Starting phenix.real_space_refine on Sun Mar 24 07:02:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r92_4766/03_2024/6r92_4766_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r92_4766/03_2024/6r92_4766.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r92_4766/03_2024/6r92_4766_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r92_4766/03_2024/6r92_4766_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r92_4766/03_2024/6r92_4766_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r92_4766/03_2024/6r92_4766.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r92_4766/03_2024/6r92_4766.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r92_4766/03_2024/6r92_4766_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r92_4766/03_2024/6r92_4766_trim_updated.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 288 5.49 5 S 66 5.16 5 C 12679 2.51 5 N 3869 2.21 5 O 4598 1.98 5 H 19019 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 358": "OD1" <-> "OD2" Residue "L PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 376": "OD1" <-> "OD2" Residue "A ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 73": "OD1" <-> "OD2" Residue "D TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "E ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F ASP 69": "OD1" <-> "OD2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "H ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 52": "OD1" <-> "OD2" Residue "K GLU 90": "OE1" <-> "OE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 117": "OE1" <-> "OE2" Residue "K ASP 243": "OD1" <-> "OD2" Residue "K PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 289": "OE1" <-> "OE2" Residue "K ASP 292": "OD1" <-> "OD2" Residue "K GLU 303": "OE1" <-> "OE2" Residue "K ASP 339": "OD1" <-> "OD2" Residue "K GLU 342": "OE1" <-> "OE2" Residue "K GLU 368": "OE1" <-> "OE2" Residue "K ASP 744": "OD1" <-> "OD2" Residue "K ASP 824": "OD1" <-> "OD2" Residue "K GLU 840": "OE1" <-> "OE2" Residue "K GLU 842": "OE1" <-> "OE2" Residue "K ASP 855": "OD1" <-> "OD2" Residue "K GLU 896": "OE1" <-> "OE2" Residue "K GLU 898": "OE1" <-> "OE2" Residue "K ASP 962": "OD1" <-> "OD2" Residue "K ASP 980": "OD1" <-> "OD2" Residue "K ASP 986": "OD1" <-> "OD2" Residue "K GLU 988": "OE1" <-> "OE2" Residue "K GLU 994": "OE1" <-> "OE2" Residue "K GLU 1045": "OE1" <-> "OE2" Residue "K GLU 1079": "OE1" <-> "OE2" Residue "K ASP 1099": "OD1" <-> "OD2" Residue "K ASP 1127": "OD1" <-> "OD2" Residue "K ASP 1128": "OD1" <-> "OD2" Residue "K GLU 1134": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40519 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 4611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4611 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 4565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4565 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "L" Number of atoms: 5642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5642 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 22, 'TRANS': 340} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1645 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1347 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1877 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "D" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1507 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1646 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1348 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1878 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "H" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1555 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "K" Number of atoms: 12898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 12898 Classifications: {'peptide': 825} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 797} Chain breaks: 1 Time building chain proxies: 17.20, per 1000 atoms: 0.42 Number of scatterers: 40519 At special positions: 0 Unit cell: (131.58, 179.74, 145.34, 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 66 16.00 P 288 15.00 O 4598 8.00 N 3869 7.00 C 12679 6.00 H 19019 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 38.29 Conformation dependent library (CDL) restraints