Starting phenix.real_space_refine on Mon Mar 11 03:10:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmj_3532/03_2024/5mmj_3532.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmj_3532/03_2024/5mmj_3532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmj_3532/03_2024/5mmj_3532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmj_3532/03_2024/5mmj_3532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmj_3532/03_2024/5mmj_3532.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmj_3532/03_2024/5mmj_3532.pdb" } resolution = 3.6 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= 0.001 sd= 0.010 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: 6 Type Number sf(0) Gaussians P 1484 5.49 5 Mg 185 5.21 5 S 80 5.16 5 C 28819 2.51 5 N 10362 2.21 5 O 14385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c GLU 172": "OE1" <-> "OE2" Residue "d GLU 62": "OE1" <-> "OE2" Residue "d GLU 195": "OE1" <-> "OE2" Residue "e GLU 196": "OE1" <-> "OE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "h GLU 128": "OE1" <-> "OE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "m GLU 95": "OE1" <-> "OE2" Residue "p TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 42": "OE1" <-> "OE2" Residue "s PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 168": "OE1" <-> "OE2" Residue "u GLU 94": "OE1" <-> "OE2" Residue "v PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 55315 Number of models: 1 Model: "" Number of chains: 31 Chain: "0" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 98 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "8" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 870 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'TRANS': 173} Chain breaks: 2 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 522 Unresolved non-hydrogen dihedrals: 174 Planarities with less than four sites: {'UNK:plan-1': 174} Unresolved non-hydrogen planarities: 174 Chain: "a" Number of atoms: 31868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1484, 31868 Classifications: {'RNA': 1484} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 80, 'rna3p_pur': 734, 'rna3p_pyr': 552} Link IDs: {'rna2p': 198, 'rna3p': 1285} Chain: "b" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1844 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain: "c" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1736 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "d" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1633 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain: "e" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1331 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 181} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "f" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 911 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "g" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1210 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain: "h" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1079 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "i" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1119 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "j" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 805 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "k" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 882 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 959 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 113} Chain: "m" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "n" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 820 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "o" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 635 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "p" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 664 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "q" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 7, 'TRANS': 78} Chain: "r" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 490 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "s" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 853 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 2, 'TRANS': 104} Chain: "u" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 568 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "v" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 613 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 686 Classifications: {'peptide': 82} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 74} Chain: "x" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 309 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 5, 'TRANS': 34} Chain: "y" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 919 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "a" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 182 Unusual residues: {' MG': 182} Classifications: {'undetermined': 182} Link IDs: {None: 181} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.05, per 1000 atoms: 0.40 Number of scatterers: 55315 At special positions: 0 Unit cell: (186.26, 180.7, 243.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 1484 15.00 Mg 185 11.99 O 14385 8.00 N 10362 7.00 C 28819 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: 21.53 Conformation dependent library (CDL) restraints added in 3.2 seconds 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5566 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 27 sheets defined 47.7% alpha, 21.2% beta 452 base pairs and 809 stacking pairs defined. Time for finding SS restraints: 19.33 Creating SS restraints... Processing helix chain '0' and resid 93 through 101 removed outlier: 3.625A pdb=" N LYS 0 100 " --> pdb=" O LYS 0 96 " (cutoff:3.500A) Processing helix chain '8' and resid 1039 through 1043 removed outlier: 3.533A pdb=" N UNK 81042 " --> pdb=" O UNK 81039 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N UNK 81043 " --> pdb=" O UNK 81040 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 1039 through 1043' Processing helix chain '8' and resid 1102 through 1126 Processing helix chain '8' and resid 1134 through 1141 removed outlier: 3.892A pdb=" N UNK 81138 " --> pdb=" O UNK 81134 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N UNK 81141 " --> pdb=" O UNK 81137 " (cutoff:3.500A) Processing helix chain '8' and resid 1221 through 1230 Processing helix chain '8' and resid 1237 through 1245 Processing helix chain '8' and resid 1246 through 1258 Processing helix chain 'b' and resid 9 through 17 removed outlier: 3.505A pdb=" N GLY b 17 " --> pdb=" O MET b 13 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 32 Processing helix chain 'b' and resid 46 through 68 removed outlier: 3.777A pdb=" N ARG b 52 " --> pdb=" O THR b 48 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 92 removed outlier: 3.819A pdb=" N ASP b 82 " --> pdb=" O ASN b 78 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG b 86 " --> pdb=" O ASP b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 128 removed outlier: 3.904A pdb=" N THR b 111 " --> pdb=" O ASN b 107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR b 126 " --> pdb=" O ARG b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 134 through 153 Processing helix chain 'b' and resid 173 through 184 Processing helix chain 'b' and resid 210 through 235 Processing helix chain 'c' and resid 6 through 11 removed outlier: 3.645A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 52 removed outlier: 4.343A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL c 47 " --> pdb=" O ILE c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 103 removed outlier: 3.940A pdb=" N ASN c 98 " --> pdb=" O ASP c 94 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 Processing helix chain 'c' and resid 140 through 155 Processing helix chain 'c' and resid 168 through 171 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.049A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 42 through 59 Processing helix chain 'd' and resid 61 through 75 removed outlier: 3.548A pdb=" N LYS d 67 " --> pdb=" O ARG d 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 78 through 89 Processing helix chain 'd' and resid 90 through 98 Processing helix chain 'd' and resid 103 through 113 Processing helix chain 'd' and resid 141 through 154 Processing helix chain 'd' and resid 180 through 184 removed outlier: 3.753A pdb=" N VAL d 184 " --> pdb=" O SER d 181 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 197 removed outlier: 3.738A pdb=" N VAL d 193 " --> pdb=" O ASN d 189 " (cutoff:3.500A) Processing helix chain 'd' and resid 198 through 200 No H-bonds generated for 'chain 'd' and resid 198 through 200' Processing helix chain 'e' and resid 124 through 136 removed outlier: 3.586A pdb=" N ALA e 128 " --> pdb=" O ASN e 124 " (cutoff:3.500A) Processing helix chain 'e' and resid 146 through 150 Processing helix chain 'e' and resid 196 through 212 Processing helix chain 'e' and resid 250 through 261 Processing helix chain 'e' and resid 274 through 288 Processing helix chain 'e' and resid 291 through 300 Processing helix chain 'e' and resid 302 through 308 removed outlier: 3.634A pdb=" N LEU e 306 " --> pdb=" O PRO e 302 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS e 308 " --> pdb=" O GLU e 304 " (cutoff:3.500A) Processing helix chain 'f' and resid 119 through 137 Processing helix chain 'f' and resid 184 through 195 removed outlier: 4.374A pdb=" N LEU f 188 " --> pdb=" O SER f 184 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU f 189 " --> pdb=" O ILE f 185 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA f 190 " --> pdb=" O SER f 186 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP f 195 " --> pdb=" O ALA f 191 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 30 removed outlier: 3.858A pdb=" N ASN g 24 " --> pdb=" O ASN g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.800A pdb=" N GLN g 41 " --> pdb=" O SER g 37 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.889A pdb=" N ARG g 63 " --> pdb=" O LEU g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 110 Processing helix chain 'g' and resid 115 through 129 Processing helix chain 'g' and resid 132 through 147 removed outlier: 3.611A pdb=" N LYS g 138 " --> pdb=" O ALA g 134 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 152 Processing helix chain 'h' and resid 4 through 19 removed outlier: 3.700A pdb=" N ASP h 8 " --> pdb=" O ASP h 4 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 92 through 96 removed outlier: 3.586A pdb=" N ILE h 96 " --> pdb=" O TYR h 93 " (cutoff:3.500A) Processing helix chain 'h' and resid 99 through 103 Processing helix chain 'h' and resid 116 through 124 Processing helix chain 'i' and resid 66 through 74 Processing helix chain 'i' and resid 112 through 116 Processing helix chain 'i' and resid 119 through 132 Proline residue: i 129 - end of helix removed outlier: 3.656A pdb=" N THR i 132 " --> pdb=" O THR i 128 " (cutoff:3.500A) Processing helix chain 'i' and resid 149 through 169 Processing helix chain 'i' and resid 172 through 180 Processing helix chain 'j' and resid 107 through 125 removed outlier: 3.685A pdb=" N ILE j 111 " --> pdb=" O TRP j 107 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR j 125 " --> pdb=" O ALA j 121 " (cutoff:3.500A) Processing helix chain 'j' and resid 173 through 182 Processing helix chain 'k' and resid 64 through 67 Processing helix chain 'k' and resid 68 through 86 removed outlier: 3.951A pdb=" N THR k 82 " --> pdb=" O ASN k 78 " (cutoff:3.500A) Processing helix chain 'k' and resid 100 through 112 removed outlier: 3.805A pdb=" N ALA k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU k 106 " --> pdb=" O ARG k 102 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG k 107 " --> pdb=" O ASP k 103 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA k 108 " --> pdb=" O ALA k 104 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 8 Processing helix chain 'l' and resid 21 through 25 Processing helix chain 'l' and resid 113 through 118 removed outlier: 3.911A pdb=" N TYR l 117 " --> pdb=" O GLY l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 54 removed outlier: 3.532A pdb=" N VAL m 53 " --> pdb=" O VAL m 50 " (cutoff:3.500A) Processing helix chain 'm' and resid 60 through 66 Processing helix chain 'm' and resid 73 through 83 Processing helix chain 'm' and resid 94 through 106 Processing helix chain 'm' and resid 110 through 129 Processing helix chain 'm' and resid 130 through 139 Processing helix chain 'm' and resid 151 through 156 Processing helix chain 'n' and resid 3 through 34 removed outlier: 3.680A pdb=" N ILE n 7 " --> pdb=" O ARG n 3 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU n 22 " --> pdb=" O GLN n 18 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ILE n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 36 through 48 removed outlier: 4.423A pdb=" N GLU n 42 " --> pdb=" O SER n 38 " (cutoff:3.500A) Processing helix chain 'n' and resid 51 through 59 Proline residue: n 56 - end of helix Processing helix chain 'n' and resid 79 through 89 Processing helix chain 'o' and resid 21 through 43 removed outlier: 4.069A pdb=" N LEU o 38 " --> pdb=" O ARG o 34 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N HIS o 39 " --> pdb=" O ARG o 35 " (cutoff:3.500A) Processing helix chain 'o' and resid 46 through 71 removed outlier: 3.561A pdb=" N GLN o 50 " --> pdb=" O ASP o 46 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY o 52 " --> pdb=" O SER o 48 " (cutoff:3.500A) Processing helix chain 'o' and resid 71 through 82 Processing helix chain 'p' and resid 49 through 59 removed outlier: 3.529A pdb=" N ILE p 53 " --> pdb=" O ASN p 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS p 59 " --> pdb=" O ASP p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 64 through 74 Processing helix chain 'p' and resid 75 through 80 removed outlier: 4.191A pdb=" N GLU p 79 " --> pdb=" O GLU p 75 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE p 80 " --> pdb=" O VAL p 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 75 through 80' Processing helix chain 'q' and resid 102 through 105 removed outlier: 4.527A pdb=" N GLN q 105 " --> pdb=" O PRO q 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 102 through 105' Processing helix chain 'r' and resid 32 through 39 removed outlier: 3.632A pdb=" N PHE r 39 " --> pdb=" O LEU r 35 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 53 Processing helix chain 'r' and resid 55 through 72 Processing helix chain 's' and resid 12 through 25 Processing helix chain 's' and resid 63 through 67 removed outlier: 3.777A pdb=" N VAL s 67 " --> pdb=" O ASP s 64 " (cutoff:3.500A) Processing helix chain 's' and resid 71 through 75 removed outlier: 3.634A pdb=" N ALA s 75 " --> pdb=" O GLY s 72 " (cutoff:3.500A) Processing helix chain 't' and resid 76 through 117 removed outlier: 3.552A pdb=" N ALA t 80 " --> pdb=" O ALA t 76 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL t 100 " --> pdb=" O ARG t 96 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS t 117 " --> pdb=" O ALA t 113 " (cutoff:3.500A) Processing helix chain 't' and resid 120 through 145 removed outlier: 4.730A pdb=" N VAL t 126 " --> pdb=" O THR t 122 " (cutoff:3.500A) Proline residue: t 127 - end of helix Processing helix chain 't' and resid 149 through 172 removed outlier: 3.778A pdb=" N ARG t 155 " --> pdb=" O ASN t 151 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU t 168 " --> pdb=" O LYS t 164 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE t 169 " --> pdb=" O LYS t 165 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS t 170 " --> pdb=" O VAL t 166 " (cutoff:3.500A) Processing helix chain 'u' and resid 95 through 111 removed outlier: 3.564A pdb=" N LEU u 99 " --> pdb=" O ASN u 95 " (cutoff:3.500A) Processing helix chain 'u' and resid 111 through 119 Processing helix chain 'u' and resid 124 through 146 removed outlier: 3.626A pdb=" N GLY u 146 " --> pdb=" O ARG u 142 " (cutoff:3.500A) Processing helix chain 'v' and resid 196 through 204 Processing helix chain 'v' and resid 234 through 245 removed outlier: 3.709A pdb=" N ALA v 244 " --> pdb=" O ALA v 240 " (cutoff:3.500A) Processing helix chain 'w' and