d 143 ASP cc_start: 0.6993 (m-30) cc_final: 0.6349 (p0) REVERT: d 166 GLU cc_start: 0.6390 (pm20) cc_final: 0.6128 (pp20) REVERT: d 171 ASP cc_start: 0.4717 (m-30) cc_final: 0.4297 (p0) REVERT: d 172 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.5015 (mpm) REVERT: d 176 ILE cc_start: 0.8571 (tp) cc_final: 0.8289 (pp) REVERT: d 242 VAL cc_start: 0.8672 (m) cc_final: 0.8355 (p) REVERT: d 261 MET cc_start: 0.7155 (mpt) cc_final: 0.6559 (mpp) REVERT: e 73 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7941 (mm) REVERT: e 234 PHE cc_start: 0.3097 (m-10) cc_final: 0.2413 (m-10) REVERT: e 260 LEU cc_start: 0.2806 (OUTLIER) cc_final: 0.2278 (pt) REVERT: h 70 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9197 (tm) REVERT: h 118 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8115 (p-80) REVERT: p 47 LYS cc_start: 0.9342 (mttp) cc_final: 0.9054 (mttm) REVERT: p 59 TRP cc_start: 0.9186 (OUTLIER) cc_final: 0.8874 (m100) REVERT: p 118 LYS cc_start: 0.8610 (mttt) cc_final: 0.8278 (ttmm) REVERT: p 125 ASN cc_start: 0.9213 (m-40) cc_final: 0.8960 (m-40) REVERT: q 125 MET cc_start: 0.8305 (mmm) cc_final: 0.7978 (mmt) REVERT: r 110 GLU cc_start: 0.7425 (pm20) cc_final: 0.7135 (pm20) REVERT: s 341 MET cc_start: 0.8978 (mtp) cc_final: 0.8657 (mtt) REVERT: u 96 MET cc_start: 0.8845 (mmm) cc_final: 0.8614 (tpp) REVERT: u 151 CYS cc_start: 0.7153 (m) cc_final: 0.6794 (t) REVERT: v 27 ASP cc_start: 0.8365 (t0) cc_final: 0.8137 (t0) REVERT: v 39 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7462 (m-80) REVERT: v 56 GLU cc_start: 0.9175 (tp30) cc_final: 0.8924 (tp30) REVERT: x 118 VAL cc_start: 0.1179 (OUTLIER) cc_final: 0.0610 (p) REVERT: x 173 LEU cc_start: 0.8493 (mm) cc_final: 0.8176 (tp) outliers start: 261 outliers final: 139 residues processed: 1502 average time/residue: 1.7747 time to fit residues: 3674.6951 Evaluate side-chains 1493 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1329 time to evaluate : 7.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 47 ASP Chi-restraints excluded: chain 5 residue 208 THR Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 366 CYS Chi-restraints excluded: chain 6 residue 179 VAL Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 276 ASP Chi-restraints excluded: chain 6 residue 320 GLN Chi-restraints excluded: chain 6 residue 324 ASP Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 7 residue 181 TYR Chi-restraints excluded: chain 7 residue 269 ILE Chi-restraints excluded: chain 8 residue 145 GLU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 339 GLN Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 114 ASP Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 195 HIS Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain V residue 198 VAL Chi-restraints excluded: chain V residue 200 GLU Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 85 LYS Chi-restraints excluded: chain X residue 15 GLN Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 60 GLU Chi-restraints excluded: chain X residue 74 GLU Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 143 ASP Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain c residue 276 CYS Chi-restraints excluded: chain d residue 156 ASP Chi-restraints excluded: chain d residue 172 MET Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain e residue 151 ARG Chi-restraints excluded: chain e residue 152 LYS Chi-restraints excluded: chain e residue 204 PHE Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 260 LEU Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 108 THR Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain h residue 135 GLN Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain j residue 43 LEU Chi-restraints excluded: chain j residue 67 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain p residue 59 TRP Chi-restraints excluded: chain p residue 100 GLU Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain r residue 72 ILE Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 111 GLU Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 173 SER Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 131 SER Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 200 ASP Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 39 PHE Chi-restraints excluded: chain v residue 62 LEU Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain x residue 81 CYS Chi-restraints excluded: chain x residue 94 SER Chi-restraints excluded: chain x residue 118 VAL Chi-restraints excluded: chain x residue 142 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 911 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 538 optimal weight: 5.9990 chunk 690 optimal weight: 10.0000 chunk 534 optimal weight: 0.8980 chunk 795 optimal weight: 0.0870 chunk 527 optimal weight: 20.0000 chunk 941 optimal weight: 8.9990 chunk 589 optimal weight: 0.7980 chunk 574 optimal weight: 0.9980 chunk 434 optimal weight: 5.9990 overall best weight: 1.3560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 GLN 6 191 ASN ** 7 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 90 GLN C 85 HIS C 304 HIS E 52 HIS ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN F 257 GLN H 93 ASN H 136 ASN I 45 GLN ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN L 48 ASN L 80 GLN M 289 ASN O 100 GLN P 147 GLN T 101 GLN T 133 ASN Y 88 GLN Y 147 GLN Y 183 GLN Z 126 GLN b 66 ASN c 172 ASN ** c 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN h 99 ASN ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 113 GLN v 63 ASN x 84 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 106223 Z= 0.190 Angle : 0.608 14.173 150405 Z= 0.313 Chirality : 0.038 0.401 17588 Planarity : 0.005 0.117 14010 Dihedral : 20.704 179.968 30990 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.59 % Allowed : 17.94 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.94 (0.09), residues: 8496 helix: 1.52 (0.09), residues: 3037 sheet: 0.00 (0.15), residues: 1109 loop : 0.27 (0.10), residues: 4350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP 6 235 HIS 0.015 0.001 HIS C 266 PHE 0.035 0.001 PHE e 215 TYR 0.044 0.001 TYR v 13 ARG 0.018 0.000 ARG 1 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1601 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1403 time to evaluate : 7.180 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: 1 45 HIS cc_start: 0.7518 (t70) cc_final: 0.7226 (t70) REVERT: 4 77 LYS cc_start: 0.9065 (tttt) cc_final: 0.8845 (mttt) REVERT: 5 64 MET cc_start: 0.8365 (mtm) cc_final: 0.8081 (ttm) REVERT: 5 183 ASN cc_start: 0.9120 (m-40) cc_final: 0.8841 (m-40) REVERT: 5 223 ARG cc_start: 0.7647 (mtm-85) cc_final: 0.7417 (mtm110) REVERT: 6 320 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7129 (mm110) REVERT: 6 339 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: 6 355 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8677 (mtpp) REVERT: 8 109 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7875 (tm-30) REVERT: 8 145 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5325 (pm20) REVERT: 8 147 LEU cc_start: 0.5613 (OUTLIER) cc_final: 0.5162 (pt) REVERT: 9 41 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8519 (tp) REVERT: 9 59 GLU cc_start: 0.7976 (tt0) cc_final: 0.7733 (tt0) REVERT: 9 69 LYS cc_start: 0.8207 (ptmm) cc_final: 0.7855 (ptmm) REVERT: C 52 TYR cc_start: 0.8504 (m-10) cc_final: 0.8266 (m-80) REVERT: C 215 LYS cc_start: 0.9022 (tttp) cc_final: 0.8697 (tppt) REVERT: C 314 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.6882 (t70) REVERT: C 349 MET cc_start: 0.8538 (tpp) cc_final: 0.8261 (tpp) REVERT: C 369 MET cc_start: 0.7881 (mmm) cc_final: 0.7604 (mmm) REVERT: D 156 ASN cc_start: 0.8928 (m-40) cc_final: 0.8695 (m-40) REVERT: D 161 ASP cc_start: 0.8450 (m-30) cc_final: 0.8225 (m-30) REVERT: F 63 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8396 (mt0) REVERT: F 241 ASN cc_start: 0.8645 (m110) cc_final: 0.8329 (m110) REVERT: G 125 LEU cc_start: 0.9088 (tp) cc_final: 0.8885 (pp) REVERT: G 126 ASP cc_start: 0.8086 (m-30) cc_final: 0.7325 (m-30) REVERT: G 161 LYS cc_start: 0.9301 (ttmm) cc_final: 0.9012 (tptt) REVERT: H 84 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: H 89 ARG cc_start: 0.8360 (mtt90) cc_final: 0.8011 (mtm-85) REVERT: H 126 GLN cc_start: 0.8695 (mt0) cc_final: 0.8480 (mt0) REVERT: I 161 VAL cc_start: 0.4822 (OUTLIER) cc_final: 0.4573 (p) REVERT: K 94 GLN cc_start: 0.8759 (mt0) cc_final: 0.8475 (mt0) REVERT: K 160 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8085 (tp-100) REVERT: M 228 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8606 (mtmt) REVERT: N 80 THR cc_start: 0.9130 (m) cc_final: 0.8730 (t) REVERT: N 86 ASN cc_start: 0.7500 (p0) cc_final: 0.7192 (p0) REVERT: N 118 MET cc_start: 0.3936 (mmt) cc_final: 0.3225 (mmt) REVERT: N 178 GLN cc_start: 0.8230 (mt0) cc_final: 0.7959 (mt0) REVERT: N 197 LYS cc_start: 0.9028 (ttpt) cc_final: 0.8692 (tmmm) REVERT: N 201 ASP cc_start: 0.8176 (m-30) cc_final: 0.7911 (m-30) REVERT: N 202 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8068 (tp-100) REVERT: N 247 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7408 (mpt) REVERT: P 58 LEU cc_start: 0.9301 (mt) cc_final: 0.9050 (mt) REVERT: P 89 HIS cc_start: 0.7562 (m-70) cc_final: 0.6669 (m-70) REVERT: Q 239 ASN cc_start: 0.8793 (t0) cc_final: 0.8508 (t0) REVERT: T 198 GLU cc_start: 0.7331 (tm-30) cc_final: 0.7097 (pp20) REVERT: U 129 MET cc_start: -0.6332 (ttt) cc_final: -0.6672 (tmm) REVERT: V 175 LYS cc_start: 0.8757 (mttt) cc_final: 0.8504 (mtpt) REVERT: V 181 ASP cc_start: 0.8419 (m-30) cc_final: 0.8195 (m-30) REVERT: W 56 MET cc_start: 0.9078 (mmt) cc_final: 0.8059 (mmt) REVERT: W 85 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8723 (mtpp) REVERT: W 110 ASN cc_start: 0.8951 (t0) cc_final: 0.8494 (t0) REVERT: W 118 THR cc_start: 0.9123 (m) cc_final: 0.8884 (p) REVERT: Y 143 ASP cc_start: 0.8268 (t0) cc_final: 0.7914 (m-30) REVERT: Y 157 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8152 (mm-40) REVERT: Z 62 ASN cc_start: 0.8525 (t0) cc_final: 0.8267 (t0) REVERT: b 85 ARG cc_start: 0.7649 (mtp85) cc_final: 0.7369 (mtp180) REVERT: c 67 ASP cc_start: 0.8596 (t0) cc_final: 0.8391 (t0) REVERT: d 136 ASP cc_start: 0.6191 (m-30) cc_final: 0.5474 (t0) REVERT: d 143 ASP cc_start: 0.6944 (m-30) cc_final: 0.6345 (p0) REVERT: d 172 MET cc_start: 0.5572 (OUTLIER) cc_final: 0.5115 (mpm) REVERT: d 176 ILE cc_start: 0.8551 (tp) cc_final: 0.8307 (pp) REVERT: d 225 TYR cc_start: 0.8642 (m-80) cc_final: 0.8409 (m-80) REVERT: d 227 ARG cc_start: 0.8780 (mtm110) cc_final: 0.8567 (mtm110) REVERT: d 242 VAL cc_start: 0.8654 (m) cc_final: 0.8366 (p) REVERT: d 261 MET cc_start: 0.7236 (mpt) cc_final: 0.6558 (mpp) REVERT: e 151 ARG cc_start: 0.1381 (OUTLIER) cc_final: 0.0659 (tpp-160) REVERT: e 260 LEU cc_start: 0.2841 (OUTLIER) cc_final: 0.2391 (pt) REVERT: h 71 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7914 (mm-30) REVERT: h 86 TRP cc_start: 0.7949 (p-90) cc_final: 0.7314 (p-90) REVERT: h 118 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.8134 (p-80) REVERT: h 153 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8417 (mmmm) REVERT: k 86 MET cc_start: 0.9115 (mtm) cc_final: 0.8866 (mtm) REVERT: p 47 LYS cc_start: 0.9338 (mttp) cc_final: 0.9063 (mttm) REVERT: p 152 GLN cc_start: 0.9037 (tp40) cc_final: 0.7837 (tp40) REVERT: p 156 ASP cc_start: 0.8307 (m-30) cc_final: 0.7313 (m-30) REVERT: q 125 MET cc_start: 0.8459 (mmm) cc_final: 0.8191 (mmt) REVERT: s 341 MET cc_start: 0.9012 (mtp) cc_final: 0.8645 (mtt) REVERT: u 151 CYS cc_start: 0.7042 (m) cc_final: 0.6704 (t) REVERT: u 153 ARG cc_start: 0.8524 (pmm-80) cc_final: 0.8137 (ptp90) REVERT: u 154 ASP cc_start: 0.7081 (p0) cc_final: 0.6418 (p0) REVERT: v 39 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: v 56 GLU cc_start: 0.9176 (tp30) cc_final: 0.8922 (tp30) REVERT: w 145 VAL cc_start: 0.5128 (t) cc_final: 0.4907 (p) REVERT: x 118 VAL cc_start: 0.1155 (OUTLIER) cc_final: 0.0653 (p) REVERT: x 173 LEU cc_start: 0.8497 (mm) cc_final: 0.8202 (tp) outliers start: 198 outliers final: 105 residues processed: 1508 average time/residue: 1.8624 time to fit residues: 3906.3377 Evaluate side-chains 1480 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1356 time to evaluate : 7.