added in 3.1 seconds 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3670 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 23 sheets defined 29.8% alpha, 21.5% beta 138 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 23.83 Creating SS restraints... Processing helix chain 'L' and resid 69 through 77 Processing helix chain 'L' and resid 83 through 100 removed outlier: 3.769A pdb=" N SER L 100 " --> pdb=" O HIS L 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 65 through 79 removed outlier: 3.527A pdb=" N PHE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 32 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.869A pdb=" N TYR B 52 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B 53 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 48 through 73 Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 57 through 84 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 105 through 124 Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 65 through 79 removed outlier: 3.527A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 114 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 32 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.870A pdb=" N TYR F 52 " --> pdb=" O GLY F 49 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU F 53 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 93 Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.054A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 114 through 116 No H-bonds generated for 'chain 'G' and resid 114 through 116' Processing helix chain 'H' and resid 39 through 49 Processing helix chain 'H' and resid 57 through 84 Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'H' and resid 105 through 124 Processing helix chain 'K' and resid 251 through 255 removed outlier: 3.873A pdb=" N GLN K 255 " --> pdb=" O ILE K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 382 through 384 No H-bonds generated for 'chain 'K' and resid 382 through 384' Processing helix chain 'K' and resid 728 through 730 No H-bonds generated for 'chain 'K' and resid 728 through 730' Processing helix chain 'K' and resid 756 through 758 No H-bonds generated for 'chain 'K' and resid 756 through 758' Processing helix chain 'K' and resid 986 through 989 No H-bonds generated for 'chain 'K' and resid 986 through 989' Processing helix chain 'K' and resid 1045 through 1059 Processing helix chain 'K' and resid 1070 through 1074 Processing helix chain 'K' and resid 1091 through 1099 removed outlier: 3.676A pdb=" N PHE K1097 " --> pdb=" O LEU K1093 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU K1098 " --> pdb=" O ILE K1094 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP K1099 " --> pdb=" O GLU K1095 " (cutoff:3.500A) Processing helix chain 'K' and resid 1102 through 1108 Processing helix chain 'K' and resid 1126 through 1139 removed outlier: 3.912A pdb=" N ILE K1139 " --> pdb=" O GLU K1135 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'L' and resid 117 through 119 Processing sheet with id= B, first strand: chain 'L' and resid 159 through 164 removed outlier: 6.562A pdb=" N SER L 175 " --> pdb=" O THR L 160 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU L 162 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR L 173 " --> pdb=" O LEU L 162 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE L 164 " --> pdb=" O GLN L 171 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLN L 171 " --> pdb=" O PHE L 164 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP L 185 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE L 190 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 207 through 209 Processing sheet with id= D, first strand: chain 'L' and resid 283 through 286 removed outlier: 4.753A pdb=" N THR L 266 " --> pdb=" O SER L 262 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER L 262 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA L 259 " --> pdb=" O ALA L 249 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA L 249 " --> pdb=" O ALA L 259 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS L 247 " --> pdb=" O ALA L 261 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 312 through 316 removed outlier: 