resid 136 through 148 removed outlier: 3.560A pdb=" N LYS w 148 " --> pdb=" O LEU w 144 " (cutoff:3.500A) Processing helix chain 'w' and resid 152 through 173 removed outlier: 3.578A pdb=" N LEU w 159 " --> pdb=" O GLN w 155 " (cutoff:3.500A) Processing helix chain 'x' and resid 61 through 69 Processing helix chain 'y' and resid 87 through 106 removed outlier: 3.605A pdb=" N SER y 101 " --> pdb=" O LYS y 97 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS y 104 " --> pdb=" O LYS y 100 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N HIS y 105 " --> pdb=" O SER y 101 " (cutoff:3.500A) Processing helix chain 'y' and resid 152 through 177 removed outlier: 3.579A pdb=" N ARG y 166 " --> pdb=" O SER y 162 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP y 177 " --> pdb=" O ASP y 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '8' and resid 1002 through 1010 removed outlier: 6.898A pdb=" N UNK 81016 " --> pdb=" O UNK 81008 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N UNK 81010 " --> pdb=" O UNK 81014 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N UNK 81014 " --> pdb=" O UNK 81010 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N UNK 81064 " --> pdb=" O UNK 81024 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N UNK 81066 " --> pdb=" O UNK 81026 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N UNK 81028 " --> pdb=" O UNK 81066 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N UNK 81063 " --> pdb=" O UNK 81057 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N UNK 81057 " --> pdb=" O UNK 81063 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N UNK 81065 " --> pdb=" O UNK 81055 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '8' and resid 1205 through 1207 Processing sheet with id=AA3, first strand: chain 'b' and resid 94 through 96 removed outlier: 6.314A pdb=" N PHE b 71 " --> pdb=" O HIS b 94 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL b 96 " --> pdb=" O PHE b 71 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE b 73 " --> pdb=" O VAL b 96 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU b 72 " --> pdb=" O ILE b 166 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR b 187 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE b 204 " --> pdb=" O THR b 187 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS b 189 " --> pdb=" O ILE b 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 60 through 67 removed outlier: 6.343A pdb=" N ILE c 72 " --> pdb=" O ASN c 111 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ALA c 113 " --> pdb=" O ILE c 72 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL c 74 " --> pdb=" O ALA c 113 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR c 115 " --> pdb=" O VAL c 74 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE c 76 " --> pdb=" O THR c 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 175 through 182 Processing sheet with id=AA6, first strand: chain 'd' and resid 116 through 118 Processing sheet with id=AA7, first strand: chain 'e' and resid 153 through 165 removed outlier: 5.338A pdb=" N GLU e 154 " --> pdb=" O GLY e 181 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLY e 181 " --> pdb=" O GLU e 154 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL e 156 " --> pdb=" O VAL e 179 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL e 179 " --> pdb=" O VAL e 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 227 through 231 Processing sheet with id=AA9, first strand: chain 'f' and resid 140 through 147 removed outlier: 5.625A pdb=" N TYR f 141 " --> pdb=" O PHE f 179 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE f 179 " --> pdb=" O TYR f 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 156 through 159 removed outlier: 3.692A pdb=" N ILE f 156 " --> pdb=" O TYR f 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'g' and resid 76 through 80 Processing sheet with id=AB3, first strand: chain 'h' and resid 23 through 27 removed outlier: 3.623A pdb=" N ASN h 47 " --> pdb=" O THR h 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 79 through 81 Processing sheet with id=AB5, first strand: chain 'h' and resid 79 through 81 removed outlier: 6.943A pdb=" N ILE h 107 " --> pdb=" O LEU h 130 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TYR h 132 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE h 105 " --> pdb=" O TYR h 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'i' and resid 84 through 89 Processing sheet with id=AB7, first strand: chain 'j' and resid 129 through 145 removed outlier: 5.424A pdb=" N ASP j 168 " --> pdb=" O MET j 130 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU j 166 " --> pdb=" O PRO j 132 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLN j 164 " --> pdb=" O PRO j 134 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR j 162 " --> pdb=" O PRO j 136 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS j 138 " --> pdb=" O ILE j 160 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE j 160 " --> pdb=" O LYS j 138 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG j 140 " --> pdb=" O PHE j 158 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE j 158 " --> pdb=" O ARG j 140 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR j 142 " --> pdb=" O PHE j 156 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE j 156 " --> pdb=" O TYR j 142 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'j' and resid 129 through 145 removed outlier: 5.424A pdb=" N ASP j 168 " --> pdb=" O MET j 130 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU j 166 " --> pdb=" O PRO j 132 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLN j 164 " --> pdb=" O PRO j 134 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR j 162 " --> pdb=" O PRO j 136 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS j 138 " --> pdb=" O ILE j 160 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE j 160 " --> pdb=" O LYS j 138 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG j 140 " --> pdb=" O PHE j 158 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE j 158 " --> pdb=" O ARG j 140 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR j 142 " --> pdb=" O PHE j 156 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE j 156 " --> pdb=" O TYR j 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'k' and resid 49 through 55 removed outlier: 5.772A pdb=" N VAL k 50 " --> pdb=" O ASP k 45 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP k 45 " --> pdb=" O VAL k 50 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA k 91 " --> pdb=" O PHE k 118 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ARG k 120 " --> pdb=" O ALA k 91 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL k 93 " --> pdb=" O ARG k 120 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL u 86 " --> pdb=" O ASP k 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'l' and resid 29 through 40 removed outlier: 6.549A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL l 37 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL l 52 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR l 39 " --> pdb=" O ARG l 50 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG l 50 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR l 95 " --> pdb=" O THR l 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'p' and resid 46 through 47 removed outlier: 5.684A pdb=" N LYS p 35 " --> pdb=" O ALA p 21 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA p 21 " --> pdb=" O LYS p 35 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL p 2 " --> pdb=" O GLN p 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'q' and resid 61 through 67 removed outlier: 7.003A pdb=" N GLN q 62 " --> pdb=" O VAL q 79 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL q 79 " --> pdb=" O GLN q 62 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN q 75 " --> pdb=" O ILE q 66 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE q 126 " --> pdb=" O GLN q 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 's' and resid 31 through 33 removed outlier: 5.984A pdb=" N ILE s 31 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N HIS s 52 " --> pdb=" O ILE s 31 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N THR s 33 " --> pdb=" O HIS s 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'v' and resid 210 through 217 removed outlier: 4.715A pdb=" N PHE v 227 " --> pdb=" O GLN v 216 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'v' and resid 249 through 250 Processing sheet with id=AC7, first strand: chain 'w' and resid 98 through 105 Processing sheet with id=AC8, first strand: chain 'w' and resid 98 through 105 Processing sheet with id=AC9, first strand: chain 'y' and resid 76 through 81 removed outlier: 3.754A pdb=" N GLU y 111 " --> pdb=" O PHE y 137 " (cutoff:3.500A) 1190 hydrogen bonds defined for protein. 3417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1123 hydrogen bonds 1874 hydrogen bond angles 0 basepair planarities 452 basepair parallelities 809 stacking parallelities Total time for adding SS restraints: 41.98 Time building geometry restraints manager: 23.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7934 1.33 - 1.46: 25174 1.46 - 1.59: 23253 1.59 - 1.72: 2812 1.72 - 1.85: 127 Bond restraints: 59300 Sorted by residual: bond pdb=" CA ALA x 88 " pdb=" CB ALA x 88 " ideal model delta sigma weight residual 1.534 1.643 -0.109 1.18e-02 7.18e+03 8.46e+01 bond pdb=" CA ALA x 88 " pdb=" C ALA x 88 " ideal model delta sigma weight residual 1.521 1.614 -0.092 1.17e-02 7.31e+03 6.23e+01 bond pdb=" CA ILE b 35 " pdb=" CB ILE b 35 " ideal model delta sigma weight residual 1.540 1.607 -0.067 1.36e-02 5.41e+03 2.43e+01 bond pdb=" N ALA x 88 " pdb=" CA ALA x 88 " ideal model delta sigma weight residual 1.462 1.504 -0.042 9.50e-03 1.11e+04 1.99e+01 bond pdb=" CA VAL i 168 " pdb=" CB VAL i 168 " ideal model delta sigma weight residual 1.539 1.591 -0.052 1.20e-02 6.94e+03 1.85e+01 ... (remaining 59295 not shown) Histogram of bond angle deviations from ideal: 96.96 - 105.18: 7398 105.18 - 113.41: 36136 113.41 - 121.63: 29244 121.63 - 129.85: 13619 129.85 - 138.08: 1030 Bond angle restraints: 87427 Sorted by residual: angle pdb=" C GLY k 97 " pdb=" N PRO k 98 " pdb=" CA PRO k 98 " ideal model delta sigma weight residual 119.87 132.84 -12.97 1.04e+00 9.25e-01 1.56e+02 angle pdb=" C LYS c 119 " pdb=" N PRO c 120 " pdb=" CA PRO c 120 " ideal model delta sigma weight residual 119.56 129.50 -9.94 1.01e+00 9.80e-01 9.68e+01 angle pdb=" C ALA x 88 " pdb=" N PRO x 89 " pdb=" CA PRO x 89 " ideal model delta sigma weight residual 120.13 109.17 10.96 1.13e+00 7.83e-01 9.40e+01 angle pdb=" N GLY s 82 " pdb=" CA GLY s 82 " pdb=" C GLY s 82 " ideal model delta sigma weight residual 112.65 124.38 -11.73 1.30e+00 5.92e-01 8.14e+01 angle pdb=" N ASN m 52 " pdb=" CA ASN m 52 " pdb=" C ASN m 52 " ideal model delta sigma weight residual 111.30 121.78 -10.48 1.36e+00 5.41e-01 5.94e+01 ... (remaining 87422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 33518 35.91 - 71.83: 3909 71.83 - 107.74: 451 107.74 - 143.66: 16 143.66 - 179.57: 5 Dihedral angle restraints: 37899 sinusoidal: 29303 harmonic: 8596 Sorted by residual: dihedral pdb=" CA TRP t 173 " pdb=" C TRP t 173 " pdb=" N TYR t 174 " pdb=" CA TYR t 174 " ideal model delta harmonic sigma weight residual 180.00 135.36 44.64 0 5.00e+00 4.00e-02 7.97e+01 dihedral pdb=" O4' C a 702 " pdb=" C1' C a 702 " pdb=" N1 C a 702 " pdb=" C2 C a 702 " ideal model delta sinusoidal sigma weight residual 200.00 56.99 143.01 1 1.50e+01 4.44e-03 7.67e+01 dihedral pdb=" O4' U a 336 " pdb=" C1' U a 336 " pdb=" N1 U a 336 " pdb=" C2 U a 336 " ideal model delta sinusoidal sigma weight residual 200.00 58.72 141.28 1 1.50e+01 4.44e-03 7.60e+01 ... (remaining 37896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 10473 0.096 - 0.192: 483 0.192 - 0.289: 27 0.289 - 0.385: 5 0.385 - 0.481: 1 Chirality restraints: 10989 Sorted by residual: chirality pdb=" CB ILE i 107 " pdb=" CA ILE i 107 " pdb=" CG1 ILE i 107 " pdb=" CG2 ILE i 107 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" CA ILE b 35 " pdb=" N ILE b 35 " pdb=" C ILE b 35 " pdb=" CB ILE b 35 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CB ILE s 41 " pdb=" CA ILE s 41 " pdb=" CG1 ILE s 41 " pdb=" CG2 ILE s 41 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 10986 not shown) Planarity restraints: 5570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA g 152 " -0.026 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C ALA g 152 " 0.088 2.00e-02 2.50e+03 pdb=" O ALA g 152 " -0.034 2.00e-02 2.50e+03 pdb=" N HIS g 153 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G a1006 " 0.024 2.00e-02 2.50e+03 2.54e-02 1.94e+01 pdb=" N9 G a1006 " -0.023 2.00e-02 2.50e+03 pdb=" C8 G a1006 " 0.017 2.00e-02 2.50e+03 pdb=" N7 G a1006 " 0.013 2.00e-02 2.50e+03 pdb=" C5 G a1006 " -0.046 2.00e-02 2.50e+03 pdb=" C6 G a1006 " -0.043 2.00e-02 2.50e+03 pdb=" O6 G a1006 " 0.034 2.00e-02 2.50e+03 pdb=" N1 G a1006 " 0.031 2.00e-02 2.50e+03 pdb=" C2 G a1006 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G a1006 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G a1006 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G a1006 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA i 174 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO i 175 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO i 175 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO i 175 " 0.047 5.00e-02 4.00e+02 ... (remaining 5567 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 199 2.40 - 3.02: 28994 3.02 - 3.65: 93384 3.65 - 4.27: 152294 4.27 - 4.90: 210564 Nonbonded interactions: 485435 Sorted by model distance: nonbonded pdb=" OP1 A a 707 " pdb="MG MG a1544 " model vdw 1.774 2.170 nonbonded pdb=" O6 G a1057 " pdb="MG MG a1637 " model vdw 1.776 2.170 nonbonded pdb=" OP2 A a1059 " pdb="MG MG a1526 " model vdw 1.816 2.170 nonbonded pdb=" OP1 G a1172 " pdb="MG MG a1539 " model vdw 1.837 2.170 nonbonded pdb=" OP2 U a1032 " pdb="MG MG a1513 " model vdw 1.840 2.170 ... (remaining 485430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.030 Extract box with map and model: 8.490 Check model and map are aligned: 0.650 Set scattering table: 0.390 Process input model: 146.530 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 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 : 0.008 0.109 59300 Z= 0.510 Angle : 1.155 14.342 87427 Z= 0.685 Chirality : 0.047 0.481 10989 Planarity : 0.005 0.078 5570 Dihedral : 23.407 179.571 32333 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.90 % Favored : 94.85 % Rotamer: Outliers : 7.28 % Allowed : 11.72 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.46 (0.13), residues: 2756 helix: -3.09 (0.10), residues: 1140 sheet: -0.66 (0.21), residues: 470 loop : -1.95 (0.15), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP b 6 HIS 0.012 0.002 HIS y 105 PHE 0.031 0.003 PHE x 91 TYR 0.027 0.003 TYR c 195 ARG 0.010 0.001 ARG n 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 997 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 7 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.6959 (t0) REVERT: b 28 ASN cc_start: 0.9284 (t0) cc_final: 0.8324 (t0) REVERT: b 70 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7430 (mm-40) REVERT: b 74 VAL cc_start: 0.9244 (t) cc_final: 0.8967 (p) REVERT: b 82 ASP cc_start: 0.9147 (m-30) cc_final: 0.8926 (m-30) REVERT: b 99 LYS cc_start: 0.7657 (tttt) cc_final: 0.7281 (tppt) REVERT: b 108 TRP cc_start: 0.8112 (t-100) cc_final: 0.7771 (t-100) REVERT: b 110 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8823 (m) REVERT: b 116 HIS cc_start: 0.8680 (m170) cc_final: 0.8334 (m-70) REVERT: b 118 PHE cc_start: 0.8892 (t80) cc_final: 0.8690 (t80) REVERT: b 119 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.6734 (tpt170) REVERT: b 158 MET cc_start: 0.8592 (ttp) cc_final: 0.8137 (tpp) REVERT: c 4 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8188 (mptt) REVERT: c 72 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9128 (mm) REVERT: c 209 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9249 (mt) REVERT: d 8 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8669 (ptt180) REVERT: d 11 LYS cc_start: 0.9491 (mmtt) cc_final: 0.9241 (mmtm) REVERT: d 23 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7739 (p0) REVERT: d 51 LYS cc_start: 0.9282 (ttpp) cc_final: 0.8806 (tttp) REVERT: d 58 TYR cc_start: 0.9078 (m-80) cc_final: 0.8739 (m-80) REVERT: d 62 GLU cc_start: 0.8680 (tp30) cc_final: 0.8219 (tp30) REVERT: d 68 TYR cc_start: 0.9241 (m-80) cc_final: 0.8856 (m-80) REVERT: d 159 GLU cc_start: 0.8656 (tp30) cc_final: 0.8451 (pp20) REVERT: e 155 ASN cc_start: 0.8884 (t0) cc_final: 0.8573 (t0) REVERT: e 163 THR cc_start: 0.8954 (m) cc_final: 0.8608 (m) REVERT: e 172 MET cc_start: 0.8925 (mmt) cc_final: 0.8546 (mmt) REVERT: e 211 ASN cc_start: 0.9007 (t0) cc_final: 0.8588 (t0) REVERT: e 213 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8863 (pp) REVERT: e 237 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8678 (tmm) REVERT: e 259 MET cc_start: 0.9225 (tpp) cc_final: 0.8974 (mmt) REVERT: e 263 GLU cc_start: 0.8706 (tp30) cc_final: 0.8400 (tp30) REVERT: e 289 MET cc_start: 0.9174 (tpp) cc_final: 0.8946 (mmt) REVERT: e 294 ASP cc_start: 0.8949 (m-30) cc_final: 0.8523 (m-30) REVERT: f 107 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: f 111 MET cc_start: 0.9078 (tpp) cc_final: 0.8438 (tpp) REVERT: f 124 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8728 (pp) REVERT: f 145 PHE cc_start: 0.8565 (t80) cc_final: 0.8354 (t80) REVERT: f 166 ASN cc_start: 0.7525 (m-40) cc_final: 0.7153 (m-40) REVERT: f 167 ASN cc_start: 0.8993 (t0) cc_final: 0.8739 (m-40) REVERT: f 170 ASP cc_start: 0.8753 (m-30) cc_final: 0.8539 (t0) REVERT: f 177 THR cc_start: 0.8784 (m) cc_final: 0.8064 (p) REVERT: f 178 TYR cc_start: 0.8526 (p90) cc_final: 0.7347 (p90) REVERT: f 194 THR cc_start: 0.9451 (m) cc_final: 0.9241 (t) REVERT: f 202 SER cc_start: 0.8401 (p) cc_final: 0.8110 (p) REVERT: f 208 LYS cc_start: 0.8283 (pttt) cc_final: 0.8045 (mmmt) REVERT: g 10 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.6808 (mtmm) REVERT: g 18 TYR cc_start: 0.9130 (m-80) cc_final: 0.8862 (m-80) REVERT: g 24 ASN cc_start: 0.8821 (t0) cc_final: 0.8573 (t0) REVERT: g 44 TYR cc_start: 0.8241 (m-10) cc_final: 0.7792 (m-10) REVERT: g 50 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8975 (mm) REVERT: g 76 LYS cc_start: 0.8489 (tptt) cc_final: 0.8244 (mmtm) REVERT: g 126 ASP cc_start: 0.8897 (m-30) cc_final: 0.8408 (m-30) REVERT: g 151 PHE cc_start: 0.8827 (m-80) cc_final: 0.8581 (m-80) REVERT: h 19 ASN cc_start: 0.8890 (t0) cc_final: 0.8545 (t0) REVERT: h 77 PHE cc_start: 0.8977 (t80) cc_final: 0.8582 (t80) REVERT: h 80 LYS cc_start: 0.9265 (tttt) cc_final: 0.9061 (tttp) REVERT: i 132 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.8045 (p) REVERT: i 150 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9386 (mp) REVERT: j 159 GLU cc_start: 0.8628 (pt0) cc_final: 0.8377 (pt0) REVERT: j 183 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7459 (mt) REVERT: k 33 GLN cc_start: 0.9084 (tt0) cc_final: 0.8844 (tt0) REVERT: k 78 ASN cc_start: 0.8986 (t0) cc_final: 0.8702 (t0) REVERT: k 82 THR cc_start: 0.9438 (m) cc_final: 0.9234 (p) REVERT: k 112 SER cc_start: 0.8794 (m) cc_final: 0.8577 (p) REVERT: k 114 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8283 (mm) REVERT: k 116 LEU cc_start: 0.8759 (mt) cc_final: 0.8559 (mm) REVERT: l 19 THR cc_start: 0.9121 (p) cc_final: 0.8865 (m) REVERT: l 29 GLN cc_start: 0.9393 (mp10) cc_final: 0.9135 (mp10) REVERT: l 35 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8491 (t) REVERT: l 49 LEU cc_start: 0.9283 (tp) cc_final: 0.8777 (tp) REVERT: l 101 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8618 (t) REVERT: l 103 ASP cc_start: 0.8187 (m-30) cc_final: 0.7899 (m-30) REVERT: m 50 VAL cc_start: 0.8993 (t) cc_final: 0.8731 (t) REVERT: m 104 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7859 (mt-10) REVERT: m 137 ILE cc_start: 0.9301 (mt) cc_final: 0.8517 (mt) REVERT: n 8 GLN cc_start: 0.9380 (mm-40) cc_final: 0.9178 (mm-40) REVERT: n 79 SER cc_start: 0.9386 (t) cc_final: 0.9168 (m) REVERT: o 22 VAL cc_start: 0.8839 (t) cc_final: 0.8611 (p) REVERT: o 23 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8441 (mp0) REVERT: o 27 PHE cc_start: 0.9278 (t80) cc_final: 0.8945 (t80) REVERT: o 34 ARG cc_start: 0.8897 (mtt180) cc_final: 0.8303 (mtp-110) REVERT: o 78 LEU cc_start: 0.9242 (tp) cc_final: 0.8854 (mp) REVERT: p 28 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8398 (ttp-170) REVERT: p 34 GLN cc_start: 0.9142 (tp40) cc_final: 0.8862 (tp-100) REVERT: q 67 CYS cc_start: 0.8407 (t) cc_final: 0.8071 (t) REVERT: q 79 VAL cc_start: 0.9345 (t) cc_final: 0.9111 (t) REVERT: r 38 ARG cc_start: 0.8699 (mtm180) cc_final: 0.8310 (mtm-85) REVERT: s 22 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8780 (mp) REVERT: s 62 ILE cc_start: 0.9138 (mm) cc_final: 0.8777 (tp) REVERT: s 69 HIS cc_start: 0.8391 (m170) cc_final: 0.7992 (m-70) REVERT: s 71 LEU cc_start: 0.9696 (mt) cc_final: 0.9348 (mp) REVERT: t 91 LEU cc_start: 0.9649 (mt) cc_final: 0.9415 (mt) REVERT: t 100 VAL cc_start: 0.9469 (t) cc_final: 0.9188 (t) REVERT: t 101 LYS cc_start: 0.9149 (tptt) cc_final: 0.8809 (tttp) REVERT: t 130 ASN cc_start: 0.9077 (m-40) cc_final: 0.8540 (m-40) REVERT: t 145 LYS cc_start: 0.9213 (mmtt) cc_final: 0.8860 (mttt) REVERT: u 85 ASN cc_start: 0.8176 (m-40) cc_final: 0.7791 (m110) REVERT: u 101 ASN cc_start: 0.9004 (m-40) cc_final: 0.8589 (m110) REVERT: u 103 PHE cc_start: 0.9223 (t80) cc_final: 0.9004 (t80) REVERT: u 120 ARG cc_start: 0.8948 (tpt170) cc_final: 0.8610 (ttt180) REVERT: u 129 LYS cc_start: 0.9246 (mttt) cc_final: 0.8982 (mmmm) REVERT: u 131 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8618 (ttp-110) REVERT: u 132 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8463 (mmmm) REVERT: w 145 LEU cc_start: -0.1012 (mt) cc_final: -0.1233 (mm) REVERT: y 76 LYS cc_start: 0.8113 (mttt) cc_final: 0.7600 (mtpt) REVERT: y 78 ILE cc_start: 0.8965 (mm) cc_final: 0.8449 (mp) REVERT: y 89 ASN cc_start: 0.8461 (m-40) cc_final: 0.8257 (p0) REVERT: y 132 CYS cc_start: 0.8798 (m) cc_final: 0.8234 (m) REVERT: y 149 ASP cc_start: 0.8561 (m-30) cc_final: 0.8360 (m-30) REVERT: y 154 TYR cc_start: 0.8492 (m-80) cc_final: 0.7947 (m-10) REVERT: y 180 ARG cc_start: 0.6568 (mtt180) cc_final: 0.6272 (mtt180) outliers start: 174 outliers final: 58 residues processed: 1112 average time/residue: 0.6475 time to fit residues: 1115.4073 Evaluate side-chains 748 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 667 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 7 ASN Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 79 LYS Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 194 ASN Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain c residue 4 LYS Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 103 LEU Chi-restraints excluded: chain c residue 196 CYS Chi-restraints excluded: chain c residue 202 THR Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain c residue 209 ILE Chi-restraints excluded: chain d residue 8 ARG Chi-restraints excluded: chain d residue 9 PHE Chi-restraints excluded: chain d residue 12 ILE Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 109 GLN Chi-restraints excluded: chain d residue 134 ASP Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain e residue 162 VAL Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain e residue 201 VAL Chi-restraints excluded: chain e residue 213 ILE Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 237 MET Chi-restraints excluded: chain e residue 266 LEU Chi-restraints excluded: chain f residue 107 GLN Chi-restraints excluded: chain f residue 124 LEU Chi-restraints excluded: chain g residue 10 LYS Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 25 MET Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 72 ASP Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 76 THR Chi-restraints excluded: chain i residue 132 THR Chi-restraints excluded: chain i residue 150 LEU Chi-restraints excluded: chain i residue 206 SER Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 115 CYS Chi-restraints excluded: chain j residue 143 CYS Chi-restraints excluded: chain j residue 183 LEU Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 114 ILE Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain l residue 101 THR Chi-restraints excluded: chain m residue 69 HIS Chi-restraints excluded: chain m residue 118 ASN Chi-restraints excluded: chain m residue 142 CYS Chi-restraints excluded: chain m residue 151 CYS Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 49 SER Chi-restraints excluded: chain n residue 54 SER Chi-restraints excluded: chain n residue 63 CYS Chi-restraints excluded: chain n residue 90 CYS Chi-restraints excluded: chain n residue 92 LEU Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain p residue 33 LEU Chi-restraints excluded: chain p residue 49 ASN Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain q residue 112 VAL Chi-restraints excluded: chain q residue 142 LYS Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 32 ASN Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 53 ASN Chi-restraints excluded: chain t residue 143 VAL Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain u residue 124 ASN Chi-restraints excluded: chain u residue 131 ARG Chi-restraints excluded: chain y residue 122 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 367 optimal weight: 4.9990 chunk 329 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 340 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 395 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 78 ASN b 94 HIS ** b 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 ASN ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 GLN e 211 ASN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 277 ASN ** f 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 ASN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 ASN h 30 ASN h 75 ASN i 81 GLN ** i 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 153 GLN j 149 HIS j 151 HIS ** k 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 10 ASN m 138 GLN n 72 ASN n 81 HIS o 43 HIS ** p 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 70 ASN ** q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 98 GLN s 47 HIS u 133 HIS u 140 ASN ** v 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 162 GLN w 168 ASN y 89 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 59300 Z= 0.328 Angle : 0.708 8.995 87427 Z= 0.366 Chirality : 0.039 0.391 10989 Planarity : 0.006 0.065 5570 Dihedral : 23.814 178.590 26711 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.45 % Favored : 96.37 % Rotamer: Outliers : 6.65 % Allowed : 21.76 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.14), residues: 2756 helix: -0.67 (0.14), residues: 1145 sheet: -0.34 (0.22), residues: 482 loop : -1.70 (0.16), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP e 307 HIS 0.007 0.001 HIS n 21 PHE 0.021 0.002 PHE 0 97 TYR 0.027 0.002 TYR b 232 ARG 0.013 0.001 ARG k 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 740 time to evaluate : 3.412 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: b 104 MET cc_start: 0.9295 (mmm) cc_final: 0.9092 (mmm) REVERT: b 107 ASN cc_start: 0.8497 (t0) cc_final: 0.8294 (t0) REVERT: b 112 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8098 (pt0) REVERT: b 116 HIS cc_start: 0.8445 (m170) cc_final: 0.8208 (m-70) REVERT: b 119 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.6717 (tpt170) REVERT: b 163 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7003 (t70) REVERT: b 178 ARG cc_start: 0.8783 (mmp-170) cc_final: 0.8343 (mtm110) REVERT: b 185 ILE cc_start: 0.8458 (mt) cc_final: 0.8232 (mm) REVERT: c 184 VAL cc_start: 0.9625 (t) cc_final: 0.9397 (p) REVERT: d 58 TYR cc_start: 0.8659 (m-80) cc_final: 0.8306 (m-80) REVERT: d 88 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8717 (mm-30) REVERT: d 123 VAL cc_start: 0.9543 (t) cc_final: 0.9225 (m) REVERT: d 124 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7769 (t0) REVERT: d 175 VAL cc_start: 0.9468 (t) cc_final: 0.9264 (p) REVERT: e 211 ASN cc_start: 0.8980 (t0) cc_final: 0.8419 (t0) REVERT: e 263 GLU cc_start: 0.8338 (tp30) cc_final: 0.8091 (tp30) REVERT: e 292 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8707 (t80) REVERT: f 107 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8454 (tm-30) REVERT: f 111 MET cc_start: 0.8982 (tpp) cc_final: 0.8422 (tpp) REVERT: f 120 GLU cc_start: 0.8912 (tp30) cc_final: 0.8034 (tp30) REVERT: f 123 ARG cc_start: 0.8711 (ttt-90) cc_final: 0.8222 (ttp80) REVERT: f 124 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8533 (pp) REVERT: f 128 GLN cc_start: 0.9216 (tm-30) cc_final: 0.8955 (pp30) REVERT: f 159 LYS cc_start: 0.9001 (mmmm) cc_final: 0.8800 (mmmt) REVERT: f 170 ASP cc_start: 0.8777 (m-30) cc_final: 0.8336 (t0) REVERT: f 178 TYR cc_start: 0.8329 (p90) cc_final: 0.7601 (p90) REVERT: f 181 LYS cc_start: 0.9017 (ttmm) cc_final: 0.7943 (ttmm) REVERT: g 10 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.6913 (mtmm) REVERT: g 18 TYR cc_start: 0.9122 (m-80) cc_final: 0.8809 (m-80) REVERT: g 24 ASN cc_start: 0.8803 (t0) cc_final: 0.8218 (t0) REVERT: g 59 LEU cc_start: 0.8592 (mt) cc_final: 0.8332 (mt) REVERT: g 76 LYS cc_start: 0.8492 (tptt) cc_final: 0.8228 (mmtm) REVERT: g 126 ASP cc_start: 0.8904 (m-30) cc_final: 0.8576 (m-30) REVERT: g 151 PHE cc_start: 0.8853 (m-80) cc_final: 0.8197 (m-80) REVERT: h 4 ASP cc_start: 0.7678 (t0) cc_final: 0.7367 (t0) REVERT: h 77 PHE cc_start: 0.8881 (t80) cc_final: 0.8622 (t80) REVERT: i 124 GLN cc_start: 0.9096 (pt0) cc_final: 0.8817 (pt0) REVERT: j 112 GLU cc_start: 0.8905 (pt0) cc_final: 0.8590 (mt-10) REVERT: j 123 ARG cc_start: 0.8843 (tpm170) cc_final: 0.8547 (tpm170) REVERT: j 125 THR cc_start: 0.7184 (OUTLIER) cc_final: 0.6853 (p) REVERT: j 159 GLU cc_start: 0.8648 (pt0) cc_final: 0.8391 (pt0) REVERT: j 194 LYS cc_start: 0.8334 (mmmt) cc_final: 0.8100 (mmmm) REVERT: k 33 GLN cc_start: 0.8996 (tt0) cc_final: 0.8314 (tm-30) REVERT: k 78 ASN cc_start: 0.8834 (t0) cc_final: 0.8475 (t0) REVERT: k 83 VAL cc_start: 0.8442 (m) cc_final: 0.8220 (m) REVERT: k 88 MET cc_start: 0.7755 (ptp) cc_final: 0.7541 (ttm) REVERT: k 112 SER cc_start: 0.8635 (m) cc_final: 0.8414 (p) REVERT: k 116 LEU cc_start: 0.8578 (mt) cc_final: 0.8169 (mm) REVERT: l 16 ARG cc_start: 0.8683 (mmm160) cc_final: 0.8454 (mmm160) REVERT: l 29 GLN cc_start: 0.9188 (mp10) cc_final: 0.8972 (mp10) REVERT: l 49 LEU cc_start: 0.9207 (tp) cc_final: 0.8779 (tp) REVERT: m 84 THR cc_start: 0.9184 (m) cc_final: 0.8765 (m) REVERT: m 86 GLU cc_start: 0.7550 (tp30) cc_final: 0.7345 (tp30) REVERT: m 99 LEU cc_start: 0.8918 (mt) cc_final: 0.8663 (mt) REVERT: o 34 ARG cc_start: 0.8871 (mtt180) cc_final: 0.8473 (mtp-110) REVERT: o 35 ARG cc_start: 0.8655 (ttp80) cc_final: 0.8413 (tmm160) REVERT: o 71 ASN cc_start: 0.7981 (t0) cc_final: 0.7599 (t0) REVERT: o 74 ARG cc_start: 0.8999 (mtp180) cc_final: 0.8523 (mtm180) REVERT: p 25 ARG cc_start: 0.8754 (mmp80) cc_final: 0.8452 (mmp80) REVERT: p 43 LYS cc_start: 0.9196 (mmmt) cc_final: 0.8958 (tttm) REVERT: p 47 TYR cc_start: 0.8694 (p90) cc_final: 0.8484 (p90) REVERT: q 67 CYS cc_start: 0.8281 (t) cc_final: 0.8034 (t) REVERT: q 114 LEU cc_start: 0.8812 (tp) cc_final: 0.8514 (tp) REVERT: s 62 ILE cc_start: 0.9231 (mm) cc_final: 0.8765 (tp) REVERT: s 69 HIS cc_start: 0.8307 (m170) cc_final: 0.7797 (m-70) REVERT: t 134 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8541 (pt0) REVERT: u 97 GLU cc_start: 0.7334 (pm20) cc_final: 0.6877 (pm20) REVERT: u 120 ARG cc_start: 0.8808 (tpt170) cc_final: 0.8438 (ttt180) REVERT: u 131 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8571 (tmm-80) REVERT: w 144 LEU cc_start: 0.2678 (mt) cc_final: 0.2443 (mt) REVERT: y 76 LYS cc_start: 0.8185 (mttt) cc_final: 0.7766 (mttt) REVERT: y 111 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7409 (tm-30) REVERT: y 132 CYS cc_start: 0.8519 (m) cc_final: 0.8261 (m) REVERT: y 154 TYR cc_start: 0.8182 (m-80) cc_final: 0.7528 (m-10) outliers start: 159 outliers final: 80 residues processed: 836 average time/residue: 0.5670 time to fit residues: 777.3131 Evaluate side-chains 701 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 