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 6 residue 179 VAL Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 320 GLN Chi-restraints excluded: chain 6 residue 339 GLU Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 269 ILE Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 145 GLU Chi-restraints excluded: chain 8 residue 147 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 130 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 195 HIS Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain V residue 198 VAL Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 85 LYS Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain c residue 215 ILE Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain c residue 276 CYS Chi-restraints excluded: chain d residue 156 ASP Chi-restraints excluded: chain d residue 172 MET Chi-restraints excluded: chain d residue 226 ASP Chi-restraints excluded: chain e residue 151 ARG Chi-restraints excluded: chain e residue 152 LYS Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 260 LEU Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain h residue 135 GLN Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain j residue 67 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain r residue 72 ILE Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 111 GLU Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 173 SER Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain s residue 419 LEU Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 131 SER Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 177 ILE Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 39 PHE Chi-restraints excluded: chain v residue 65 LYS Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain x residue 81 CYS Chi-restraints excluded: chain x residue 94 SER Chi-restraints excluded: chain x residue 118 VAL Chi-restraints excluded: chain x residue 142 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 582 optimal weight: 3.9990 chunk 376 optimal weight: 7.9990 chunk 562 optimal weight: 30.0000 chunk 283 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 598 optimal weight: 8.9990 chunk 641 optimal weight: 3.9990 chunk 465 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 740 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 37 ASN 6 191 ASN ** 7 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 304 HIS ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN F 228 GLN F 257 GLN H 93 ASN H 100 GLN H 136 ASN ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN L 80 GLN M 219 ASN ** T 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 133 ASN Y 88 GLN Y 147 GLN Z 47 GLN b 66 ASN c 172 ASN ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 GLN h 99 ASN q 51 GLN r 76 ASN ** u 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 106223 Z= 0.422 Angle : 0.674 15.304 150405 Z= 0.346 Chirality : 0.043 0.406 17588 Planarity : 0.005 0.123 14010 Dihedral : 20.650 179.919 30990 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.88 % Allowed : 18.05 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.87 (0.09), residues: 8496 helix: 1.42 (0.09), residues: 3038 sheet: -0.02 (0.15), residues: 1111 loop : 0.26 (0.10), residues: 4347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP 6 235 HIS 0.013 0.001 HIS C 85 PHE 0.034 0.002 PHE e 215 TYR 0.044 0.002 TYR v 13 ARG 0.019 0.001 ARG 1 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1573 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1353 time to evaluate : 7.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 45 HIS cc_start: 0.7485 (t70) cc_final: 0.7184 (t70) REVERT: 4 77 LYS cc_start: 0.9099 (tttt) cc_final: 0.8889 (mttt) REVERT: 5 64 MET cc_start: 0.8441 (mtm) cc_final: 0.8170 (ttm) REVERT: 5 142 ASP cc_start: 0.4871 (OUTLIER) cc_final: 0.4636 (p0) REVERT: 5 183 ASN cc_start: 0.9119 (m-40) cc_final: 0.8859 (m-40) REVERT: 6 320 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7153 (mm110) REVERT: 6 355 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8736 (mtpp) REVERT: 7 113 TRP cc_start: 0.8639 (t-100) cc_final: 0.8069 (t-100) REVERT: 8 109 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7870 (tm-30) REVERT: 8 145 GLU cc_start: 0.5807 (OUTLIER) cc_final: 0.5393 (pm20) REVERT: 8 147 LEU cc_start: 0.5661 (OUTLIER) cc_final: 0.5203 (pt) REVERT: 9 41 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8539 (tp) REVERT: 9 59 GLU cc_start: 0.8029 (tt0) cc_final: 0.7791 (tt0) REVERT: 9 69 LYS cc_start: 0.8225 (ptmm) cc_final: 0.8005 (ptmm) REVERT: C 158 MET cc_start: 0.8375 (ppp) cc_final: 0.8059 (ppp) REVERT: C 215 LYS cc_start: 0.9035 (tttp) cc_final: 0.8715 (tppt) REVERT: C 314 HIS cc_start: 0.7669 (OUTLIER) cc_final: 0.6906 (t70) REVERT: C 349 MET cc_start: 0.8528 (tpp) cc_final: 0.8273 (tpp) REVERT: C 369 MET cc_start: 0.7965 (mmm) cc_final: 0.7761 (mmm) REVERT: D 156 ASN cc_start: 0.8952 (m-40) cc_final: 0.8667 (m-40) REVERT: D 161 ASP cc_start: 0.8498 (m-30) cc_final: 0.8271 (m-30) REVERT: D 287 ARG cc_start: 0.7624 (mtt180) cc_final: 0.7138 (mtt180) REVERT: E 63 GLN cc_start: 0.7787 (tp40) cc_final: 0.7583 (tp40) REVERT: F 63 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8410 (mt0) REVERT: G 126 ASP cc_start: 0.8140 (m-30) cc_final: 0.7391 (m-30) REVERT: G 161 LYS cc_start: 0.9305 (ttmm) cc_final: 0.9021 (tptt) REVERT: H 84 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7169 (tt0) REVERT: H 89 ARG cc_start: 0.8436 (mtt90) cc_final: 0.8122 (mtm-85) REVERT: H 126 GLN cc_start: 0.8728 (mt0) cc_final: 0.8499 (mt0) REVERT: I 161 VAL cc_start: 0.4660 (OUTLIER) cc_final: 0.4386 (p) REVERT: J 51 LYS cc_start: 0.7492 (mppt) cc_final: 0.7078 (pmtt) REVERT: J 92 LYS cc_start: 0.1764 (mmtt) cc_final: 0.0529 (mttp) REVERT: J 157 LYS cc_start: 0.5401 (pmtt) cc_final: 0.4788 (tmmm) REVERT: K 94 GLN cc_start: 0.8870 (mt0) cc_final: 0.8589 (mt0) REVERT: K 111 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7854 (mtt) REVERT: N 80 THR cc_start: 0.9163 (m) cc_final: 0.8739 (t) REVERT: N 86 ASN cc_start: 0.7539 (p0) cc_final: 0.7259 (p0) REVERT: N 118 MET cc_start: 0.4106 (mmt) cc_final: 0.3742 (mmt) REVERT: N 178 GLN cc_start: 0.8280 (mt0) cc_final: 0.7988 (mt0) REVERT: N 197 LYS cc_start: 0.9069 (ttpt) cc_final: 0.8813 (tmmm) REVERT: N 201 ASP cc_start: 0.8308 (m-30) cc_final: 0.8054 (m-30) REVERT: N 247 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.7316 (mpt) REVERT: P 89 HIS cc_start: 0.7592 (m-70) cc_final: 0.6668 (m-70) REVERT: Q 239 ASN cc_start: 0.8836 (t0) cc_final: 0.8545 (t0) REVERT: T 163 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7732 (mmm160) REVERT: U 129 MET cc_start: -0.6286 (ttt) cc_final: -0.6628 (tmm) REVERT: W 110 ASN cc_start: 0.9004 (t0) cc_final: 0.8474 (t0) REVERT: X 60 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7334 (pm20) REVERT: Y 143 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: Z 62 ASN cc_start: 0.8553 (t0) cc_final: 0.8276 (t0) REVERT: Z 92 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6091 (pp20) REVERT: b 36 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: b 74 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7186 (mtp-110) REVERT: b 85 ARG cc_start: 0.7709 (mtp85) cc_final: 0.7471 (mtp180) REVERT: c 47 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7975 (ttp80) REVERT: c 67 ASP cc_start: 0.8688 (t0) cc_final: 0.8448 (t0) REVERT: d 136 ASP cc_start: 0.6146 (m-30) cc_final: 0.5393 (t0) REVERT: d 143 ASP cc_start: 0.7042 (m-30) cc_final: 0.6413 (p0) REVERT: d 166 GLU cc_start: 0.6242 (pm20) cc_final: 0.5983 (pp20) REVERT: d 172 MET cc_start: 0.5570 (OUTLIER) cc_final: 0.5077 (mpm) REVERT: d 176 ILE cc_start: 0.8564 (tp) cc_final: 0.8294 (pp) REVERT: d 232 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8738 (ptp) REVERT: d 237 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7775 (p0) REVERT: d 242 VAL cc_start: 0.8658 (m) cc_final: 0.8366 (p) REVERT: d 261 MET cc_start: 0.7265 (mpt) cc_final: 0.6626 (mpp) REVERT: e 73 LEU cc_start: 0.7984 (pp) cc_final: 0.7312 (mm) REVERT: e 151 ARG cc_start: 0.1316 (OUTLIER) cc_final: 0.0370 (tpp-160) REVERT: e 260 LEU cc_start: 0.3030 (OUTLIER) cc_final: 0.2618 (pt) REVERT: g 49 GLU cc_start: 0.8353 (mp0) cc_final: 0.8133 (mp0) REVERT: g 76 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8396 (ptp-170) REVERT: h 88 ASP cc_start: 0.8025 (t70) cc_final: 0.7779 (t0) REVERT: h 118 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.8159 (p-80) REVERT: h 153 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8551 (mmmm) REVERT: k 86 MET cc_start: 0.9075 (mtm) cc_final: 0.8853 (mtm) REVERT: p 47 LYS cc_start: 0.9330 (mttp) cc_final: 0.9033 (mttm) REVERT: p 152 GLN cc_start: 0.9050 (tp40) cc_final: 0.7832 (tp40) REVERT: p 156 ASP cc_start: 0.8298 (m-30) cc_final: 0.7270 (m-30) REVERT: q 125 MET cc_start: 0.8305 (mmm) cc_final: 0.8046 (mmt) REVERT: r 103 LYS cc_start: 0.8086 (tptt) cc_final: 0.7822 (tptt) REVERT: r 110 GLU cc_start: 0.7404 (pm20) cc_final: 0.7175 (pm20) REVERT: s 341 MET cc_start: 0.9009 (mtp) cc_final: 0.8662 (mtt) REVERT: u 151 CYS cc_start: 0.7122 (m) cc_final: 0.6891 (t) REVERT: u 153 ARG cc_start: 0.8516 (pmm-80) cc_final: 0.8139 (ptp90) REVERT: u 154 ASP cc_start: 0.7007 (p0) cc_final: 0.6383 (p0) REVERT: v 39 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: v 56 GLU cc_start: 0.9186 (tp30) cc_final: 0.8927 (tp30) REVERT: x 118 VAL cc_start: 0.1688 (OUTLIER) cc_final: 0.1126 (p) REVERT: x 173 LEU cc_start: 0.8477 (mm) cc_final: 0.8223 (tp) outliers start: 220 outliers final: 129 residues processed: 1463 average time/residue: 1.7891 time to fit residues: 3606.0765 Evaluate side-chains 1484 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1328 time to evaluate : 7.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 5 residue 142 ASP Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 366 CYS Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 179 VAL Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 320 GLN Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 7 residue 269 ILE Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 145 GLU Chi-restraints excluded: chain 8 residue 147 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 130 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 195 HIS Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 87 ILE Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain V residue 198 VAL Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 85 LYS Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 60 GLU Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 143 ASP Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 74 ARG Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain c residue 276 CYS Chi-restraints excluded: chain d residue 156 ASP Chi-restraints excluded: chain d residue 172 MET Chi-restraints excluded: chain d residue 226 ASP Chi-restraints excluded: chain d residue 232 MET Chi-restraints excluded: chain d residue 237 ASP Chi-restraints excluded: chain e residue 151 ARG Chi-restraints excluded: chain e residue 152 LYS Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 260 LEU Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain h residue 135 GLN Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain j residue 43 LEU