3.667A pdb=" N ALA L 293 " --> pdb=" O THR L 306 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 350 through 354 removed outlier: 5.547A pdb=" N ASP L 376 " --> pdb=" O MET L 382 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N MET L 382 " --> pdb=" O ASP L 376 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 414 through 417 Processing sheet with id= H, first strand: chain 'K' and resid 1088 through 1090 removed outlier: 7.026A pdb=" N ASN K 4 " --> pdb=" O ILE K1089 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR K 3 " --> pdb=" O LEU K1043 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE K1037 " --> pdb=" O ALA K 9 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 17 through 21 removed outlier: 3.533A pdb=" N GLY K 17 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL K 43 " --> pdb=" O PRO K 51 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 61 through 67 removed outlier: 6.323A pdb=" N LEU K 80 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET K 64 " --> pdb=" O PHE K 78 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE K 78 " --> pdb=" O MET K 64 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU K 66 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU K 76 " --> pdb=" O LEU K 66 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN K 85 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU K 90 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THR K 102 " --> pdb=" O GLU K 90 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS K 92 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE K 100 " --> pdb=" O LYS K 92 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER K 94 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ILE K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 121 through 124 Processing sheet with id= L, first strand: chain 'K' and resid 201 through 204 removed outlier: 3.586A pdb=" N ASP K 166 " --> pdb=" O VAL K 181 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN K 183 " --> pdb=" O VAL K 164 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL K 164 " --> pdb=" O GLN K 183 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'K' and resid 218 through 221 Processing sheet with id= N, first strand: chain 'K' and resid 258 through 263 removed outlier: 7.061A pdb=" N GLY K 274 " --> pdb=" O VAL K 259 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N HIS K 261 " --> pdb=" O LEU K 272 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU K 272 " --> pdb=" O HIS K 261 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ARG K 263 " --> pdb=" O ARG K 270 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ARG K 270 " --> pdb=" O ARG K 263 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG K 279 " --> pdb=" O ASP K 275 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N MET K 282 " --> pdb=" O LEU K 304 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU K 304 " --> pdb=" O MET K 282 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU K 284 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL K 302 " --> pdb=" O LEU K 284 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU K 286 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU K 300 " --> pdb=" O GLU K 286 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 287 through 289 Processing sheet with id= P, first strand: chain 'K' and resid 313 through 316 removed outlier: 5.818A pdb=" N LYS K 335 " --> pdb=" O ALA K 349 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ALA K 349 " --> pdb=" O LYS K 335 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 711 through 716 removed outlier: 3.746A pdb=" N ASP K 361 " --> pdb=" O CYS K 378 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'K' and resid 749 through 751 removed outlier: 6.801A pdb=" N ASP K 795 " --> pdb=" O VAL K 801 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL K 801 " --> pdb=" O ASP K 795 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER K 762 " --> pdb=" O ALA K 804 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLN K 806 " --> pdb=" O SER K 762 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER K 764 " --> pdb=" O GLN K 806 