611 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 94 VAL Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 112 GLU Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain b residue 163 ASP Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 232 TYR Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 152 THR Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain d residue 109 GLN Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 152 LEU Chi-restraints excluded: chain d residue 180 ASP Chi-restraints excluded: chain e residue 197 VAL Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 284 VAL Chi-restraints excluded: chain e residue 292 PHE Chi-restraints excluded: chain f residue 107 GLN Chi-restraints excluded: chain f residue 124 LEU Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 155 SER Chi-restraints excluded: chain f residue 184 SER Chi-restraints excluded: chain f residue 186 SER Chi-restraints excluded: chain g residue 10 LYS Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 75 ASN Chi-restraints excluded: chain h residue 76 THR Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain i residue 111 ASP Chi-restraints excluded: chain i residue 125 TYR Chi-restraints excluded: chain i residue 153 GLN Chi-restraints excluded: chain i residue 168 VAL Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 115 CYS Chi-restraints excluded: chain j residue 118 ILE Chi-restraints excluded: chain j residue 125 THR Chi-restraints excluded: chain j residue 143 CYS Chi-restraints excluded: chain j residue 147 SER Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain m residue 98 LEU Chi-restraints excluded: chain m residue 142 CYS Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 49 SER Chi-restraints excluded: chain n residue 54 SER Chi-restraints excluded: chain n residue 63 CYS Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 92 LEU Chi-restraints excluded: chain n residue 96 THR Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 33 LEU Chi-restraints excluded: chain q residue 70 ASN Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain t residue 126 VAL Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 86 VAL Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain u residue 124 ASN Chi-restraints excluded: chain u residue 130 LYS Chi-restraints excluded: chain u residue 131 ARG Chi-restraints excluded: chain u residue 141 SER Chi-restraints excluded: chain w residue 94 MET Chi-restraints excluded: chain w residue 99 LEU Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain y residue 95 GLU Chi-restraints excluded: chain y residue 108 LEU Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 123 LEU Chi-restraints excluded: chain y residue 171 ILE Chi-restraints excluded: chain y residue 175 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 219 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 328 optimal weight: 4.9990 chunk 268 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 395 optimal weight: 0.9990 chunk 427 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 chunk 392 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 317 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 94 HIS b 144 GLN ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 16 GLN ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 ASN h 75 ASN ** i 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 164 GLN ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 138 GLN p 13 GLN q 70 ASN q 84 HIS r 59 GLN ** v 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 59300 Z= 0.258 Angle : 0.628 8.981 87427 Z= 0.324 Chirality : 0.037 0.344 10989 Planarity : 0.005 0.064 5570 Dihedral : 23.641 179.888 26616 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.88 % Favored : 95.94 % Rotamer: Outliers : 6.78 % Allowed : 23.89 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.77 (0.15), residues: 2756 helix: 0.19 (0.14), residues: 1165 sheet: -0.05 (0.23), residues: 470 loop : -1.40 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP e 307 HIS 0.010 0.001 HIS y 105 PHE 0.027 0.002 PHE 0 97 TYR 0.025 0.002 TYR b 232 ARG 0.009 0.001 ARG n 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 675 time to evaluate : 3.005 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: b 25 ARG cc_start: 0.8165 (mtp180) cc_final: 0.7823 (mmm160) REVERT: b 70 GLN cc_start: 0.7534 (mm-40) cc_final: 0.7304 (mm-40) REVERT: b 112 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8031 (pt0) REVERT: b 116 HIS cc_start: 0.8296 (m170) cc_final: 0.8039 (m-70) REVERT: b 119 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.6672 (tpt170) REVERT: b 169 ASP cc_start: 0.7895 (m-30) cc_final: 0.7585 (m-30) REVERT: b 178 ARG cc_start: 0.8698 (mmp-170) cc_final: 0.8240 (mtm110) REVERT: b 185 ILE cc_start: 0.8415 (mt) cc_final: 0.8142 (mm) REVERT: b 187 THR cc_start: 0.9053 (m) cc_final: 0.8684 (p) REVERT: b 232 TYR cc_start: 0.5978 (OUTLIER) cc_final: 0.4909 (p90) REVERT: c 36 ASP cc_start: 0.8302 (m-30) cc_final: 0.8028 (m-30) REVERT: c 184 VAL cc_start: 0.9637 (t) cc_final: 0.9411 (p) REVERT: d 58 TYR cc_start: 0.8632 (m-80) cc_final: 0.8262 (m-80) REVERT: d 88 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8610 (mm-30) REVERT: d 89 MET cc_start: 0.9358 (mmt) cc_final: 0.9147 (mmm) REVERT: d 124 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7730 (t0) REVERT: e 211 ASN cc_start: 0.9129 (t0) cc_final: 0.8568 (t0) REVERT: e 263 GLU cc_start: 0.8538 (tp30) cc_final: 0.8180 (tp30) REVERT: e 287 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8776 (pt0) REVERT: f 107 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8311 (tm-30) REVERT: f 111 MET cc_start: 0.8782 (tpp) cc_final: 0.8395 (tpp) REVERT: f 120 GLU cc_start: 0.8853 (tp30) cc_final: 0.8104 (tp30) REVERT: f 124 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8460 (pp) REVERT: f 128 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8427 (pp30) REVERT: f 131 GLU cc_start: 0.8820 (pp20) cc_final: 0.8350 (pp20) REVERT: f 170 ASP cc_start: 0.8804 (m-30) cc_final: 0.8381 (t70) REVERT: f 181 LYS cc_start: 0.9229 (ttmm) cc_final: 0.8936 (ttmm) REVERT: g 10 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.6916 (mtmm) REVERT: g 18 TYR cc_start: 0.9138 (m-80) cc_final: 0.8647 (m-80) REVERT: g 76 LYS cc_start: 0.8606 (tptt) cc_final: 0.8216 (mmtm) REVERT: g 88 PRO cc_start: 0.8878 (Cg_exo) cc_final: 0.8590 (Cg_endo) REVERT: g 101 ILE cc_start: 0.9493 (mt) cc_final: 0.9191 (tt) REVERT: g 126 ASP cc_start: 0.8867 (m-30) cc_final: 0.8557 (m-30) REVERT: g 151 PHE cc_start: 0.8759 (m-80) cc_final: 0.8439 (m-80) REVERT: h 4 ASP cc_start: 0.7683 (t0) cc_final: 0.7296 (t0) REVERT: h 19 ASN cc_start: 0.8987 (t0) cc_final: 0.8694 (t0) REVERT: h 37 LYS cc_start: 0.9492 (mtpp) cc_final: 0.9156 (mtmm) REVERT: h 77 PHE cc_start: 0.8834 (t80) cc_final: 0.8465 (t80) REVERT: i 124 GLN cc_start: 0.9134 (pt0) cc_final: 0.8914 (pt0) REVERT: j 159 GLU cc_start: 0.8655 (pt0) cc_final: 0.8378 (pt0) REVERT: j 164 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7616 (mt0) REVERT: j 192 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7414 (tm-30) REVERT: j 194 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8342 (mmmm) REVERT: k 33 GLN cc_start: 0.9018 (tt0) cc_final: 0.8204 (tm-30) REVERT: k 78 ASN cc_start: 0.8813 (t0) cc_final: 0.8553 (t0) REVERT: k 110 ARG cc_start: 0.8506 (tpt90) cc_final: 0.7968 (mmm-85) REVERT: k 112 SER cc_start: 0.8713 (m) cc_final: 0.8487 (p) REVERT: l 16 ARG cc_start: 0.8937 (mmm160) cc_final: 0.8676 (mmm160) REVERT: l 29 GLN cc_start: 0.8987 (mp10) cc_final: 0.8659 (mp10) REVERT: l 43 LYS cc_start: 0.8570 (mttt) cc_final: 0.8222 (mttp) REVERT: l 76 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7504 (mm-30) REVERT: m 86 GLU cc_start: 0.7703 (tp30) cc_final: 0.7414 (tp30) REVERT: m 99 LEU cc_start: 0.8925 (mt) cc_final: 0.8668 (mt) REVERT: m 137 ILE cc_start: 0.9256 (mt) cc_final: 0.9040 (pt) REVERT: n 18 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8865 (mm-40) REVERT: n 37 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6570 (mp) REVERT: n 59 LEU cc_start: 0.9290 (mt) cc_final: 0.9068 (tp) REVERT: o 34 ARG cc_start: 0.8765 (mtt180) cc_final: 0.8211 (mtp-110) REVERT: o 35 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8373 (tmm160) REVERT: p 47 TYR cc_start: 0.8638 (p90) cc_final: 0.8270 (p90) REVERT: q 67 CYS cc_start: 0.8171 (t) cc_final: 0.7951 (t) REVERT: q 103 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7815 (t70) REVERT: r 60 ARG cc_start: 0.9138 (mtm-85) cc_final: 0.8899 (mtp85) REVERT: s 28 LYS cc_start: 0.8561 (mttt) cc_final: 0.8307 (mmtm) REVERT: s 66 MET cc_start: 0.9059 (mmm) cc_final: 0.8843 (mtp) REVERT: t 140 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8412 (t70) REVERT: u 90 VAL cc_start: 0.8508 (t) cc_final: 0.6873 (t) REVERT: u 97 GLU cc_start: 0.7668 (pm20) cc_final: 0.7178 (pm20) REVERT: u 120 ARG cc_start: 0.8880 (tpt170) cc_final: 0.8419 (ttt180) REVERT: u 135 GLU cc_start: 0.8448 (tp30) cc_final: 0.8165 (tp30) REVERT: y 111 GLU cc_start: 0.7770 (tm-30) cc_final: 0.6922 (tm-30) REVERT: y 132 CYS cc_start: 0.8541 (m) cc_final: 0.8321 (m) REVERT: y 135 THR cc_start: 0.9150 (m) cc_final: 0.8831 (m) REVERT: y 148 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6827 (mm-30) REVERT: y 154 TYR cc_start: 0.7766 (m-80) cc_final: 0.7485 (m-10) outliers start: 162 outliers final: 102 residues processed: 767 average time/residue: 0.5868 time to fit residues: 742.3527 Evaluate side-chains 721 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 606 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 94 VAL Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 76 THR Chi-restraints excluded: chain b residue 82 ASP Chi-restraints excluded: chain b residue 112 GLU Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 232 TYR Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 202 THR Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain e residue 167 LYS Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain e residue 203 LYS Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 284 VAL Chi-restraints excluded: chain e residue 287 GLN Chi-restraints excluded: chain f residue 107 GLN Chi-restraints excluded: chain f residue 124 LEU Chi-restraints excluded: chain f residue 155 SER Chi-restraints excluded: chain f residue 186 SER Chi-restraints excluded: chain g residue 10 LYS Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 76 THR Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 121 LEU Chi-restraints excluded: chain i residue 125 TYR Chi-restraints excluded: chain i residue 137 THR Chi-restraints excluded: chain i residue 138 ASN Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 115 CYS Chi-restraints excluded: chain j residue 118 ILE Chi-restraints excluded: chain j residue 128 LYS Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain j residue 146 LYS Chi-restraints excluded: chain j residue 153 ASP Chi-restraints excluded: chain j residue 164 GLN Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 19 THR Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain m residue 52 ASN Chi-restraints excluded: chain m residue 57 ASN Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 87 ASN Chi-restraints excluded: chain m residue 142 CYS Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain n residue 12 LYS Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain n residue 35 THR Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 49 SER Chi-restraints excluded: chain n residue 54 SER Chi-restraints excluded: chain n residue 63 CYS Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 92 LEU Chi-restraints excluded: chain n residue 96 THR Chi-restraints excluded: chain o residue 27 PHE Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain p residue 53 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain q residue 103 ASP Chi-restraints excluded: chain q residue 112 VAL Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 83 THR Chi-restraints excluded: chain t residue 126 VAL Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain t residue 130 ASN Chi-restraints excluded: chain t residue 140 ASP Chi-restraints excluded: chain t residue 143 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain u residue 124 ASN Chi-restraints excluded: chain u residue 141 SER Chi-restraints excluded: chain v residue 250 LEU Chi-restraints excluded: chain w residue 94 MET Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain y residue 95 GLU Chi-restraints excluded: chain y residue 108 LEU Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 148 GLU Chi-restraints excluded: chain y residue 153 LEU Chi-restraints excluded: chain y residue 171 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 390 optimal weight: 6.9990 chunk 297 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 397 optimal weight: 2.9990 chunk 420 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 376 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 93 GLN b 94 HIS b 144 GLN ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 16 GLN c 98 ASN ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 160 ASN g 24 ASN ** g 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 ASN ** i 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 164 GLN ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 136 HIS m 138 GLN n 48 GLN n 60 HIS p 45 GLN q 70 ASN ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 HIS ** u 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 168 ASN x 68 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 59300 Z= 0.337 Angle : 0.663 11.291 87427 Z= 0.339 Chirality : 0.038 0.351 10989 Planarity : 0.005 0.058 5570 Dihedral : 23.614 178.384 26601 Min Nonbonded Distance : 1.586 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.57 % Favored : 95.25 % Rotamer: Outliers : 7.45 % Allowed : 24.60 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.59 (0.15), residues: 2756 helix: 0.43 (0.15), residues: 1169 sheet: -0.17 (0.23), residues: 473 loop : -1.30 (0.17), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP b 6 HIS 0.006 0.001 HIS h 65 PHE 0.026 0.002 PHE 0 97 TYR 0.035 0.002 TYR b 232 ARG 0.011 0.001 ARG k 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 651 time to evaluate : 2.911 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: 0 100 LYS cc_start: 0.7140 (tptt) cc_final: 0.6798 (tptt) REVERT: b 25 ARG cc_start: 0.8151 (mtp180) cc_final: 0.7790 (mmm160) REVERT: b 46 ASN cc_start: 0.8363 (t0) cc_final: 0.8126 (t0) REVERT: b 119 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.6616 (tpt170) REVERT: b 169 ASP cc_start: 0.7914 (m-30) cc_final: 0.7582 (m-30) REVERT: b 178 ARG cc_start: 0.8640 (mmp-170) cc_final: 0.8167 (mtm110) REVERT: b 187 THR cc_start: 0.8565 (m) cc_final: 0.7897 (p) REVERT: c 36 ASP cc_start: 0.8305 (m-30) cc_final: 0.7979 (m-30) REVERT: c 94 ASP cc_start: 0.8391 (t0) cc_final: 0.8118 (t0) REVERT: c 179 ILE cc_start: 0.9479 (mt) cc_final: 0.9261 (mm) REVERT: c 184 VAL cc_start: 0.9637 (t) cc_final: 0.9383 (p) REVERT: d 58 TYR cc_start: 0.8640 (m-80) cc_final: 0.8184 (m-80) REVERT: d 88 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8493 (mm-30) REVERT: d 89 MET cc_start: 0.9292 (mmt) cc_final: 0.9046 (mmm) REVERT: d 124 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7846 (t70) REVERT: e 202 GLN cc_start: 0.8801 (mp10) cc_final: 0.8595 (mp10) REVERT: e 211 ASN cc_start: 0.9069 (t0) cc_final: 0.8596 (t0) REVERT: e 263 GLU cc_start: 0.8489 (tp30) cc_final: 0.8036 (tp30) REVERT: e 287 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8790 (pt0) REVERT: e 292 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8513 (t80) REVERT: e 303 MET cc_start: 0.8893 (tpp) cc_final: 0.8512 (tpp) REVERT: f 101 CYS cc_start: 0.7691 (m) cc_final: 0.7322 (t) REVERT: f 107 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8738 (tm-30) REVERT: f 111 MET cc_start: 0.8802 (tpp) cc_final: 0.8367 (tpp) REVERT: f 141 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7853 (t80) REVERT: f 170 ASP cc_start: 0.9004 (m-30) cc_final: 0.8560 (t70) REVERT: g 52 GLN cc_start: 0.9148 (mt0) cc_final: 0.8821 (mt0) REVERT: g 63 