Chi-restraints excluded: chain j residue 67 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain j residue 93 LEU Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain p residue 98 LYS Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain r residue 72 ILE Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 111 GLU Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 173 SER Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 271 LEU Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 131 SER Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 200 ASP Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 39 PHE Chi-restraints excluded: chain v residue 65 LYS Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain x residue 81 CYS Chi-restraints excluded: chain x residue 94 SER Chi-restraints excluded: chain x residue 118 VAL Chi-restraints excluded: chain x residue 142 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 856 optimal weight: 0.9990 chunk 902 optimal weight: 0.0870 chunk 823 optimal weight: 9.9990 chunk 877 optimal weight: 1.9990 chunk 901 optimal weight: 8.9990 chunk 528 optimal weight: 30.0000 chunk 382 optimal weight: 0.9980 chunk 689 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 chunk 792 optimal weight: 50.0000 chunk 829 optimal weight: 4.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 191 ASN ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 304 HIS D 195 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN F 228 GLN F 257 GLN ** G 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN H 136 ASN ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN L 80 GLN O 100 GLN ** T 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 133 ASN Y 88 GLN Y 147 GLN b 66 ASN c 172 ASN ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 GLN h 99 ASN ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN ** u 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 106223 Z= 0.211 Angle : 0.623 14.290 150405 Z= 0.320 Chirality : 0.039 0.397 17588 Planarity : 0.005 0.117 14010 Dihedral : 20.672 179.891 30990 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.97 % Favored : 97.02 % Rotamer: Outliers : 2.38 % Allowed : 18.90 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.92 (0.09), residues: 8496 helix: 1.48 (0.09), residues: 3035 sheet: -0.01 (0.15), residues: 1104 loop : 0.27 (0.10), residues: 4357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP 6 235 HIS 0.013 0.001 HIS C 85 PHE 0.035 0.001 PHE e 215 TYR 0.024 0.001 TYR 5 176 ARG 0.019 0.000 ARG 1 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1567 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1385 time to evaluate : 7.188 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: 4 76 CYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8121 (p) REVERT: 4 77 LYS cc_start: 0.9057 (tttt) cc_final: 0.8810 (mttt) REVERT: 5 64 MET cc_start: 0.8344 (mtm) cc_final: 0.8057 (ttm) REVERT: 5 183 ASN cc_start: 0.9119 (m-40) cc_final: 0.8865 (m-40) REVERT: 5 223 ARG cc_start: 0.7492 (mtm-85) cc_final: 0.7096 (mtm110) REVERT: 6 320 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7152 (mm110) REVERT: 6 355 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8690 (mtpp) REVERT: 7 113 TRP cc_start: 0.8653 (t-100) cc_final: 0.8135 (t-100) REVERT: 8 109 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7867 (tm-30) REVERT: 8 145 GLU cc_start: 0.5913 (OUTLIER) cc_final: 0.5507 (pm20) REVERT: 8 147 LEU cc_start: 0.5338 (OUTLIER) cc_final: 0.4882 (pt) REVERT: 9 41 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8501 (tp) REVERT: 9 59 GLU cc_start: 0.7979 (tt0) cc_final: 0.7742 (tt0) REVERT: 9 120 GLU cc_start: 0.8235 (pm20) cc_final: 0.7573 (pm20) REVERT: C 153 MET cc_start: 0.7335 (mmp) cc_final: 0.7030 (mmp) REVERT: C 158 MET cc_start: 0.8356 (ppp) cc_final: 0.7936 (ppp) REVERT: C 215 LYS cc_start: 0.9008 (tttp) cc_final: 0.8672 (tppt) REVERT: C 314 HIS cc_start: 0.7625 (OUTLIER) cc_final: 0.6782 (t70) REVERT: C 349 MET cc_start: 0.8518 (tpp) cc_final: 0.8266 (tpp) REVERT: D 156 ASN cc_start: 0.8928 (m-40) cc_final: 0.8643 (m-40) REVERT: D 161 ASP cc_start: 0.8425 (m-30) cc_final: 0.8209 (m-30) REVERT: D 287 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7457 (mtt180) REVERT: F 241 ASN cc_start: 0.8651 (m110) cc_final: 0.8333 (m110) REVERT: G 161 LYS cc_start: 0.9312 (ttmm) cc_final: 0.9001 (tptt) REVERT: H 84 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: H 89 ARG cc_start: 0.8424 (mtt90) cc_final: 0.8117 (mtm-85) REVERT: H 126 GLN cc_start: 0.8679 (mt0) cc_final: 0.8470 (mt0) REVERT: I 161 VAL cc_start: 0.4777 (OUTLIER) cc_final: 0.4475 (p) REVERT: J 157 LYS cc_start: 0.5488 (pmtt) cc_final: 0.4773 (tmmm) REVERT: K 94 GLN cc_start: 0.8762 (mt0) cc_final: 0.8468 (mt0) REVERT: L 120 LYS cc_start: 0.8730 (tptm) cc_final: 0.8482 (tppp) REVERT: N 80 THR cc_start: 0.9079 (m) cc_final: 0.8643 (t) REVERT: N 86 ASN cc_start: 0.7560 (p0) cc_final: 0.7301 (p0) REVERT: N 114 ASP cc_start: 0.7704 (p0) cc_final: 0.7472 (p0) REVERT: N 118 MET cc_start: 0.3963 (mmt) cc_final: 0.3656 (mmt) REVERT: N 197 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8733 (tmmm) REVERT: N 201 ASP cc_start: 0.8213 (m-30) cc_final: 0.7965 (m-30) REVERT: N 202 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8137 (tp-100) REVERT: N 247 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.7405 (mpt) REVERT: P 89 HIS cc_start: 0.7596 (m-70) cc_final: 0.6755 (m-70) REVERT: Q 239 ASN cc_start: 0.8790 (t0) cc_final: 0.8509 (t0) REVERT: R 124 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7608 (ttm-80) REVERT: S 153 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8948 (tp) REVERT: T 163 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7817 (mmm160) REVERT: T 198 GLU cc_start: 0.7328 (tm-30) cc_final: 0.7095 (pp20) REVERT: U 129 MET cc_start: -0.6320 (ttt) cc_final: -0.6638 (tmm) REVERT: W 56 MET cc_start: 0.9079 (mmt) cc_final: 0.8080 (mmt) REVERT: W 85 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8653 (mtpp) REVERT: W 110 ASN cc_start: 0.8959 (t0) cc_final: 0.8448 (t0) REVERT: Y 143 ASP cc_start: 0.8292 (t0) cc_final: 0.7928 (m-30) REVERT: Y 157 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8166 (mm-40) REVERT: Z 62 ASN cc_start: 0.8496 (t0) cc_final: 0.8266 (t0) REVERT: b 85 ARG cc_start: 0.7712 (mtp85) cc_final: 0.7418 (mtp180) REVERT: c 67 ASP cc_start: 0.8596 (t0) cc_final: 0.8369 (t0) REVERT: c 294 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: d 136 ASP cc_start: 0.6189 (m-30) cc_final: 0.5452 (t0) REVERT: d 143 ASP cc_start: 0.7120 (m-30) cc_final: 0.6540 (p0) REVERT: d 166 GLU cc_start: 0.6187 (pm20) cc_final: 0.5901 (pp20) REVERT: d 172 MET cc_start: 0.5541 (OUTLIER) cc_final: 0.5123 (mpm) REVERT: d 176 ILE cc_start: 0.8682 (tp) cc_final: 0.8447 (pp) REVERT: d 227 ARG cc_start: 0.8801 (ttp80) cc_final: 0.8497 (ttp80) REVERT: d 261 MET cc_start: 0.7335 (mpt) cc_final: 0.6785 (mmt) REVERT: d 277 LEU cc_start: 0.8696 (mm) cc_final: 0.8469 (mp) REVERT: e 73 LEU cc_start: 0.7996 (pp) cc_final: 0.7298 (mm) REVERT: e 151 ARG cc_start: 0.1083 (OUTLIER) cc_final: 0.0456 (tpp-160) REVERT: e 260 LEU cc_start: 0.2994 (OUTLIER) cc_final: 0.2598 (pt) REVERT: g 40 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6832 (tm-30) REVERT: h 71 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8017 (mm-30) REVERT: h 118 HIS cc_start: 0.8550 (OUTLIER) cc_final: 0.8142 (p-80) REVERT: h 153 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8438 (mmmm) REVERT: p 47 LYS cc_start: 0.9326 (mttp) cc_final: 0.9031 (mttm) REVERT: p 152 GLN cc_start: 0.9021 (tp40) cc_final: 0.7877 (tp40) REVERT: p 156 ASP cc_start: 0.8264 (m-30) cc_final: 0.7324 (m-30) REVERT: q 59 LYS cc_start: 0.8861 (mttm) cc_final: 0.8544 (mttm) REVERT: q 125 MET cc_start: 0.8288 (mmm) cc_final: 0.8039 (mmt) REVERT: r 72 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9254 (mp) REVERT: s 341 MET cc_start: 0.9008 (mtp) cc_final: 0.8635 (mtt) REVERT: s 385 GLN cc_start: 0.7278 (pm20) cc_final: 0.7000 (pm20) REVERT: u 151 CYS cc_start: 0.6958 (m) cc_final: 0.6685 (t) REVERT: u 153 ARG cc_start: 0.8478 (pmm-80) cc_final: 0.8110 (ptp90) REVERT: u 154 ASP cc_start: 0.7100 (p0) cc_final: 0.6438 (p0) REVERT: v 39 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: v 56 GLU cc_start: 0.9178 (tp30) cc_final: 0.8910 (tp30) REVERT: w 145 VAL cc_start: 0.5133 (t) cc_final: 0.4912 (p) REVERT: x 118 VAL cc_start: 0.1919 (OUTLIER) cc_final: 0.1457 (p) REVERT: x 173 LEU cc_start: 0.8503 (mm) cc_final: 0.8242 (tp) outliers start: 182 outliers final: 115 residues processed: 1486 average time/residue: 1.7713 time to fit residues: 3650.0432 Evaluate side-chains 1487 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1351 time to evaluate : 7.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 CYS Chi-restraints excluded: chain 4 residue 76 CYS Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 179 VAL Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 320 GLN Chi-restraints excluded: chain 6 residue 339 GLU Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 7 residue 269 ILE Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 145 GLU Chi-restraints excluded: chain 8 residue 147 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain 9 residue 130 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 121 ASP Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 195 HIS Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain V residue 198 VAL Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 85 LYS Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 215 ILE Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain c residue 276 CYS Chi-restraints excluded: chain c residue 294 GLU Chi-restraints excluded: chain d residue 156 ASP Chi-restraints excluded: chain d residue 172 MET Chi-restraints excluded: chain d residue 226 ASP Chi-restraints excluded: chain e residue 151 ARG Chi-restraints excluded: chain e residue 152 LYS Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 260 LEU Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain h residue 135 GLN Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain j residue 67 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain r residue 72 ILE Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 173 SER Chi-restraints excluded: chain s residue 215 GLU Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 271 LEU Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 39 PHE Chi-restraints excluded: chain v residue 65 LYS Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain x residue 81 CYS Chi-restraints excluded: chain x residue 94 SER Chi-restraints excluded: chain x residue 118 VAL Chi-restraints excluded: chain x residue 142 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 874 optimal weight: 20.0000 chunk 576 optimal weight: 0.9980 chunk 927 optimal weight: 30.0000 chunk 566 optimal weight: 7.9990 chunk 440 optimal weight: 6.9990 chunk 645 optimal weight: 0.7980 chunk 973 optimal weight: 7.9990 chunk 895 optimal weight: 10.0000 chunk 775 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 598 optimal weight: 3.