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 811 through 819 removed outlier: 6.704A pdb=" N GLY K 832 " --> pdb=" O LEU K 814 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU K 816 " --> pdb=" O ILE K 830 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE K 830 " --> pdb=" O LEU K 816 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER K 818 " --> pdb=" O TYR K 828 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR K 828 " --> pdb=" O SER K 818 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG K 847 " --> pdb=" O THR K 833 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN K 852 " --> pdb=" O THR K 860 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N THR K 860 " --> pdb=" O GLN K 852 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N SER K 854 " --> pdb=" O LEU K 858 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU K 858 " --> pdb=" O SER K 854 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 870 through 876 removed outlier: 6.679A pdb=" N SER K 883 " --> pdb=" O TYR K 871 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET K 873 " --> pdb=" O LEU K 881 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU K 881 " --> pdb=" O MET K 873 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLU K 875 " --> pdb=" O LYS K 879 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS K 879 " --> pdb=" O GLU K 875 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS K 903 " --> pdb=" O LEU K 890 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLU K 892 " --> pdb=" O THR K 901 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR K 901 " --> pdb=" O GLU K 892 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 911 through 917 removed outlier: 6.677A pdb=" N GLY K 924 " --> pdb=" O LEU K 912 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU K 914 " --> pdb=" O LEU K 922 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU K 922 " --> pdb=" O LEU K 914 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N THR K 916 " --> pdb=" O PHE K 920 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE K 920 " --> pdb=" O THR K 916 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA K 934 " --> pdb=" O GLU K 944 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLU K 944 " --> pdb=" O ALA K 934 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LYS K 936 " --> pdb=" O PHE K 942 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE K 942 " --> pdb=" O LYS K 936 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 954 through 959 removed outlier: 6.781A pdb=" N ALA K 968 " --> pdb=" O SER K 955 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL K 957 " --> pdb=" O LEU K 966 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU K 966 " --> pdb=" O VAL K 957 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN K 973 " --> pdb=" O GLU K 969 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN K 978 " --> pdb=" O GLU K 994 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLU K 994 " --> pdb=" O GLN K 978 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 720 through 727 removed outlier: 6.505A pdb=" N LEU K 736 " --> pdb=" O ARG K 722 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE K 724 " --> pdb=" O GLY K 734 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY K 734 " --> pdb=" O ILE K 724 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TYR K 726 " --> pdb=" O CYS K 732 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N CYS K 732 " --> pdb=" O TYR K 726 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 332 hydrogen bonds 664 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 21.93 Time building geometry restraints manager: 39.