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7796 (mmt90) REVERT: g 76 LYS cc_start: 0.8603 (tptt) cc_final: 0.8208 (mmtm) REVERT: g 88 PRO cc_start: 0.8879 (Cg_exo) cc_final: 0.8627 (Cg_endo) REVERT: g 126 ASP cc_start: 0.8838 (m-30) cc_final: 0.8554 (m-30) REVERT: g 151 PHE cc_start: 0.8744 (m-80) cc_final: 0.8416 (m-80) REVERT: h 4 ASP cc_start: 0.7756 (t0) cc_final: 0.7489 (t0) REVERT: h 19 ASN cc_start: 0.8604 (t0) cc_final: 0.8203 (p0) REVERT: h 77 PHE cc_start: 0.8784 (t80) cc_final: 0.8451 (t80) REVERT: i 105 PHE cc_start: 0.8318 (m-80) cc_final: 0.8097 (m-80) REVERT: i 124 GLN cc_start: 0.9184 (pt0) cc_final: 0.8945 (pt0) REVERT: j 115 CYS cc_start: 0.8980 (p) cc_final: 0.8637 (p) REVERT: j 192 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7471 (tm-30) REVERT: j 194 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8100 (mtmt) REVERT: k 33 GLN cc_start: 0.9084 (tt0) cc_final: 0.8177 (tm-30) REVERT: k 78 ASN cc_start: 0.8865 (t0) cc_final: 0.8466 (t0) REVERT: k 110 ARG cc_start: 0.8649 (tpt90) cc_final: 0.8422 (mmm-85) REVERT: l 16 ARG cc_start: 0.8880 (mmm160) cc_final: 0.8642 (mmm160) REVERT: m 86 GLU cc_start: 0.7763 (tp30) cc_final: 0.7415 (tp30) REVERT: m 137 ILE cc_start: 0.9226 (mt) cc_final: 0.8947 (pt) REVERT: n 18 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8904 (mm-40) REVERT: n 59 LEU cc_start: 0.9312 (mt) cc_final: 0.9080 (tp) REVERT: o 34 ARG cc_start: 0.8659 (mtt180) cc_final: 0.8292 (mtp-110) REVERT: o 45 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8100 (ttpp) REVERT: o 53 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8950 (tp) REVERT: p 7 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8697 (ttmm) REVERT: p 25 ARG cc_start: 0.8885 (mmp80) cc_final: 0.8440 (mmp80) REVERT: p 59 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8902 (mmmt) REVERT: p 75 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7975 (tp30) REVERT: q 67 CYS cc_start: 0.8163 (t) cc_final: 0.7904 (t) REVERT: q 70 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7645 (t0) REVERT: r 38 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.7783 (mtm-85) REVERT: r 49 ARG cc_start: 0.9209 (tmm-80) cc_final: 0.8984 (tmm-80) REVERT: r 60 ARG cc_start: 0.9165 (mtm-85) cc_final: 0.8833 (mtp85) REVERT: t 140 ASP cc_start: 0.8690 (m-30) cc_final: 0.8389 (t0) REVERT: u 120 ARG cc_start: 0.8825 (tpt170) cc_final: 0.8361 (ttt180) REVERT: u 135 GLU cc_start: 0.8602 (tp30) cc_final: 0.8191 (tp30) REVERT: w 115 ASP cc_start: 0.5092 (m-30) cc_final: 0.3942 (p0) REVERT: x 59 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8158 (mtt-85) REVERT: y 163 ILE cc_start: 0.9492 (mt) cc_final: 0.9237 (mp) outliers start: 178 outliers final: 117 residues processed: 753 average time/residue: 0.5634 time to fit residues: 701.1073 Evaluate side-chains 730 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 602 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 94 VAL Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 76 THR Chi-restraints excluded: chain b residue 82 ASP Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 157 THR Chi-restraints excluded: chain c residue 202 THR Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain e residue 167 LYS Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 284 VAL Chi-restraints excluded: chain e residue 287 GLN Chi-restraints excluded: chain e residue 292 PHE Chi-restraints excluded: chain f residue 107 GLN Chi-restraints excluded: chain f residue 141 TYR Chi-restraints excluded: chain f residue 184 SER Chi-restraints excluded: chain f residue 186 SER Chi-restraints excluded: chain g residue 10 LYS Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 63 ARG Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 75 ASN Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 78 PHE Chi-restraints excluded: chain i residue 121 LEU Chi-restraints excluded: chain i residue 125 TYR Chi-restraints excluded: chain i residue 137 THR Chi-restraints excluded: chain i residue 138 ASN Chi-restraints excluded: chain i residue 168 VAL Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 125 THR Chi-restraints excluded: chain j residue 146 LYS Chi-restraints excluded: chain j residue 147 SER Chi-restraints excluded: chain j residue 153 ASP Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 19 THR Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain m residue 52 ASN Chi-restraints excluded: chain m residue 57 ASN Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 87 ASN Chi-restraints excluded: chain m residue 96 ASP Chi-restraints excluded: chain m residue 97 GLU Chi-restraints excluded: chain m residue 138 GLN Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain n residue 12 LYS Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 54 SER Chi-restraints excluded: chain n residue 63 CYS Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 92 LEU Chi-restraints excluded: chain n residue 96 THR Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain o residue 27 PHE Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 53 LEU Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain p residue 7 LYS Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 33 LEU Chi-restraints excluded: chain p residue 53 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain q residue 70 ASN Chi-restraints excluded: chain q residue 112 VAL Chi-restraints excluded: chain q residue 142 LYS Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain t residue 83 THR Chi-restraints excluded: chain t residue 87 GLU Chi-restraints excluded: chain t residue 126 VAL Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain t residue 130 ASN Chi-restraints excluded: chain t residue 143 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain u residue 124 ASN Chi-restraints excluded: chain u residue 141 SER Chi-restraints excluded: chain v residue 250 LEU Chi-restraints excluded: chain w residue 94 MET Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 126 LEU Chi-restraints excluded: chain x residue 59 ARG Chi-restraints excluded: chain y residue 95 GLU Chi-restraints excluded: chain y residue 108 LEU Chi-restraints excluded: chain y residue 113 ASP Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 136 LEU Chi-restraints excluded: chain y residue 148 GLU Chi-restraints excluded: chain y residue 153 LEU Chi-restraints excluded: chain y residue 171 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 350 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 6 optimal weight: 50.0000 chunk 313 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 358 optimal weight: 2.9990 chunk 290 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 377 optimal weight: 0.5980 chunk 106 optimal weight: 8.9990 overall best weight: 2.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 94 HIS ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 16 GLN c 98 ASN ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 133 GLN d 176 ASN ** e 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** g 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 ASN ** i 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 204 GLN j 175 GLN ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 138 GLN p 45 GLN q 70 ASN ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 140 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 59300 Z= 0.216 Angle : 0.597 14.197 87427 Z= 0.307 Chirality : 0.035 0.324 10989 Planarity : 0.005 0.070 5570 Dihedral : 23.557 177.709 26593 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.92 % Favored : 95.90 % Rotamer: Outliers : 6.49 % Allowed : 26.90 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.35 (0.15), residues: 2756 helix: 0.71 (0.15), residues: 1164 sheet: -0.07 (0.23), residues: 469 loop : -1.27 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP b 6 HIS 0.004 0.001 HIS d 163 PHE 0.026 0.002 PHE k 118 TYR 0.025 0.002 TYR b 232 ARG 0.018 0.001 ARG o 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 648 time to evaluate : 2.909 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: b 25 ARG cc_start: 0.8106 (mtp180) cc_final: 0.7837 (mmm160) REVERT: b 70 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7546 (mm-40) REVERT: b 119 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.6647 (tpt170) REVERT: b 167 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8186 (tp) REVERT: b 169 ASP cc_start: 0.8031 (m-30) cc_final: 0.7611 (m-30) REVERT: b 178 ARG cc_start: 0.8580 (mmp-170) cc_final: 0.8098 (mtm110) REVERT: b 187 THR cc_start: 0.8427 (m) cc_final: 0.7664 (p) REVERT: c 36 ASP cc_start: 0.8297 (m-30) cc_final: 0.7935 (m-30) REVERT: c 179 ILE cc_start: 0.9409 (mt) cc_final: 0.9183 (mm) REVERT: c 184 VAL cc_start: 0.9612 (t) cc_final: 0.9393 (p) REVERT: d 33 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.6318 (ttm170) REVERT: d 58 TYR cc_start: 0.8557 (m-80) cc_final: 0.8109 (m-10) REVERT: d 88 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8502 (mm-30) REVERT: d 89 MET cc_start: 0.9252 (mmt) cc_final: 0.8728 (mmm) REVERT: d 124 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7817 (t70) REVERT: e 202 GLN cc_start: 0.8824 (mp10) cc_final: 0.8600 (mp10) REVERT: e 211 ASN cc_start: 0.9139 (t0) cc_final: 0.8620 (t0) REVERT: e 237 MET cc_start: 0.9106 (tmm) cc_final: 0.8731 (tmm) REVERT: e 263 GLU cc_start: 0.8340 (tp30) cc_final: 0.8044 (tp30) REVERT: e 289 MET cc_start: 0.8634 (mtp) cc_final: 0.8363 (mtp) REVERT: f 101 CYS cc_start: 0.7614 (m) cc_final: 0.7327 (t) REVERT: f 107 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8334 (tm-30) REVERT: f 111 MET cc_start: 0.8774 (tpp) cc_final: 0.8397 (tpp) REVERT: f 124 LEU cc_start: 0.8956 (pp) cc_final: 0.8748 (pp) REVERT: f 141 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.7966 (t80) REVERT: f 170 ASP cc_start: 0.8891 (m-30) cc_final: 0.8506 (t70) REVERT: g 10 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7079 (mtmm) REVERT: g 52 GLN cc_start: 0.9123 (mt0) cc_final: 0.8807 (mt0) REVERT: g 63 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7808 (mmt90) REVERT: g 76 LYS cc_start: 0.8622 (tptt) cc_final: 0.8224 (mmtm) REVERT: g 88 PRO cc_start: 0.8975 (Cg_exo) cc_final: 0.8603 (Cg_endo) REVERT: g 116 MET cc_start: 0.8384 (mmp) cc_final: 0.8165 (mmm) REVERT: g 120 LEU cc_start: 0.9372 (tt) cc_final: 0.9144 (tt) REVERT: g 126 ASP cc_start: 0.8796 (m-30) cc_final: 0.8420 (m-30) REVERT: g 151 PHE cc_start: 0.8615 (m-80) cc_final: 0.8312 (m-80) REVERT: h 4 ASP cc_start: 0.7742 (t0) cc_final: 0.7467 (t0) REVERT: h 29 THR cc_start: 0.8845 (m) cc_final: 0.8641 (m) REVERT: i 124 GLN cc_start: 0.9173 (pt0) cc_final: 0.8917 (pt0) REVERT: i 178 GLN cc_start: 0.8285 (pm20) cc_final: 0.8030 (pm20) REVERT: j 115 CYS cc_start: 0.9156 (p) cc_final: 0.8826 (p) REVERT: j 192 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7178 (tm-30) REVERT: j 194 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8200 (mtmt) REVERT: k 33 GLN cc_start: 0.8866 (tt0) cc_final: 0.8079 (mt0) REVERT: k 78 ASN cc_start: 0.8877 (t0) cc_final: 0.8454 (t0) REVERT: l 76 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7381 (mm-30) REVERT: m 86 GLU cc_start: 0.7970 (tp30) cc_final: 0.7672 (tp30) REVERT: m 88 LYS cc_start: 0.8906 (ttpp) cc_final: 0.8387 (pttt) REVERT: n 5 SER cc_start: 0.9054 (OUTLIER) cc_final: 0.8009 (t) REVERT: n 18 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8883 (mm-40) REVERT: n 59 LEU cc_start: 0.9305 (mt) cc_final: 0.9070 (tp) REVERT: o 34 ARG cc_start: 0.8658 (mtt180) cc_final: 0.8251 (mtp-110) REVERT: o 45 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8224 (ttpp) REVERT: o 53 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8857 (tp) REVERT: p 7 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8686 (ttmm) REVERT: p 75 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7900 (tp30) REVERT: q 67 CYS cc_start: 0.8071 (t) cc_final: 0.7866 (t) REVERT: r 24 SER cc_start: 0.8946 (m) cc_final: 0.8604 (p) REVERT: r 56 LEU cc_start: 0.9082 (tp) cc_final: 0.8789 (mp) REVERT: r 60 ARG cc_start: 0.9163 (mtm-85) cc_final: 0.8770 (mtp85) REVERT: t 131 LEU cc_start: 0.9552 (mt) cc_final: 0.9350 (mm) REVERT: t 173 TRP cc_start: 0.7880 (OUTLIER) cc_final: 0.6284 (p-90) REVERT: u 95 ASN cc_start: 0.8054 (p0) cc_final: 0.7768 (p0) REVERT: u 120 ARG cc_start: 0.8798 (tpt170) cc_final: 0.8361 (ttt180) REVERT: w 115 ASP cc_start: 0.5114 (m-30) cc_final: 0.3937 (p0) REVERT: y 119 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7710 (ttt180) REVERT: y 178 HIS cc_start: 0.6391 (m170) cc_final: 0.6107 (m-70) outliers start: 155 outliers final: 113 residues processed: 731 average time/residue: 0.5639 time to fit residues: 679.2028 Evaluate side-chains 722 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 596 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 94 VAL Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 76 THR Chi-restraints excluded: chain b residue 82 ASP Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain b residue 163 ASP Chi-restraints excluded: chain b residue 167 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 202 THR Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain e residue 167 LYS Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 292 PHE Chi-restraints excluded: chain f residue 107 GLN Chi-restraints excluded: chain f residue 141 TYR Chi-restraints excluded: chain f residue 184 SER Chi-restraints excluded: chain f residue 186 SER Chi-restraints excluded: chain f residue 203 SER Chi-restraints excluded: chain g residue 10 LYS Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 63 ARG Chi-restraints excluded: chain g residue 72 ASP Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 78 PHE Chi-restraints excluded: chain i residue 121 LEU Chi-restraints excluded: chain i residue 137 THR Chi-restraints excluded: chain i residue 138 ASN Chi-restraints excluded: chain i residue 168 VAL Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain j residue 146 LYS Chi-restraints excluded: chain j residue 147 SER Chi-restraints excluded: chain j residue 153 ASP Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain k residue 130 CYS Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 19 THR Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain m residue 48 VAL Chi-restraints excluded: chain m residue 52 ASN Chi-restraints excluded: chain m residue 57 ASN Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 87 ASN Chi-restraints excluded: chain m residue 96 ASP Chi-restraints excluded: chain m residue 138 GLN Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 12 LYS Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 54 SER Chi-restraints excluded: chain n residue 63 CYS Chi-restraints excluded: chain n residue 92 LEU Chi-restraints excluded: chain n residue 96 THR Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain o residue 27 PHE Chi-restraints excluded: chain o residue 33 ILE Chi-restraints excluded: chain o residue 53 LEU Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain p residue 7 LYS Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 53 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain q residue 70 ASN Chi-restraints excluded: chain q residue 112 VAL Chi-restraints excluded: chain q residue 120 ILE Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain t residue 126 VAL Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain t residue 130 ASN Chi-restraints excluded: chain t residue 143 VAL Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain u residue 124 ASN Chi-restraints excluded: chain u residue 141 SER Chi-restraints excluded: chain v residue 250 LEU Chi-restraints excluded: chain w residue 94 MET Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 126 LEU Chi-restraints excluded: chain y residue 95 GLU Chi-restraints excluded: chain y residue 108 LEU Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 119 ARG Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 136 LEU Chi-restraints excluded: chain y residue 148 GLU Chi-restraints excluded: chain y residue 153 LEU Chi-restraints excluded: chain y residue 171 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 141 optimal weight: 10.0000 chunk 378 optimal weight: 0.0970 chunk 83 optimal weight: 10.0000 