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 GLN ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 304 HIS ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN F 257 GLN ** G 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 GLN L 43 ASN L 80 GLN N 117 ASN N 178 GLN ** T 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN X 240 GLN Y 88 GLN Y 147 GLN b 66 ASN ** c 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 211 GLN ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 GLN h 119 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 76 ASN ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN ** u 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 113 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 106223 Z= 0.365 Angle : 0.664 14.866 150405 Z= 0.341 Chirality : 0.042 0.397 17588 Planarity : 0.005 0.120 14010 Dihedral : 20.619 179.741 30990 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.16 % Allowed : 19.21 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.87 (0.09), residues: 8496 helix: 1.40 (0.09), residues: 3048 sheet: -0.01 (0.15), residues: 1108 loop : 0.27 (0.10), residues: 4340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP h 86 HIS 0.013 0.001 HIS C 85 PHE 0.039 0.002 PHE 1 30 TYR 0.050 0.002 TYR v 13 ARG 0.020 0.001 ARG 1 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16992 Ramachandran restraints generated. 8496 Oldfield, 0 Emsley, 8496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1497 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1332 time to evaluate : 7.433 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: 4 76 CYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8051 (p) REVERT: 4 77 LYS cc_start: 0.9101 (tttt) cc_final: 0.8865 (mttt) REVERT: 5 64 MET cc_start: 0.8395 (mtm) cc_final: 0.8138 (ttm) REVERT: 5 183 ASN cc_start: 0.9108 (m-40) cc_final: 0.8842 (m-40) REVERT: 5 223 ARG cc_start: 0.7534 (mtm-85) cc_final: 0.7146 (mtm110) REVERT: 6 279 ILE cc_start: 0.4676 (OUTLIER) cc_final: 0.4470 (mp) REVERT: 6 320 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7114 (mm110) REVERT: 6 355 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8733 (mtpp) REVERT: 7 113 TRP cc_start: 0.8653 (t-100) cc_final: 0.8150 (t-100) REVERT: 7 235 TYR cc_start: 0.8144 (m-80) cc_final: 0.7771 (m-80) REVERT: 8 109 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7837 (tm-30) REVERT: 8 145 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.5470 (pm20) REVERT: 8 147 LEU cc_start: 0.5381 (OUTLIER) cc_final: 0.4915 (pt) REVERT: 9 41 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8522 (tp) REVERT: 9 59 GLU cc_start: 0.8000 (tt0) cc_final: 0.7761 (tt0) REVERT: C 153 MET cc_start: 0.7473 (mmp) cc_final: 0.7104 (mmp) REVERT: C 158 MET cc_start: 0.8348 (ppp) cc_final: 0.7926 (ppp) REVERT: C 215 LYS cc_start: 0.8993 (tttp) cc_final: 0.8666 (tppt) REVERT: C 314 HIS cc_start: 0.7626 (OUTLIER) cc_final: 0.6791 (t70) REVERT: C 349 MET cc_start: 0.8521 (tpp) cc_final: 0.8269 (tpp) REVERT: D 156 ASN cc_start: 0.8953 (m-40) cc_final: 0.8657 (m-40) REVERT: D 161 ASP cc_start: 0.8450 (m-30) cc_final: 0.8232 (m-30) REVERT: G 161 LYS cc_start: 0.9312 (ttmm) cc_final: 0.9043 (tptt) REVERT: H 84 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: H 89 ARG cc_start: 0.8445 (mtt90) cc_final: 0.8137 (mtm-85) REVERT: H 126 GLN cc_start: 0.8708 (mt0) cc_final: 0.8442 (mt0) REVERT: I 161 VAL cc_start: 0.4687 (OUTLIER) cc_final: 0.4410 (p) REVERT: J 157 LYS cc_start: 0.5251 (pmtt) cc_final: 0.4620 (tmmm) REVERT: K 94 GLN cc_start: 0.8850 (mt0) cc_final: 0.8582 (mt0) REVERT: N 80 THR cc_start: 0.9157 (m) cc_final: 0.8720 (t) REVERT: N 86 ASN cc_start: 0.7593 (p0) cc_final: 0.7329 (p0) REVERT: N 118 MET cc_start: 0.4229 (mmt) cc_final: 0.3808 (mmt) REVERT: N 178 GLN cc_start: 0.8274 (mt0) cc_final: 0.8055 (mt0) REVERT: N 197 LYS cc_start: 0.9065 (ttpt) cc_final: 0.8799 (tmmm) REVERT: N 201 ASP cc_start: 0.8294 (m-30) cc_final: 0.8039 (m-30) REVERT: N 202 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8178 (tp-100) REVERT: N 247 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7379 (mpt) REVERT: P 40 GLU cc_start: 0.7355 (pm20) cc_final: 0.7112 (pp20) REVERT: P 89 HIS cc_start: 0.7616 (m-70) cc_final: 0.6694 (m-70) REVERT: Q 239 ASN cc_start: 0.8820 (t0) cc_final: 0.8533 (t0) REVERT: R 124 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7681 (ttm-80) REVERT: S 153 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9007 (tp) REVERT: T 163 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7767 (mmm160) REVERT: U 129 MET cc_start: -0.6293 (ttt) cc_final: -0.6658 (tmm) REVERT: W 110 ASN cc_start: 0.8938 (t0) cc_final: 0.8419 (t0) REVERT: X 60 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: Y 143 ASP cc_start: 0.8336 (t0) cc_final: 0.7976 (m-30) REVERT: Z 62 ASN cc_start: 0.8518 (t0) cc_final: 0.8279 (t0) REVERT: Z 92 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6153 (pp20) REVERT: b 85 ARG cc_start: 0.7751 (mtp85) cc_final: 0.7451 (mtp180) REVERT: c 47 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7968 (ttp80) REVERT: c 294 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: d 166 GLU cc_start: 0.6205 (pm20) cc_final: 0.5931 (pp20) REVERT: d 176 ILE cc_start: 0.8689 (tp) cc_final: 0.8450 (pp) REVERT: d 227 ARG cc_start: 0.8878 (ttp80) cc_final: 0.8502 (ttp80) REVERT: d 237 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7797 (p0) REVERT: d 261 MET cc_start: 0.7372 (mpt) cc_final: 0.6808 (mmm) REVERT: d 264 LYS cc_start: 0.6808 (mtpt) cc_final: 0.6387 (mptt) REVERT: d 277 LEU cc_start: 0.8709 (mm) cc_final: 0.8485 (mp) REVERT: e 73 LEU cc_start: 0.8005 (pp) cc_final: 0.7453 (mp) REVERT: e 260 LEU cc_start: 0.3010 (OUTLIER) cc_final: 0.2569 (tp) REVERT: g 76 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8366 (ptp-170) REVERT: h 118 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.8130 (p-80) REVERT: p 47 LYS cc_start: 0.9335 (mttp) cc_final: 0.9026 (mttm) REVERT: p 152 GLN cc_start: 0.9033 (tp40) cc_final: 0.7893 (tp40) REVERT: p 156 ASP cc_start: 0.8271 (m-30) cc_final: 0.7168 (m-30) REVERT: q 59 LYS cc_start: 0.8889 (mttm) cc_final: 0.8561 (mttm) REVERT: q 125 MET cc_start: 0.8245 (mmm) cc_final: 0.8014 (mmt) REVERT: s 341 MET cc_start: 0.9020 (mtp) cc_final: 0.8672 (mtt) REVERT: s 385 GLN cc_start: 0.7395 (pm20) cc_final: 0.7145 (pm20) REVERT: u 151 CYS cc_start: 0.7000 (m) cc_final: 0.6735 (t) REVERT: u 153 ARG cc_start: 0.8485 (pmm-80) cc_final: 0.8129 (ptp90) REVERT: u 154 ASP cc_start: 0.6988 (p0) cc_final: 0.6321 (p0) REVERT: v 39 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: v 56 GLU cc_start: 0.9189 (tp30) cc_final: 0.8910 (tp30) REVERT: w 120 MET cc_start: 0.7233 (mmp) cc_final: 0.7028 (mmm) REVERT: x 118 VAL cc_start: 0.2058 (OUTLIER) cc_final: 0.1510 (p) REVERT: x 173 LEU cc_start: 0.8489 (mm) cc_final: 0.8272 (tp) outliers start: 165 outliers final: 116 residues processed: 1421 average time/residue: 1.8237 time to fit residues: 3580.1355 Evaluate side-chains 1461 residues out of total 7632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1323 time to evaluate : 7.