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 18993 1.03 - 1.23: 525 1.23 - 1.43: 9671 1.43 - 1.63: 12225 1.63 - 1.83: 106 Bond restraints: 41520 Sorted by residual: bond pdb=" C4' 3DR J 93 " pdb=" O4' 3DR J 93 " ideal model delta sigma weight residual 1.664 1.436 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C4' 3DR J 94 " pdb=" O4' 3DR J 94 " ideal model delta sigma weight residual 1.664 1.441 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C4' 3DR J 93 " pdb=" C3' 3DR J 93 " ideal model delta sigma weight residual 1.336 1.524 -0.188 2.00e-02 2.50e+03 8.88e+01 bond pdb=" C4' 3DR J 94 " pdb=" C3' 3DR J 94 " ideal model delta sigma weight residual 1.336 1.524 -0.188 2.00e-02 2.50e+03 8.88e+01 bond pdb=" O4' 3DR J 93 " pdb=" C1' 3DR J 93 " ideal model delta sigma weight residual 1.309 1.428 -0.119 2.00e-02 2.50e+03 3.56e+01 ... (remaining 41515 not shown) Histogram of bond angle deviations from ideal: 72.32 - 85.68: 14 85.68 - 99.05: 39 99.05 - 112.41: 47819 112.41 - 125.77: 25953 125.77 - 139.13: 1358 Bond angle restraints: 75183 Sorted by residual: angle pdb=" OG1 THR B 81 " pdb=" CB THR B 81 " pdb=" HB THR B 81 " ideal model delta sigma weight residual 109.00 72.53 36.47 3.00e+00 1.11e-01 1.48e+02 angle pdb=" CG2 THR B 81 " pdb=" CB THR B 81 " pdb=" HB THR B 81 " ideal model delta sigma weight residual 108.00 72.32 35.68 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C SER C 123 " pdb=" CA SER C 123 " pdb=" HA SER C 123 " ideal model delta sigma weight residual 109.00 78.08 30.92 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C GLU C 122 " pdb=" CA GLU C 122 " pdb=" HA GLU C 122 " ideal model delta sigma weight residual 109.00 80.31 28.69 3.00e+00 1.11e-01 9.14e+01 angle pdb=" CA THR B 81 " pdb=" CB THR B 81 " pdb=" HB THR B 81 " ideal model delta sigma weight residual 109.00 80.98 28.02 3.00e+00 1.11e-01 8.72e+01 ... (remaining 75178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.07: 16377 34.07 - 68.14: 1942 68.14 - 102.21: 58 102.21 - 136.28: 0 136.28 - 170.35: 6 Dihedral angle restraints: 18383 sinusoidal: 11872 harmonic: 6511 Sorted by residual: dihedral pdb=" C LYS C 126 " pdb=" N LYS C 126 " pdb=" CA LYS C 126 " pdb=" CB LYS C 126 " ideal model delta harmonic sigma weight residual -122.60 -164.65 42.05 0 2.50e+00 1.60e-01 2.83e+02 dihedral pdb=" N LYS C 126 " pdb=" C LYS C 126 " pdb=" CA LYS C 126 " pdb=" CB LYS C 126 " ideal model delta harmonic sigma weight residual 122.80 164.42 -41.62 0 2.50e+00 1.60e-01 2.77e+02 dihedral pdb=" C SER C 123 " pdb=" N SER C 123 " pdb=" CA SER C 123 " pdb=" CB SER C 123 " ideal model delta harmonic sigma weight residual -122.60 -160.13 37.53 0 2.50e+00 1.60e-01 2.25e+02 ... (remaining 18380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.368: 3568 0.368 - 0.735: 2 0.735 - 1.103: 0 1.103 - 1.470: 1 1.470 - 1.838: 4 Chirality restraints: 3575 Sorted by residual: chirality pdb=" CA LYS C 126 " pdb=" N LYS C 126 " pdb=" C LYS C 126 " pdb=" CB LYS C 126 " both_signs ideal model delta sigma weight residual False 2.51 0.67 1.84 2.00e-01 2.50e+01 8.44e+01 chirality pdb=" CG LEU L 63 " pdb=" CB LEU L 63 " pdb=" CD1 LEU L 63 " pdb=" CD2 LEU L 63 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.66e+01 chirality pdb=" CA SER C 123 " pdb=" N SER C 123 " pdb=" C SER C 123 " pdb=" CB SER C 123 " both_signs ideal model delta sigma weight residual False 2.51 0.90 1.61 2.00e-01 2.50e+01 6.50e+01 ... (remaining 3572 not shown) Planarity restraints: 5131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 62 " -0.023 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C PHE F 62 " 0.081 2.00e-02 2.50e+03 pdb=" O PHE F 62 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU F 63 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 65 " -0.023 2.00e-02 2.50e+03 4.65e-02 2.17e+01 pdb=" C ASN B 65 " 0.081 2.00e-02 2.50e+03 pdb=" O ASN B 65 " -0.030 2.00e-02 2.50e+03 pdb=" N VAL B 66 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 65 " 0.023 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C ASN F 65 " -0.080 2.00e-02 2.50e+03 pdb=" O ASN F 65 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL F 66 " 0.027 2.00e-02 2.50e+03 ... (remaining 5128 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 2045 2.18 - 2.79: 76479 2.79 - 3.39: 110181 3.39 - 4.00: 153335 4.00 - 4.60: 228465 Nonbonded interactions: 570505 Sorted by model distance: nonbonded pdb=" HZ2 LYS K 383 " pdb=" OE2 GLU K 384 " model vdw 1.577 1.850 nonbonded pdb=" O3' DA J 81 " pdb="HH22 ARG A 41 " model vdw 1.600 1.850 nonbonded pdb=" OG1 THR K 118 " pdb="HH22 ARG K 134 " model vdw 1.628 1.850 nonbonded pdb=" O PHE K 67 " pdb=" H LEU K 76 " model vdw 1.629 1.850 nonbonded pdb=" O GLU K 286 " pdb=" H LYS K 