chunk 246 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 420 optimal weight: 9.9990 chunk 349 optimal weight: 0.0010 chunk 194 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 220 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 16 GLN ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 287 GLN g 24 ASN g 51 GLN h 75 ASN ** i 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 70 ASN q 98 GLN ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 59300 Z= 0.251 Angle : 0.612 13.964 87427 Z= 0.313 Chirality : 0.035 0.315 10989 Planarity : 0.005 0.052 5570 Dihedral : 23.513 176.960 26593 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.39 % Favored : 95.43 % Rotamer: Outliers : 6.74 % Allowed : 27.32 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.29 (0.16), residues: 2756 helix: 0.69 (0.15), residues: 1170 sheet: 0.08 (0.24), residues: 455 loop : -1.20 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 212 HIS 0.006 0.001 HIS d 113 PHE 0.035 0.002 PHE c 141 TYR 0.025 0.002 TYR b 232 ARG 0.010 0.001 ARG o 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 635 time to evaluate : 2.928 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: 0 98 ARG cc_start: 0.8979 (ttp80) cc_final: 0.8777 (ttp80) REVERT: 0 100 LYS cc_start: 0.7574 (tptt) cc_final: 0.7221 (tptt) REVERT: b 45 ILE cc_start: 0.8571 (pt) cc_final: 0.8133 (mp) REVERT: b 70 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7543 (mm-40) REVERT: b 119 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.6685 (tpt170) REVERT: b 178 ARG cc_start: 0.8546 (mmp-170) cc_final: 0.8028 (mtp180) REVERT: b 187 THR cc_start: 0.8454 (m) cc_final: 0.7694 (p) REVERT: c 36 ASP cc_start: 0.8223 (m-30) cc_final: 0.7824 (m-30) REVERT: c 184 VAL cc_start: 0.9608 (t) cc_final: 0.9393 (p) REVERT: d 33 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6360 (ttm170) REVERT: d 58 TYR cc_start: 0.8559 (m-80) cc_final: 0.8188 (m-10) REVERT: d 88 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8464 (mm-30) REVERT: d 124 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7932 (t70) REVERT: e 211 ASN cc_start: 0.9156 (t0) cc_final: 0.8666 (t0) REVERT: e 237 MET cc_start: 0.9083 (tmm) cc_final: 0.8713 (tmm) REVERT: e 263 GLU cc_start: 0.8360 (tp30) cc_final: 0.8041 (tp30) REVERT: e 289 MET cc_start: 0.8619 (mtp) cc_final: 0.8353 (mtp) REVERT: f 107 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8403 (tm-30) REVERT: f 111 MET cc_start: 0.8776 (tpp) cc_final: 0.8379 (tpp) REVERT: f 123 ARG cc_start: 0.8726 (ptm-80) cc_final: 0.8515 (ptm-80) REVERT: f 128 GLN cc_start: 0.9149 (pp30) cc_final: 0.8532 (pp30) REVERT: f 131 GLU cc_start: 0.8979 (pp20) cc_final: 0.8749 (pp20) REVERT: f 141 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7957 (t80) REVERT: f 170 ASP cc_start: 0.8911 (m-30) cc_final: 0.8484 (t70) REVERT: f 178 TYR cc_start: 0.8025 (p90) cc_final: 0.7058 (p90) REVERT: g 24 ASN cc_start: 0.8662 (t160) cc_final: 0.8461 (t0) REVERT: g 52 GLN cc_start: 0.9106 (mt0) cc_final: 0.8800 (mt0) REVERT: g 63 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7767 (mmt90) REVERT: g 76 LYS cc_start: 0.8616 (tptt) cc_final: 0.8186 (mmtm) REVERT: g 88 PRO cc_start: 0.8973 (Cg_exo) cc_final: 0.8608 (Cg_endo) REVERT: g 126 ASP cc_start: 0.8792 (m-30) cc_final: 0.8441 (m-30) REVERT: g 151 PHE cc_start: 0.8646 (m-80) cc_final: 0.8315 (m-80) REVERT: h 4 ASP cc_start: 0.7793 (t0) cc_final: 0.7502 (t0) REVERT: h 33 GLU cc_start: 0.8900 (pp20) cc_final: 0.8689 (pp20) REVERT: h 37 LYS cc_start: 0.9419 (mtmm) cc_final: 0.8952 (mtmm) REVERT: h 77 PHE cc_start: 0.8721 (t80) cc_final: 0.8458 (t80) REVERT: h 103 MET cc_start: 0.9086 (mmp) cc_final: 0.8875 (mmp) REVERT: i 124 GLN cc_start: 0.9160 (pt0) cc_final: 0.8907 (pt0) REVERT: i 178 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8084 (pp30) REVERT: j 115 CYS cc_start: 0.9171 (p) cc_final: 0.8672 (p) REVERT: j 192 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7385 (tm-30) REVERT: j 194 LYS cc_start: 0.8538 (mmmt) cc_final: 0.8165 (mtmt) REVERT: k 33 GLN cc_start: 0.8864 (tt0) cc_final: 0.7968 (mt0) REVERT: k 78 ASN cc_start: 0.9043 (t0) cc_final: 0.8581 (t0) REVERT: l 16 ARG cc_start: 0.8775 (mmm160) cc_final: 0.8369 (mmm160) REVERT: m 86 GLU cc_start: 0.7849 (tp30) cc_final: 0.7492 (tp30) REVERT: m 88 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8021 (pttt) REVERT: n 5 SER cc_start: 0.9068 (OUTLIER) cc_final: 0.8060 (t) REVERT: n 18 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8914 (mm-40) REVERT: n 42 GLU cc_start: 0.8992 (mp0) cc_final: 0.8594 (mp0) REVERT: n 59 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9070 (tp) REVERT: o 34 ARG cc_start: 0.8531 (mtt180) cc_final: 0.8182 (mtp-110) REVERT: o 45 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8394 (ttpp) REVERT: o 53 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8888 (tp) REVERT: p 7 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8725 (ttmm) REVERT: p 25 ARG cc_start: 0.8828 (mmp80) cc_final: 0.8413 (mmp80) REVERT: p 34 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8231 (tm-30) REVERT: p 75 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7953 (tp30) REVERT: q 67 CYS cc_start: 0.8040 (t) cc_final: 0.7831 (t) REVERT: r 56 LEU cc_start: 0.9133 (tp) cc_final: 0.8716 (mp) REVERT: r 60 ARG cc_start: 0.9175 (mtm-85) cc_final: 0.8901 (mtp85) REVERT: t 132 ILE cc_start: 0.9462 (mt) cc_final: 0.9231 (pt) REVERT: t 173 TRP cc_start: 0.8228 (OUTLIER) cc_final: 0.6735 (p-90) REVERT: u 95 ASN cc_start: 0.8012 (p0) cc_final: 0.7764 (p0) REVERT: u 120 ARG cc_start: 0.8813 (tpt170) cc_final: 0.8365 (ttt180) REVERT: y 105 HIS cc_start: 0.8448 (m-70) cc_final: 0.8147 (m-70) REVERT: y 119 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7701 (ttt180) outliers start: 161 outliers final: 129 residues processed: 718 average time/residue: 0.5708 time to fit residues: 676.4716 Evaluate side-chains 744 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 602 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 94 VAL Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 76 THR Chi-restraints excluded: chain b residue 82 ASP Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain b residue 163 ASP Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain b residue 235 ASN Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 202 THR Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain e residue 167 LYS Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 292 PHE Chi-restraints excluded: chain f residue 107 GLN Chi-restraints excluded: chain f residue 141 TYR Chi-restraints excluded: chain f residue 155 SER Chi-restraints excluded: chain f residue 184 SER Chi-restraints excluded: chain f residue 186 SER Chi-restraints excluded: chain f residue 203 SER Chi-restraints excluded: chain g residue 10 LYS Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 63 ARG Chi-restraints excluded: chain g residue 72 ASP Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 75 ASN Chi-restraints excluded: chain h residue 76 THR Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain h residue 116 THR Chi-restraints excluded: chain i residue 78 PHE Chi-restraints excluded: chain i residue 121 LEU Chi-restraints excluded: chain i residue 137 THR Chi-restraints excluded: chain i residue 138 ASN Chi-restraints excluded: chain i residue 168 VAL Chi-restraints excluded: chain i residue 178 GLN Chi-restraints excluded: chain j residue 103 LEU Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain j residue 146 LYS Chi-restraints excluded: chain j residue 147 SER Chi-restraints excluded: chain j residue 153 ASP Chi-restraints excluded: chain j residue 180 LEU Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 116 LEU Chi-restraints excluded: chain k residue 130 CYS Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 19 THR Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain m residue 48 VAL Chi-restraints excluded: chain m residue 52 ASN Chi-restraints excluded: chain m residue 57 ASN Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 87 ASN Chi-restraints excluded: chain m residue 96 ASP Chi-restraints excluded: chain m residue 97 GLU Chi-restraints excluded: chain m residue 138 GLN Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 12 LYS Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 54 SER Chi-restraints excluded: chain n residue 59 LEU Chi-restraints excluded: chain n residue 63 CYS Chi-restraints excluded: chain n residue 92 LEU Chi-restraints excluded: chain n residue 96 THR Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain o residue 27 PHE Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 53 LEU Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain p residue 7 LYS Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 53 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain q residue 112 VAL Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain t residue 83 THR Chi-restraints excluded: chain t residue 126 VAL Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain t residue 143 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain u residue 115 GLU Chi-restraints excluded: chain u residue 124 ASN Chi-restraints excluded: chain u residue 141 SER Chi-restraints excluded: chain v residue 250 LEU Chi-restraints excluded: chain w residue 94 MET Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 126 LEU Chi-restraints excluded: chain y residue 95 GLU Chi-restraints excluded: chain y residue 108 LEU Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 119 ARG Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 136 LEU Chi-restraints excluded: chain y residue 148 GLU Chi-restraints excluded: chain y residue 153 LEU Chi-restraints excluded: chain y residue 171 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 405 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 239 optimal weight: 4.9990 chunk 307 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 354 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 419 optimal weight: 30.0000 chunk 262 optimal weight: 8.9990 chunk 255 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 ASN h 75 ASN ** i 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 153 GLN ** j 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 70 ASN ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 59300 Z= 0.319 Angle : 0.655 12.228 87427 Z= 0.333 Chirality : 0.037 0.310 10989 Planarity : 0.005 0.066 5570 Dihedral : 23.533 174.329 26590 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.75 % Favored : 95.07 % Rotamer: Outliers : 7.03 % Allowed : 28.37 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.32 (0.16), residues: 2756 helix: 0.58 (0.15), residues: 1156 sheet: 0.06 (0.24), residues: 470 loop : -1.10 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP c 212 HIS 0.009 0.001 HIS h 78 PHE 0.035 0.002 PHE 0 97 TYR 0.021 0.002 TYR b 232 ARG 0.015 0.001 ARG o 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 613 time to evaluate : 2.898 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: 0 100 LYS cc_start: 0.7724 (tptt) cc_final: 0.7395 (tptt) REVERT: b 13 MET cc_start: 0.8114 (ptt) cc_final: 0.7667 (ppp) REVERT: b 45 ILE cc_start: 0.8525 (pt) cc_final: 0.8180 (mp) REVERT: b 46 ASN cc_start: 0.8263 (t0) cc_final: 0.8035 (t0) REVERT: b 70 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7527 (mm-40) REVERT: b 119 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6664 (tpt170) REVERT: b 167 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8304 (tp) REVERT: b 169 ASP cc_start: 0.8011 (m-30) cc_final: 0.7664 (m-30) REVERT: b 178 ARG cc_start: 0.8449 (mmp-170) cc_final: 0.7899 (mtp85) REVERT: b 187 THR cc_start: 0.8435 (m) cc_final: 0.7598 (p) REVERT: c 184 VAL cc_start: 0.9629 (t) cc_final: 0.9413 (p) REVERT: d 33 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6430 (ttm170) REVERT: d 58 TYR cc_start: 0.8627 (m-80) cc_final: 0.8191 (m-10) REVERT: d 88 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8510 (mm-30) REVERT: d 124 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7885 (t70) REVERT: e 211 ASN cc_start: 0.9087 (t0) cc_final: 0.8627 (t0) REVERT: e 237 MET cc_start: 0.9105 (tmm) cc_final: 0.8765 (tmm) REVERT: e 263 GLU cc_start: 0.8401 (tp30) cc_final: 0.8016 (tp30) REVERT: e 289 MET cc_start: 0.8604 (mtp) cc_final: 0.8369 (mtp) REVERT: f 107 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: f 111 MET cc_start: 0.8791 (tpp) cc_final: 0.8363 (tpp) REVERT: f 141 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7881 (t80) REVERT: f 170 ASP cc_start: 0.8920 (m-30) cc_final: 0.8487 (t70) REVERT: f 178 TYR cc_start: 0.8066 (p90) cc_final: 0.7209 (p90) REVERT: f 205 LYS cc_start: 0.8507 (tppp) cc_final: 0.7914 (tppp) REVERT: g 52 GLN cc_start: 0.9117 (mt0) cc_final: 0.8819 (mt0) REVERT: g 63 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7733 (mmt90) REVERT: g 76 LYS cc_start: 0.8615 (tptt) cc_final: 0.8183 (mmtm) REVERT: g 88 PRO cc_start: 0.9006 (Cg_exo) cc_final: 0.8661 (Cg_endo) REVERT: g 126 ASP cc_start: 0.8822 (m-30) cc_final: 0.8469 (m-30) REVERT: g 151 PHE cc_start: 0.8615 (m-80) cc_final: 0.8257 (m-80) REVERT: h 33 GLU cc_start: 0.9021 (pp20) cc_final: 0.8775 (pp20) REVERT: h 37 LYS cc_start: 0.9421 (mtmm) cc_final: 0.8896 (mtmm) REVERT: h 42 GLU cc_start: 0.9000 (tp30) cc_final: 0.8743 (tp30) REVERT: h 103 MET cc_start: 0.9171 (mmp) cc_final: 0.8934 (mmp) REVERT: i 78 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7238 (t80) REVERT: i 124 GLN cc_start: 0.9151 (pt0) cc_final: 0.8892 (pt0) REVERT: i 139 TYR cc_start: 0.8870 (m-80) cc_final: 0.8663 (m-80) REVERT: i 178 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.8025 (pp30) REVERT: j 115 CYS cc_start: 0.9223 (p) cc_final: 0.8733 (p) REVERT: j 192 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7390 (tm-30) REVERT: j 194 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8176 (mtmt) REVERT: k 33 GLN cc_start: 0.8804 (tt0) cc_final: 0.8167 (tm-30) REVERT: k 78 ASN cc_start: 0.8992 (t0) cc_final: 0.8542 (t0) REVERT: l 16 ARG cc_start: 0.8941 (mmm160) cc_final: 0.8601 (mmm160) REVERT: m 86 GLU cc_start: 0.7832 (tp30) cc_final: 0.7483 (tp30) REVERT: m 88 LYS cc_start: 0.8903 (ttpp) cc_final: 0.8095 (pttt) REVERT: n 5 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8190 (t) REVERT: n 18 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8884 (mm-40) REVERT: n 39 ASP cc_start: 0.8574 (t0) cc_final: 0.8353 (t0) REVERT: n 41 TRP cc_start: 0.8580 (m100) cc_final: 0.8368 (t-100) REVERT: n 42 GLU cc_start: 0.8911 (mp0) cc_final: 0.8605 (mp0) REVERT: n 59 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9077 (tp) REVERT: o 34 ARG cc_start: 0.8630 (mtt180) cc_final: 0.8226 (mtp-110) REVERT: o 45 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8428 (ptmm) REVERT: o 66 TYR cc_start: 0.8384 (t80) cc_final: 0.8175 (t80) REVERT: o 78 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8788 (mm) REVERT: p 7 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8834 (ptmm) REVERT: p 25 ARG cc_start: 0.8847 (mmp80) cc_final: 0.8466 (mmp80) REVERT: p 34 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8228 (tm-30) REVERT: p 75 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8095 (tp30) REVERT: q 67 CYS cc_start: 0.8160 (t) cc_final: 0.7891 (t) REVERT: r 38 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.7841 (mtm-85) REVERT: r 56 LEU cc_start: 0.9194 (tp) cc_final: 0.8786 (mp) REVERT: r 60 ARG cc_start: 0.9180 (mtm-85) cc_final: 0.8799 (mtp85) REVERT: t 124 GLU cc_start: 0.7828 (pm20) cc_final: 0.7588 (pm20) REVERT: t 132 ILE cc_start: 0.9445 (mt) cc_final: 0.9243 (pt) REVERT: t 134 GLU cc_start: 0.8811 (pt0) cc_final: 0.8311 (pt0) REVERT: t 140 ASP cc_start: 0.8531 (m-30) cc_final: 0.8280 (t0) REVERT: t 173 TRP cc_start: 0.8347 (OUTLIER) cc_final: 0.7031 (p-90) REVERT: u 95 ASN cc_start: 0.7962 (p0) cc_final: 0.7724 (p0) REVERT: u 120 ARG cc_start: 0.8752 (tpt170) cc_final: 0.8363 (ttt180) REVERT: y 105 HIS cc_start: 0.8560 (m-70) cc_final: 0.8207 (m-70) REVERT: y 119 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7712 (ttt180) outliers start: 168 outliers final: 122 residues processed: 708 average time/residue: 0.5893 time to fit residues: 