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 CYS Chi-restraints excluded: chain 4 residue 76 CYS Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 179 VAL Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 279 ILE Chi-restraints excluded: chain 6 residue 320 GLN Chi-restraints excluded: chain 6 residue 355 LYS Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 180 CYS Chi-restraints excluded: chain 7 residue 269 ILE Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 145 GLU Chi-restraints excluded: chain 8 residue 147 LEU Chi-restraints excluded: chain 9 residue 41 ILE Chi-restraints excluded: chain 9 residue 84 THR Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 198 MET Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 150 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 289 SER Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 29 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain T residue 57 ILE Chi-restraints excluded: chain T residue 129 VAL Chi-restraints excluded: chain T residue 163 ARG Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 195 HIS Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 193 THR Chi-restraints excluded: chain V residue 198 VAL Chi-restraints excluded: chain V residue 207 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 85 LYS Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 60 GLU Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 235 ILE Chi-restraints excluded: chain Y residue 138 SER Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain c residue 85 LEU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 240 LEU Chi-restraints excluded: chain c residue 276 CYS Chi-restraints excluded: chain c residue 294 GLU Chi-restraints excluded: chain d residue 156 ASP Chi-restraints excluded: chain d residue 212 ILE Chi-restraints excluded: chain d residue 226 ASP Chi-restraints excluded: chain d residue 237 ASP Chi-restraints excluded: chain d residue 243 LEU Chi-restraints excluded: chain e residue 151 ARG Chi-restraints excluded: chain e residue 152 LYS Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 260 LEU Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain g residue 38 PHE Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain h residue 135 GLN Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain j residue 67 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain j residue 88 LEU Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain r residue 72 ILE Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 188 SER Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 173 SER Chi-restraints excluded: chain s residue 251 VAL Chi-restraints excluded: chain s residue 271 LEU Chi-restraints excluded: chain s residue 360 VAL Chi-restraints excluded: chain s residue 416 ASP Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 132 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 200 ASP Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 26 THR Chi-restraints excluded: chain v residue 39 PHE Chi-restraints excluded: chain w residue 112 SER Chi-restraints excluded: chain x residue 81 CYS Chi-restraints excluded: chain x residue 94 SER Chi-restraints excluded: chain x residue 118 VAL Chi-restraints excluded: chain x residue 142 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 475 optimal weight: 0.8980 chunk 615 optimal weight: 3.9990 chunk 825 optimal weight: 2.9990 chunk 237 optimal weight: 8.9990 chunk 714 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 776 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 797 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 285 ASN C 85 HIS C 304 HIS D 235 GLN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN F 228 GLN F 257 GLN ** G 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 ASN L 80 GLN ** T 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 GLN T 133 ASN ** Y 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 147 GLN b 66 ASN c 172 ASN d 211 GLN ** e 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 GLN ** h 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 GLN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN ** u 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 113 GLN x 84 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.111756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.065525 restraints weight = 195546.030| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.85 r_work: 0.2682 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 106223 Z= 0.247 Angle : 0.634 14.822 150405 Z= 0.325 Chirality : 0.040 0.390 17588 Planarity : 0.005 0.117 14010 Dihedral : 20.631 179.384 30990 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.06 % Favored : 96.93 % Rotamer: Outliers : 2.15 % Allowed : 19.52 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.88 (0.09), residues: 8496 helix: 1.42 (0.09), residues: 3046 sheet: -0.03 (0.15), residues: 1106 loop : 0.27 (0.10), residues: 4344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP 6 235 HIS 0.013 0.001 HIS C 85 PHE 0.045 0.001 PHE 1 30 TYR 0.024 0.001 TYR v 31 ARG 0.020 0.001 ARG 1 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 52826.17 seconds wall clock time: 912 minutes 31.94 seconds (54751.94 seconds total)