298 " model vdw 1.630 1.850 ... (remaining 570500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 39 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH22)) or r \ esid 44 through 136)) } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 22 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or r \ esid 29 through 103)) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 10 through 122 or (resid 123 and (name N or name CA or nam \ e C or name O or name CB or name OG or name H or name HA or name HB2 or name HB3 \ )) or resid 124 through 126)) } ncs_group { reference = chain 'D' selection = (chain 'H' and ((resid 32 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E or name HH11)) or resid 33 through 86 or (resid 87 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE )) or resid 88 through 126)) } ncs_group { reference = (chain 'I' and (resid 1 through 71 or resid 75 through 92 or resid 95 through 14 \ 5)) selection = (chain 'J' and (resid 1 through 71 or resid 75 through 92 or resid 95 through 14 \ 5)) } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.600 Extract box with map and model: 7.910 Check model and map are aligned: 0.550 Set scattering table: 0.370 Process input model: 155.590 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.170 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: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.009 0.228 22501 Z= 0.534 Angle : 1.109 22.829 31656 Z= 0.652 Chirality : 0.085 1.838 3575 Planarity : 0.007 0.083 3041 Dihedral : 23.878 170.347 9207 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.97 % Favored : 94.67 % Rotamer: Outliers : 0.36 % Allowed : 2.91 % Favored : 96.74 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 1952 helix: 0.47 (0.18), residues: 636 sheet: -0.56 (0.23), residues: 461 loop : -1.61 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP K 953 HIS 0.014 0.003 HIS C 32 PHE 0.038 0.004 PHE K 965 TYR 0.029 0.005 TYR D 84 ARG 0.032 0.002 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 638 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 632 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 GLN cc_start: 0.8793 (tt0) cc_final: 0.8566 (tm-30) REVERT: L 214 ARG cc_start: 0.9041 (mtt90) cc_final: 0.8662 (mtp-110) REVERT: L 299 ASP cc_start: 0.9034 (t0) cc_final: 0.8759 (t0) REVERT: L 420 GLN cc_start: 0.9251 (pm20) cc_final: 0.9046 (pm20) REVERT: A 59 THR cc_start: 0.9050 (p) cc_final: 0.8708 (t) REVERT: A 63 ILE cc_start: 0.6968 (mt) cc_final: 0.6764 (mm) REVERT: A 106 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8671 (tm-30) REVERT: A 111 CYS cc_start: 0.9488 (m) cc_final: 0.9150 (m) REVERT: A 121 MET cc_start: 0.7839 (mtp) cc_final: 0.7622 (mtt) REVERT: A 125 ILE cc_start: 0.9591 (mt) cc_final: 0.9123 (mm) REVERT: B 27 ILE cc_start: 0.9526 (tp) cc_final: 0.9273 (tp) REVERT: B 28 GLN cc_start: 0.9342 (mm110) cc_final: 0.8925 (mp10) REVERT: C 40 TYR cc_start: 0.8881 (m-80) cc_final: 0.8677 (m-10) REVERT: D 68 ASN cc_start: 0.8747 (m110) cc_final: 0.8334 (t0) REVERT: D 72 GLU cc_start: 0.8958 (pt0) cc_final: 0.8740 (pt0) REVERT: D 90 ILE cc_start: 0.8744 (tt) cc_final: 0.8230 (tp) REVERT: D 114 GLU cc_start: 0.9481 (mm-30) cc_final: 0.9152 (mm-30) REVERT: D 121 LYS cc_start: 0.9609 (mtpt) cc_final: 0.9118 (tppt) REVERT: E 63 ILE cc_start: 0.8760 (mt) cc_final: 0.8129 (mt) REVERT: E 75 ILE cc_start: 0.9516 (mt) cc_final: 0.9285 (tp) REVERT: E 79 PHE cc_start: 0.8836 (m-80) cc_final: 0.8292 (m-10) REVERT: E 94 GLN cc_start: 0.9600 (tt0) cc_final: 0.8143 (tp40) REVERT: E 98 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8730 (mt-10) REVERT: E 106 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8748 (tm-30) REVERT: E 113 ILE cc_start: 0.9458 (mt) cc_final: 0.9233 (mt) REVERT: F 50 LEU cc_start: 0.9378 (mt) cc_final: 0.9132 (mp) REVERT: F 54 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8903 (mm-30) REVERT: F 65 ASN cc_start: 0.9492 (m-40) cc_final: 0.9283 (m-40) REVERT: F 75 GLU cc_start: 0.9488 (tt0) cc_final: 0.8866 (tp30) REVERT: F 97 THR cc_start: 0.9132 (m) cc_final: 0.8502 (p) REVERT: G 37 LYS cc_start: 0.9436 (mttm) cc_final: 0.8846 (tmtt) REVERT: G 57 GLU cc_start: 0.8121 (tt0) cc_final: 