691.2319 Evaluate side-chains 724 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 587 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 94 VAL Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 76 THR Chi-restraints excluded: chain b residue 82 ASP Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain b residue 163 ASP Chi-restraints excluded: chain b residue 167 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 201 ASP Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain b residue 235 ASN Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 157 THR Chi-restraints excluded: chain c residue 202 THR Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain e residue 167 LYS Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 266 LEU Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 292 PHE Chi-restraints excluded: chain f residue 107 GLN Chi-restraints excluded: chain f residue 141 TYR Chi-restraints excluded: chain f residue 155 SER Chi-restraints excluded: chain f residue 184 SER Chi-restraints excluded: chain f residue 186 SER Chi-restraints excluded: chain f residue 203 SER Chi-restraints excluded: chain g residue 10 LYS Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 63 ARG Chi-restraints excluded: chain g residue 72 ASP Chi-restraints excluded: chain g residue 73 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 76 THR Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain h residue 116 THR Chi-restraints excluded: chain i residue 78 PHE Chi-restraints excluded: chain i residue 121 LEU Chi-restraints excluded: chain i residue 137 THR Chi-restraints excluded: chain i residue 138 ASN Chi-restraints excluded: chain i residue 178 GLN Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 146 LYS Chi-restraints excluded: chain j residue 147 SER Chi-restraints excluded: chain j residue 153 ASP Chi-restraints excluded: chain j residue 180 LEU Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 82 THR Chi-restraints excluded: chain k residue 116 LEU Chi-restraints excluded: chain k residue 130 CYS Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 19 THR Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain m residue 48 VAL Chi-restraints excluded: chain m residue 52 ASN Chi-restraints excluded: chain m residue 57 ASN Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 87 ASN Chi-restraints excluded: chain m residue 96 ASP Chi-restraints excluded: chain m residue 97 GLU Chi-restraints excluded: chain m residue 142 CYS Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 12 LYS Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 54 SER Chi-restraints excluded: chain n residue 59 LEU Chi-restraints excluded: chain n residue 63 CYS Chi-restraints excluded: chain n residue 92 LEU Chi-restraints excluded: chain n residue 96 THR Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain o residue 27 PHE Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain o residue 78 LEU Chi-restraints excluded: chain p residue 7 LYS Chi-restraints excluded: chain p residue 32 ASP Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 53 ILE Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain q residue 112 VAL Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 78 LEU Chi-restraints excluded: chain t residue 87 GLU Chi-restraints excluded: chain t residue 121 SER Chi-restraints excluded: chain t residue 126 VAL Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain t residue 143 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 115 GLU Chi-restraints excluded: chain u residue 124 ASN Chi-restraints excluded: chain u residue 128 GLU Chi-restraints excluded: chain u residue 141 SER Chi-restraints excluded: chain v residue 250 LEU Chi-restraints excluded: chain w residue 94 MET Chi-restraints excluded: chain w residue 126 LEU Chi-restraints excluded: chain y residue 95 GLU Chi-restraints excluded: chain y residue 108 LEU Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 119 ARG Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 136 LEU Chi-restraints excluded: chain y residue 153 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 259 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 250 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 266 optimal weight: 20.0000 chunk 285 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 329 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 16 GLN c 98 ASN c 107 ASN ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 ASN i 81 GLN ** i 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 78 GLN ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 59300 Z= 0.467 Angle : 0.770 15.579 87427 Z= 0.389 Chirality : 0.041 0.300 10989 Planarity : 0.006 0.058 5570 Dihedral : 23.696 171.406 26588 Min Nonbonded Distance : 1.369 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.02 % Favored : 93.80 % Rotamer: Outliers : 7.24 % Allowed : 28.70 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.72 (0.16), residues: 2756 helix: 0.24 (0.15), residues: 1155 sheet: -0.16 (0.24), residues: 463 loop : -1.29 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 6 HIS 0.009 0.002 HIS d 113 PHE 0.041 0.003 PHE 0 97 TYR 0.020 0.003 TYR f 130 ARG 0.014 0.001 ARG o 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 597 time to evaluate : 2.881 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: b 46 ASN cc_start: 0.8446 (t0) cc_final: 0.8195 (t0) REVERT: b 70 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7388 (mm-40) REVERT: b 119 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6668 (tpt170) REVERT: b 167 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8080 (tp) REVERT: b 178 ARG cc_start: 0.8404 (mmp-170) cc_final: 0.7867 (mtm110) REVERT: b 187 THR cc_start: 0.8479 (m) cc_final: 0.7561 (p) REVERT: d 33 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6546 (ttt180) REVERT: d 58 TYR cc_start: 0.8725 (m-80) cc_final: 0.8287 (m-80) REVERT: d 88 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8591 (mm-30) REVERT: d 124 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7910 (t0) REVERT: e 211 ASN cc_start: 0.9138 (t0) cc_final: 0.8865 (t0) REVERT: e 237 MET cc_start: 0.9134 (tmm) cc_final: 0.8822 (tmm) REVERT: e 263 GLU cc_start: 0.8447 (tp30) cc_final: 0.8037 (tp30) REVERT: e 287 GLN cc_start: 0.8885 (pt0) cc_final: 0.8416 (pt0) REVERT: f 111 MET cc_start: 0.8803 (tpp) cc_final: 0.8358 (tpp) REVERT: f 141 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7777 (t80) REVERT: f 164 GLU cc_start: 0.9032 (mp0) cc_final: 0.8670 (mp0) REVERT: f 170 ASP cc_start: 0.8994 (m-30) cc_final: 0.8544 (t70) REVERT: f 178 TYR cc_start: 0.8179 (p90) cc_final: 0.7338 (p90) REVERT: f 205 LYS cc_start: 0.8592 (tppp) cc_final: 0.8003 (tppp) REVERT: g 52 GLN cc_start: 0.9137 (mt0) cc_final: 0.8803 (mt0) REVERT: g 63 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7762 (mmt90) REVERT: g 76 LYS cc_start: 0.8527 (tptt) cc_final: 0.8126 (mmtm) REVERT: g 85 HIS cc_start: 0.7082 (m-70) cc_final: 0.6743 (m-70) REVERT: g 126 ASP cc_start: 0.8782 (m-30) cc_final: 0.8445 (m-30) REVERT: g 151 PHE cc_start: 0.8636 (m-80) cc_final: 0.8281 (m-80) REVERT: h 103 MET cc_start: 0.9261 (mmp) cc_final: 0.9051 (mmp) REVERT: i 78 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.7717 (t80) REVERT: i 124 GLN cc_start: 0.9176 (pt0) cc_final: 0.8950 (pt0) REVERT: i 139 TYR cc_start: 0.8916 (m-80) cc_final: 0.8680 (m-80) REVERT: i 178 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8106 (pp30) REVERT: j 115 CYS cc_start: 0.9252 (p) cc_final: 0.8729 (p) REVERT: k 33 GLN cc_start: 0.9020 (tt0) cc_final: 0.8197 (tm-30) REVERT: k 78 ASN cc_start: 0.9068 (t0) cc_final: 0.8759 (t0) REVERT: l 16 ARG cc_start: 0.8701 (mmm160) cc_final: 0.8418 (mmm160) REVERT: l 90 LEU cc_start: 0.9507 (mm) cc_final: 0.9285 (mm) REVERT: n 5 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.8430 (t) REVERT: n 18 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8860 (mm-40) REVERT: n 39 ASP cc_start: 0.8616 (t0) cc_final: 0.8406 (t0) REVERT: n 42 GLU cc_start: 0.8998 (mp0) cc_final: 0.8687 (mp0) REVERT: n 59 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9079 (tp) REVERT: o 45 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8468 (ptmm) REVERT: p 7 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8883 (ptmm) REVERT: p 25 ARG cc_start: 0.9043 (mmp80) cc_final: 0.8739 (mmp80) REVERT: p 58 GLU cc_start: 0.8764 (pp20) cc_final: 0.8432 (pp20) REVERT: p 75 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8348 (tp30) REVERT: q 67 CYS cc_start: 0.8121 (t) cc_final: 0.7825 (t) REVERT: r 56 LEU cc_start: 0.9182 (tp) cc_final: 0.8863 (mp) REVERT: s 70 LYS cc_start: 0.8548 (mmtt) cc_final: 0.7867 (mmtp) REVERT: t 134 GLU cc_start: 0.8865 (pt0) cc_final: 0.8362 (pt0) REVERT: t 140 ASP cc_start: 0.8559 (m-30) cc_final: 0.8280 (t0) REVERT: t 173 TRP cc_start: 0.8632 (OUTLIER) cc_final: 0.7313 (p-90) REVERT: u 95 ASN cc_start: 0.8003 (p0) cc_final: 0.7757 (p0) REVERT: u 120 ARG cc_start: 0.8692 (tpt170) cc_final: 0.8311 (ttt180) REVERT: w 115 ASP cc_start: 0.4914 (m-30) cc_final: 0.4262 (p0) REVERT: y 105 HIS cc_start: 0.8864 (m-70) cc_final: 0.8440 (m-70) REVERT: y 119 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7768 (ttt180) outliers start: 173 outliers final: 130 residues processed: 695 average time/residue: 0.5529 time to fit residues: 634.6598 Evaluate side-chains 709 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 566 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 94 VAL Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 82 ASP Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain b residue 126 THR Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain b residue 163 ASP Chi-restraints excluded: chain b residue 167 ILE Chi-restraints excluded: chain b residue 190 LEU Chi-restraints excluded: chain b residue 201 ASP Chi-restraints excluded: chain b residue 203 SER Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 235 ASN Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 157 THR Chi-restraints excluded: chain c residue 202 THR Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 195 GLU Chi-restraints excluded: chain e residue 158 GLN Chi-restraints excluded: chain e residue 167 LYS Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 266 LEU Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 284 VAL Chi-restraints excluded: chain e residue 292 PHE Chi-restraints excluded: chain f residue 107 GLN Chi-restraints excluded: chain f residue 141 TYR Chi-restraints excluded: chain f residue 155 SER Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain f residue 184 SER Chi-restraints excluded: chain f residue 186 SER Chi-restraints excluded: chain f residue 203 SER Chi-restraints excluded: chain g residue 10 LYS Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 63 ARG Chi-restraints excluded: chain g residue 72 ASP Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 75 ASN Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain h residue 116 THR Chi-restraints excluded: chain i residue 78 PHE Chi-restraints excluded: chain i residue 121 LEU Chi-restraints excluded: chain i residue 137 THR Chi-restraints excluded: chain i residue 138 ASN Chi-restraints excluded: chain i residue 178 GLN Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain j residue 146 LYS Chi-restraints excluded: chain j residue 147 SER Chi-restraints excluded: chain j residue 180 LEU Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 116 LEU Chi-restraints excluded: chain k residue 130 CYS Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 19 THR Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain m residue 48 VAL Chi-restraints excluded: chain m residue 52 ASN Chi-restraints excluded: chain m residue 57 ASN Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 87 ASN Chi-restraints excluded: chain m residue 97 GLU Chi-restraints excluded: chain m residue 142 CYS Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 12 LYS Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 54 SER Chi-restraints excluded: chain n residue 59 LEU Chi-restraints excluded: chain n residue 63 CYS Chi-restraints excluded: chain n residue 92 LEU Chi-restraints excluded: chain n residue 96 THR Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain o residue 79 ILE Chi-restraints excluded: chain p residue 7 LYS Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 53 ILE Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain q residue 112 VAL Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 78 LEU Chi-restraints excluded: chain t residue 87 GLU Chi-restraints excluded: chain t residue 121 SER Chi-restraints excluded: chain t residue 126 VAL Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain t residue 130 ASN Chi-restraints excluded: chain t residue 143 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain u residue 115 GLU Chi-restraints excluded: chain u residue 123 GLU Chi-restraints excluded: chain u residue 124 ASN Chi-restraints excluded: chain u residue 128 GLU Chi-restraints excluded: chain u residue 141 SER Chi-restraints excluded: chain v residue 250 LEU Chi-restraints excluded: chain w residue 94 MET Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 126 LEU Chi-restraints excluded: chain x residue 80 ASN Chi-restraints excluded: chain y residue 95 GLU Chi-restraints excluded: chain y residue 108 LEU Chi-restraints excluded: chain y residue 113 ASP Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 119 ARG Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 136 LEU Chi-restraints excluded: chain y residue 153 LEU Chi-restraints excluded: chain y residue 164 ILE Chi-restraints excluded: chain y residue 171 ILE Chi-restraints excluded: chain y residue 175 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 381 optimal weight: 10.0000 chunk 401 optimal weight: 3.9990 chunk 366 optimal weight: 0.9980 chunk 390 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 chunk 306 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 353 optimal weight: 2.9990 chunk 369 optimal weight: 5.9990 chunk 389 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 16 GLN ** c 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 96 HIS m 138 GLN ** y 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 59300 Z= 0.199 Angle : 0.630 13.774 87427 Z= 0.322 Chirality : 0.035 0.299 10989 Planarity : 0.005 0.058 5570 Dihedral : 23.562 177.975 26587 Min Nonbonded Distance : 1.408 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.99 % Favored : 95.79 % Rotamer: Outliers : 4.52 % Allowed : 31.63 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.36 (0.16), residues: 2756 helix: 0.54 (0.15), residues: 1153 sheet: 0.10 (0.24), residues: 465 loop : -1.13 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP n 41 HIS 0.010 0.001 HIS h 78 PHE 0.028 0.002 PHE 0 97 TYR 0.026 0.002 TYR b 232 ARG 0.010 0.001 ARG 0 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 636 time to evaluate : 3.046 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: b 13 MET cc_start: 0.8045 (ptt) cc_final: 0.7637 (ppp) REVERT: b 119 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.6589 (tpt170) REVERT: b 167 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8081 (tp) REVERT: b 169 ASP cc_start: 0.8052 (m-30) cc_final: 0.7672 (m-30) REVERT: b 187 THR cc_start: 0.8383 (m) cc_final: 0.7549 (p) REVERT: b 232 TYR cc_start: 0.5593 (OUTLIER) cc_final: 0.5270 (p90) REVERT: c 184 VAL cc_start: 0.9625 (t) cc_final: 0.9398 (p) REVERT: c 188 THR cc_start: 0.9336 (m) cc_final: 0.9067 (m) REVERT: d 33 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.6322 (ttt180) REVERT: d 58 TYR cc_start: 0.8539 (m-80) cc_final: 0.8042 (m-10) REVERT: d 88 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8548 (mm-30) REVERT: d 124 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7890 (t70) REVERT: e 211 ASN cc_start: 0.9151 (t0) cc_final: 0.8806 (t0) REVERT: e 237 MET cc_start: 0.9088 (tmm) cc_final: 0.8749 (tmm) REVERT: e 263 GLU cc_start: 0.8390 (tp30) cc_final: 0.8161 (tp30) REVERT: f 111 MET cc_start: 0.8748 (tpp) cc_final: 0.8315 (tpp) REVERT: f 141 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7924 (t80) REVERT: f 164 GLU cc_start: 0.8905 (mp0) cc_final: 0.8618 (mp0) REVERT: f 170 ASP cc_start: 0.8942 (m-30) cc_final: 0.8481 (t70) REVERT: f 173 TYR cc_start: 0.8716 (m-80) cc_final: 0.8399 (m-80) REVERT: f 178 TYR cc_start: 0.7986 (p90) cc_final: 0.7156 (p90) REVERT: f 205 LYS cc_start: 0.8533 (tppp) cc_final: 0.8015 (tppp) REVERT: g 52 GLN cc_start: 0.9052 (mt0) cc_final: 0.8751 (mt0) REVERT: g 63 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7649 (mmt90) REVERT: g 76 LYS cc_start: 0.8608 (tptt) cc_final: 0.8223 (mmtm) REVERT: g 85 HIS cc_start: 0.6989 (m-70) cc_final: 0.6686 (m-70) REVERT: g 88 PRO cc_start: 0.8963 (Cg_exo) cc_final: 0.8591 (Cg_endo) REVERT: g 126 ASP cc_start: 0.8790 (m-30) cc_final: 0.8425 (m-30) REVERT: g 151 PHE cc_start: 0.8413 (m-80) cc_final: 0.8025 (m-80) REVERT: h 42 GLU cc_start: 0.9003 (tp30) cc_final: 0.8740 (tp30) REVERT: h 57 TYR cc_start: 0.8729 (m-80) cc_final: 0.8486 (m-80) REVERT: h 103 MET cc_start: 0.9208 (mmp) cc_final: 0.8797 (mmp) REVERT: i 78 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.7527 (t80) REVERT: i 124 GLN cc_start: 0.9131 (pt0) cc_final: 0.8874 (pt0) REVERT: i 139 TYR cc_start: 0.8809 (m-80) cc_final: 0.8543 (m-80) REVERT: j 107 TRP cc_start: 0.9053 (OUTLIER) cc_final: 0.7219 (m100) REVERT: j 115 CYS cc_start: 0.9210 (p) cc_final: 0.8728 (p) REVERT: j 159 GLU cc_start: 0.8633 (pt0) cc_final: 0.8331 (pt0) REVERT: j 178 ASP cc_start: 0.9034 (m-30) cc_final: 0.8805 (p0) REVERT: k 33 GLN cc_start: 0.8968 (tt0) cc_final: 0.8210 (tm-30) REVERT: k 78 ASN cc_start: 0.9014 (t0) cc_final: 0.8654 (t0) REVERT: l 16 ARG cc_start: 0.8798 (mmm160) cc_final: 0.8539 (mmm160) REVERT: n 42 GLU cc_start: 0.9011 (mp0) cc_final: 0.8612 (mp0) REVERT: n 59 LEU cc_start: 0.9320 (mt) cc_final: 0.9081 (tp) REVERT: o 18 ASN cc_start: 0.8504 (t0) cc_final: 0.8130 (t0) REVERT: o 19 LYS cc_start: 0.7349 (pttt) cc_final: 0.7004 (pttm) REVERT: o 34 ARG cc_start: 0.8495 (mtt180) cc_final: 0.8012 (mtp-110) REVERT: o 45 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8473 (ptmm) REVERT: o 77 GLU cc_start: 0.7926 (pp20) cc_final: 0.7586 (tm-30) REVERT: p 3 LYS cc_start: 0.8859 (tttt) cc_final: 0.8654 (ttmm) REVERT: p 25 ARG cc_start: 0.9005 (mmp80) cc_final: 0.8588 (mmp80) REVERT: p 65 GLU cc_start: 0.9004 (pm20) cc_final: 0.8801 (pm20) REVERT: p 75 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8203 (tp30) REVERT: q 67 CYS cc_start: 0.7938 (t) cc_final: 0.7677 (t) REVERT: s 61 TYR cc_start: 0.8787 (t80) cc_final: 0.8494 (t80) REVERT: s 81 ARG cc_start: 0.8660 (ptp90) cc_final: 0.8430 (ptp90) REVERT: t 134 GLU cc_start: 0.8839 (pt0) cc_final: 0.8343 (pt0) REVERT: t 173 TRP cc_start: 0.8383 (OUTLIER) cc_final: 0.6892 (p-90) REVERT: u 97 GLU cc_start: 0.7979 (pm20) cc_final: 0.7778 (pm20) REVERT: u 120 ARG cc_start: 0.8721 (tpt170) cc_final: 0.8320 (ttt180) REVERT: y 105 HIS cc_start: 0.8476 (m-70) cc_final: 0.8136 (m-70) REVERT: y 119 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7607 (ttt180) REVERT: y 147 GLU cc_start: 0.7924 (pm20) cc_final: 0.7720 (pm20) outliers start: 108 outliers final: 86 residues processed: 696 average time/residue: 0.5625 time to fit residues: 644.1897 Evaluate side-chains 683 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 586 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 94 VAL Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 82 ASP Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain b residue 163 ASP Chi-restraints excluded: chain b residue 167 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain b residue 232 TYR Chi-restraints excluded: chain b residue 235 ASN Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 157 THR Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain e residue 167 LYS Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 292 PHE Chi-restraints excluded: chain f residue 107 GLN Chi-restraints excluded: chain f residue 141 TYR Chi-restraints excluded: chain f residue 186 SER Chi-restraints excluded: chain f residue 203 SER Chi-restraints excluded: chain g residue 10 LYS Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 63 ARG Chi-restraints excluded: chain g residue 73 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 76 THR Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 116 THR Chi-restraints excluded: chain i residue 78 PHE Chi-restraints excluded: chain i residue 121 LEU Chi-restraints excluded: chain i residue 137 THR Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain j residue 146 LYS Chi-restraints excluded: chain j residue 147 SER Chi-restraints excluded: chain j residue 180 LEU Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 116 LEU Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain m residue 48 VAL Chi-restraints excluded: chain m residue 52 ASN Chi-restraints excluded: chain m residue 57 ASN Chi-restraints excluded: chain m residue 66 GLN Chi-restraints excluded: chain m residue 87 ASN Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 54 SER Chi-restraints excluded: chain n residue 63 CYS Chi-restraints excluded: chain n residue 92 LEU Chi-restraints excluded: chain n residue 96 THR Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain o residue 36 LEU Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 53 ILE Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain q residue 112 VAL Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 78 LEU Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain t residue 143 VAL Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain u residue 115 GLU Chi-restraints excluded: chain u residue 124 ASN Chi-restraints excluded: chain v residue 250 LEU Chi-restraints excluded: chain w residue 94 MET Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 126 LEU Chi-restraints excluded: chain x residue 80 ASN Chi-restraints excluded: chain y residue 95 GLU Chi-restraints excluded: chain y residue 119 ARG Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 136 LEU Chi-restraints excluded: chain y residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 256 optimal weight: 20.0000 chunk 413 optimal weight: 20.0000 chunk 252 optimal weight: 1.9990 chunk 195 optimal weight: 8.9990 chunk 287 optimal weight: 1.9990 chunk 433 optimal weight: 0.9990 chunk 398 optimal weight: 8.9990 chunk 345 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 GLN d 167 ASN ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 59300 Z= 0.235 Angle : 0.632 14.238 87427 Z= 0.324 Chirality : 0.036 0.426 10989 Planarity : 0.005 0.056 5570 Dihedral : 23.491 177.189 26585 Min Nonbonded Distance : 1.391 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.01 % Favored : 94.81 % Rotamer: Outliers : 4.31 % Allowed : 31.30 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.39 (0.16), residues: 2756 helix: 0.50 (0.15), residues: 1165 sheet: 0.07 (0.24), residues: 460 loop : -1.14 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP n 41 HIS 0.005 0.001 HIS d 163 PHE 0.026 0.002 PHE c 141 TYR 0.038 0.002 TYR l 66 ARG 0.010 0.001 ARG 0 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 604 time to evaluate : 2.939 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: 0 95 GLU cc_start: 0.8634 (pm20) cc_final: 0.8314 (pm20) REVERT: b 13 MET cc_start: 0.7977 (ptt) cc_final: 0.7537 (ppp) REVERT: b 119 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6657 (tpt170) REVERT: b 167 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8017 (tp) REVERT: b 187 THR cc_start: 0.8366 (m) cc_final: 0.7424 (p) REVERT: b 232 TYR cc_start: 0.5661 (OUTLIER) cc_final: 0.5353 (p90) REVERT: c 184 VAL cc_start: 0.9616 (t) cc_final: 0.9374 (p) REVERT: c 188 THR cc_start: 0.9303 (m) cc_final: 0.9047 (m) REVERT: d 33 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6339 (ttt180) REVERT: d 58 TYR cc_start: 0.8554 (m-80) cc_final: 0.8053 (m-10) REVERT: d 88 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8502 (mm-30) REVERT: d 124 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7935 (t70) REVERT: e 161 ARG cc_start: 0.9117 (mtp85) cc_final: 0.8842 (mtp85) REVERT: e 211 ASN cc_start: 0.9143 (t0) cc_final: 0.8791 (t0) REVERT: e 237 MET cc_start: 0.9044 (tmm) cc_final: 0.8716 (tmm) REVERT: e 263 GLU cc_start: 0.8438 (tp30) cc_final: 0.8035 (tp30) REVERT: f 111 MET cc_start: 0.8774 (tpp) cc_final: 0.8357 (tpp) REVERT: f 141 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.7926 (t80) REVERT: f 164 GLU cc_start: 0.8889 (mp0) cc_final: 0.8655 (mp0) REVERT: f 170 ASP cc_start: 0.8952 (m-30) cc_final: 0.8451 (t70) REVERT: f 178 TYR cc_start: 0.8028 (p90) cc_final: 0.7243 (p90) REVERT: f 205 LYS cc_start: 0.8563 (tppp) cc_final: 0.8015 (tppp) REVERT: g 52 GLN cc_start: 0.9173 (mt0) cc_final: 0.8861 (mt0) REVERT: g 63 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7687 (mmt90) REVERT: g 76 LYS cc_start: 0.8635 (tptt) cc_final: 0.8220 (mmtm) REVERT: g 85 HIS cc_start: 0.7032 (m-70) cc_final: 0.6730 (m-70) REVERT: g 88 PRO cc_start: 0.8977 (Cg_exo) cc_final: 0.8630 (Cg_endo) REVERT: g 126 ASP cc_start: 0.8702 (m-30) cc_final: 0.8364 (m-30) REVERT: g 151 PHE cc_start: 0.8459 (m-80) cc_final: 0.8075 (m-80) REVERT: h 37 LYS cc_start: 0.9315 (mtmm) cc_final: 0.9110 (mtmm) REVERT: h 42 GLU cc_start: 0.9008 (tp30) cc_final: 0.8719 (tp30) REVERT: h 57 TYR cc_start: 0.8695 (m-80) cc_final: 0.8418 (m-80) REVERT: h 103 MET cc_start: 0.9222 (mmp) cc_final: 0.8797 (mmp) REVERT: i 78 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7905 (t80) REVERT: i 124 GLN cc_start: 0.9127 (pt0) cc_final: 0.8848 (pt0) REVERT: i 139 TYR cc_start: 0.8805 (m-80) cc_final: 0.8557 (m-80) REVERT: j 107 TRP cc_start: 0.9090 (OUTLIER) cc_final: 0.7101 (m100) REVERT: j 115 CYS cc_start: 0.9175 (p) cc_final: 0.8556 (p) REVERT: j 119 MET cc_start: 0.8854 (ppp) cc_final: 0.8634 (pmm) REVERT: j 159 GLU cc_start: 0.8623 (pt0) cc_final: 0.8324 (pt0) REVERT: j 178 ASP cc_start: 0.9030 (m-30) cc_final: 0.8762 (p0) REVERT: k 33 GLN cc_start: 0.9007 (tt0) cc_final: 0.8200 (tm-30) REVERT: k 78 ASN cc_start: 0.9030 (t0) cc_final: 0.8676 (t0) REVERT: l 16 ARG cc_start: 0.8780 (mmm160) cc_final: 0.8518 (mmm160) REVERT: n 5 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8117 (t) REVERT: n 42 GLU cc_start: 0.8948 (mp0) cc_final: 0.8554 (mp0) REVERT: n 59 LEU cc_start: 0.9306 (mt) cc_final: 0.9071 (tp) REVERT: o 18 ASN cc_start: 0.8541 (t0) cc_final: 0.8143 (t0) REVERT: o 19 LYS cc_start: 0.7443 (pttt) cc_final: 0.7048 (pttp) REVERT: o 34 ARG cc_start: 0.8520 (mtt180) cc_final: 0.8025 (mtp-110) REVERT: o 45 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8485 (ptmm) REVERT: o 77 GLU cc_start: 0.7921 (pp20) cc_final: 0.7605 (tm-30) REVERT: p 25 ARG cc_start: 0.8994 (mmp80) cc_final: 0.8639 (mmp80) REVERT: p 65 GLU cc_start: 0.9007 (pm20) cc_final: 0.8796 (pm20) REVERT: p 75 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8166 (tp30) REVERT: q 67 CYS cc_start: 0.7908 (t) cc_final: 0.7669 (t) REVERT: q 96 LYS cc_start: 0.8843 (mttt) cc_final: 0.8494 (mtmm) REVERT: s 44 MET cc_start: 0.8823 (pmm) cc_final: 0.8135 (pmm) REVERT: s 61 TYR cc_start: 0.8790 (t80) cc_final: 0.8550 (t80) REVERT: s 81 ARG cc_start: 0.8680 (ptp90) cc_final: 0.8444 (ptp90) REVERT: t 134 GLU cc_start: 0.8868 (pt0) cc_final: 0.8360 (pt0) REVERT: u 120 ARG cc_start: 0.8725 (tpt170) cc_final: 0.8324 (ttt180) REVERT: y 105 HIS cc_start: 0.8692 (m-70) cc_final: 0.8248 (m-70) REVERT: y 119 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7682 (ttt90) REVERT: y 147 GLU cc_start: 0.8088 (pm20) cc_final: 0.7374 (pm20) REVERT: y 148 GLU cc_start: 0.8469 (pm20) cc_final: 0.8238 (pp20) outliers start: 103 outliers final: 87 residues processed: 662 average time/residue: 0.5723 time to fit residues: 624.6773 Evaluate side-chains 689 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 591 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 94 VAL Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 82 ASP Chi-restraints excluded: chain b residue 119 ARG Chi-restraints excluded: chain b residue 126 THR Chi-restraints excluded: chain b residue 163 ASP Chi-restraints excluded: chain b residue 167 ILE Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain b residue 232 TYR Chi-restraints excluded: chain b residue 235 ASN Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 157 THR Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain e residue 167 LYS Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain e residue 215 VAL Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 292 PHE Chi-restraints excluded: chain f residue 107 GLN Chi-restraints excluded: chain f residue 129 LYS Chi-restraints excluded: chain f residue 141 TYR Chi-restraints excluded: chain f residue 186 SER Chi-restraints excluded: chain f residue 203 SER Chi-restraints excluded: chain g residue 10 LYS Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 63 ARG Chi-restraints excluded: chain g residue 73 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain h residue 76 THR Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 116 THR Chi-restraints excluded: chain i residue 78 PHE Chi-restraints excluded: chain i residue 121 LEU Chi-restraints excluded: chain i residue 137 THR Chi-restraints excluded: chain i residue 168 VAL Chi-restraints excluded: chain j residue 107 TRP Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain j residue 146 LYS Chi-restraints excluded: chain j residue 147 SER Chi-restraints excluded: chain j residue 180 LEU Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 116 LEU Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 11 THR Chi-restraints excluded: chain l residue 19 THR Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain m residue 48 VAL Chi-restraints excluded: chain m residue 52 ASN Chi-restraints excluded: chain m residue 57 ASN Chi-restraints excluded: chain m residue 66 GLN Chi-restraints excluded: chain m residue 87 ASN Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 54 SER Chi-restraints excluded: chain n residue 92 LEU Chi-restraints excluded: chain n residue 96 THR Chi-restraints excluded: chain o residue 22 VAL Chi-restraints excluded: chain o residue 36 LEU Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 53 ILE Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain q residue 112 VAL Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 78 LEU Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain t residue 143 VAL Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain u residue 115 GLU Chi-restraints excluded: chain u residue 124 ASN Chi-restraints excluded: chain v residue 250 LEU Chi-restraints excluded: chain w residue 94 MET Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 126 LEU Chi-restraints excluded: chain x residue 80 ASN Chi-restraints excluded: chain y residue 95 GLU Chi-restraints excluded: chain y residue 119 ARG Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 136 LEU Chi-restraints excluded: chain y residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 274 optimal weight: 7.9990 chunk 367 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 318 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 345 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 354 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.057338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.043775 restraints weight = 318409.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.044709 restraints weight = 127630.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.045291 restraints weight = 81459.349| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 59300 Z= 0.478 Angle : 0.773 15.999 87427 Z= 0.390 Chirality : 0.041 0.280 10989 Planarity : 0.006 0.057 5570 Dihedral : 23.574 172.977 26584 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.20 % Favored : 93.65 % Rotamer: Outliers : 5.10 % Allowed : 30.59 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.68 (0.16), residues: 2756 helix: 0.22 (0.15), residues: 1160 sheet: -0.09 (0.24), residues: 464 loop : -1.23 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP n 41 HIS 0.007 0.002 HIS e 225 PHE 0.026 0.003 PHE 0 97 TYR 0.033 0.002 TYR l 66 ARG 0.012 0.001 ARG 0 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11482.96 seconds wall clock time: 203 minutes 55.44 seconds (12235.44 seconds total)