0.7570 (tt0) REVERT: G 60 THR cc_start: 0.9456 (m) cc_final: 0.9255 (p) REVERT: G 101 VAL cc_start: 0.8429 (t) cc_final: 0.8123 (t) REVERT: G 103 ILE cc_start: 0.9495 (mm) cc_final: 0.8979 (tp) REVERT: H 93 ARG cc_start: 0.9322 (mtp-110) cc_final: 0.8928 (tmm-80) REVERT: H 97 THR cc_start: 0.9712 (m) cc_final: 0.9406 (p) REVERT: H 114 GLU cc_start: 0.9283 (mm-30) cc_final: 0.9008 (mm-30) REVERT: K 15 VAL cc_start: 0.7997 (t) cc_final: 0.7745 (p) REVERT: K 930 VAL cc_start: 0.7463 (m) cc_final: 0.6809 (m) REVERT: K 976 VAL cc_start: 0.9705 (t) cc_final: 0.9384 (p) REVERT: K 1070 HIS cc_start: 0.9058 (t-90) cc_final: 0.8358 (t70) REVERT: K 1120 MET cc_start: 0.8578 (mmp) cc_final: 0.7568 (tmm) REVERT: K 1127 ASP cc_start: 0.8861 (m-30) cc_final: 0.8608 (p0) outliers start: 6 outliers final: 3 residues processed: 636 average time/residue: 0.9834 time to fit residues: 872.6306 Evaluate side-chains 495 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 490 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 199 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 91 GLN ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 385 GLN ** L 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN D 68 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 ASN G 90 ASN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN K 319 ASN ** K 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 22501 Z= 0.202 Angle : 0.663 11.807 31656 Z= 0.393 Chirality : 0.057 1.702 3575 Planarity : 0.005 0.070 3041 Dihedral : 27.652 175.988 5404 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.84 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.17 (0.18), residues: 1952 helix: 1.59 (0.20), residues: 639 sheet: -0.48 (0.23), residues: 448 loop : -1.21 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 207 HIS 0.006 0.001 HIS L 345 PHE 0.017 0.002 PHE K 949 TYR 0.018 0.002 TYR H 41 ARG 0.008 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 532 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 GLN cc_start: 0.9117 (tt0) cc_final: 0.8722 (tm-30) REVERT: L 101 TYR cc_start: 0.9343 (m-10) cc_final: 0.9120 (m-80) REVERT: L 348 TYR cc_start: 0.8359 (m-80) cc_final: 0.8040 (m-80) REVERT: L 350 LEU cc_start: 0.8025 (mt) cc_final: 0.7731 (mm) REVERT: A 63 ILE cc_start: 0.7187 (mt) cc_final: 0.6753 (mm) REVERT: A 91 MET cc_start: 0.9446 (mtp) cc_final: 0.9207 (mtp) REVERT: A 106 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8722 (tm-30) REVERT: A 111 CYS cc_start: 0.9485 (m) cc_final: 0.9016 (t) REVERT: A 121 MET cc_start: 0.7953 (mtp) cc_final: 0.7523 (mtt) REVERT: B 65 ASN cc_start: 0.9679 (m-40) cc_final: 0.9472 (m-40) REVERT: B 68 ARG cc_start: 0.9434 (ttm-80) cc_final: 0.9012 (ttm-80) REVERT: C 40 TYR cc_start: 0.8800 (m-80) cc_final: 0.8542 (m-80) REVERT: C 74 ASN cc_start: 0.9571 (t0) cc_final: 0.9254 (t0) REVERT: C 88 ILE cc_start: 0.8878 (mt) cc_final: 0.8311 (tp) REVERT: D 68 ASN cc_start: 0.8673 (m-40) cc_final: 0.8332 (t0) REVERT: D 72 GLU cc_start: 0.8893 (pt0) cc_final: 0.8646 (pt0) REVERT: D 80 ARG cc_start: 0.9043 (mtp85) cc_final: 0.8264 (mtp85) REVERT: D 93 ARG cc_start: 0.9261 (ttp-170) cc_final: 0.9042 (ttp-170) REVERT: D 114 GLU cc_start: 0.9439 (mm-30) cc_final: 0.9133 (mm-30) REVERT: D 121 LYS cc_start: 0.9593 (mtpt) cc_final: 0.9129 (tppt) REVERT: E 63 ILE cc_start: 0.8584 (mt) cc_final: 0.8228 (mm) REVERT: E 79 PHE cc_start: 0.8865 (m-80) cc_final: 0.8447 (m-10) REVERT: E 94 GLN cc_start: 0.9463 (tt0) cc_final: 0.8067 (tp40) REVERT: E 98 GLU cc_start: 0.9363 (mt-10) cc_final: 0.8712 (mt-10) REVERT: E 123 LYS cc_start: 0.9418 (pttt) cc_final: 0.8931 (pttp) REVERT: E 134 GLU cc_start: 0.6863 (tp30) cc_final: 0.6381 (tp30) REVERT: F 54 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8951 (mm-30) REVERT: F 75 GLU cc_start: 0.9495 (tt0) cc_final: 0.8943 (tp30) REVERT: F 97 THR cc_start: 0.9136 (m) cc_final: 0.8572 (p) REVERT: G 37 LYS cc_start: 0.9451 (mttm) cc_final: 0.9097 (tppt) REVERT: G 103 ILE cc_start: 0.9403 (mm) cc_final: 0.8989 (tp) REVERT: H 97 THR cc_start: 0.9638 (m) cc_final: 0.9426 (p) REVERT: H 102 LEU cc_start: 0.9568 (mm) cc_final: 0.9355 (mm) REVERT: H 114 GLU cc_start: 0.9340 (mm-30) cc_final: 0.9039 (mm-30) REVERT: K 112 ILE cc_start: 0.6597 (pt) cc_final: 0.6346 (pt) REVERT: K 300 LEU cc_start: 0.9325 (mt) cc_final: 0.9059 (mt) REVERT: K 927 MET cc_start: 0.7314 (ptm) cc_final: 0.7021 (ppp) REVERT: K 976 VAL cc_start: 0.9586 (t) cc_final: 0.9284 (p) REVERT: K 1070 HIS cc_start: 0.9211 (t-90) cc_final: 0.8227 (t70) REVERT: K 1099 ASP cc_start: 0.8857 (m-30) cc_final: 0.8649 (m-30) REVERT: K 1120 MET cc_start: 0.8981 (mmp) cc_final: 0.8155 (tmm) REVERT: K 1127 ASP cc_start: 0.8781 (m-30) cc_final: 0.8493 (p0) outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.8989 time to fit residues: 680.5681 Evaluate side-chains 460 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 460 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 166 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 216 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 87 GLN ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 845 GLN K 877 ASN ** K 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 964 ASN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1055 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 22501 Z= 0.323 Angle : 0.708 12.557 31656 Z= 0.422 Chirality : 0.060 1.677 3575 Planarity : 0.005 0.066 3041 Dihedral : 27.724 172.954 5404 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.79 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.81 (0.18), residues: 1952 helix: 0.44 (0.19), residues: 648 sheet: -0.46 (0.24), residues: 451 loop : -1.28 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP K1073 HIS 0.006 0.001 HIS G 83 PHE 0.019 0.002 PHE F 101 TYR 0.019 0.002 TYR K 718 ARG 0.009 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 502 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 172 PHE cc_start: 0.7947 (p90) cc_final: 0.7026 (p90) REVERT: L 299 ASP cc_start: 0.9065 (t70) cc_final: 0.8844 (t0) REVERT: L 348 TYR cc_start: 0.8491 (m-80) cc_final: 0.8279 (m-80) REVERT: L 403 MET cc_start: 0.9457 (tpt) cc_final: 0.9122 (tpp) REVERT: A 57 LYS cc_start: 0.9522 (ttpt) cc_final: 0.9207 (tppt) REVERT: A 63 ILE cc_start: 0.7292 (mt) cc_final: 0.7038 (mm) REVERT: A 106 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8797 (tm-30) REVERT: A 124 ASP cc_start: 0.8911 (m-30) cc_final: 0.8260 (m-30) REVERT: C 30 ARG cc_start: 0.8592 (ttm170) cc_final: 0.8325 (ttm110) REVERT: C 40 TYR cc_start: 0.8964 (m-80) cc_final: 0.8649 (m-80) REVERT: C 51 TYR cc_start: 0.8984 (t80) cc_final: 0.8744 (t80) REVERT: C 88 ILE cc_start: 0.9154 (mt) cc_final: 0.8667 (tp) REVERT: D 68 ASN cc_start: 0.9030 (m-40) cc_final: 0.8371 (t0) REVERT: D 72 GLU cc_start: 0.8896 (pt0) cc_final: 0.8632 (pt0) REVERT: D 80 ARG cc_start: 0.9434 (mtp85) cc_final: 0.9124 (mtp85) REVERT: D 114 GLU cc_start: 0.9493 (mm-30) cc_final: 0.9205 (mm-30) REVERT: D 121 LYS cc_start: 0.9622 (mtpt) cc_final: 0.9180 (tppt) REVERT: E 63 ILE cc_start: 0.8764 (mt) cc_final: 0.8324 (mm) REVERT: E 77 GLN cc_start: 0.8918 (tp40) cc_final: 0.8708 (mm110) REVERT: E 94 GLN cc_start: 0.9410 (tt0) cc_final: 0.8187 (tp40) REVERT: E 98 GLU cc_start: 0.9434 (mt-10) cc_final: 0.8826 (mt-10) REVERT: E 123 LYS cc_start: 0.9421 (pttt) cc_final: 0.9096 (pttt) REVERT: E 134 GLU cc_start: 0.7196 (tp30) cc_final: 0.6546 (tp30) REVERT: F 50 LEU cc_start: 0.9363 (mp) cc_final: 0.9131 (mp) REVERT: F 51 ILE cc_start: 0.9649 (mm) cc_final: 0.9448 (mm) REVERT: F 54 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8898 (mm-30) REVERT: F 65 ASN cc_start: 0.9545 (m-40) cc_final: 0.9249 (m110) REVERT: F 75 GLU cc_start: 0.9560 (tt0) cc_final: 0.8977 (tp30) REVERT: G 103 ILE cc_start: 0.9457 (mm) cc_final: 0.9023 (tp) REVERT: H 114 GLU cc_start: 0.9558 (mm-30) cc_final: 0.9232 (mm-30) REVERT: H 117 LYS cc_start: 0.9790 (ttpt) cc_final: 0.9461 (tmtt) REVERT: K 84 TYR cc_start: 0.9112 (m-80) cc_final: 0.8755 (m-80) REVERT: K 130 MET cc_start: 0.7459 (ptp) cc_final: 0.6967 (pmm) REVERT: K 300 LEU cc_start: 0.9326 (mt) cc_final: 0.9069 (mt) REVERT: K 376 VAL cc_start: 0.8506 (t) cc_final: 0.8300 (t) REVERT: K 976 VAL cc_start: 0.9653 (t) cc_final: 0.9381 (p) REVERT: K 1070 HIS cc_start: 0.9280 (t-90) cc_final: 0.8369 (t70) REVERT: K 1120 MET cc_start: 0.9025 (mmp) cc_final: 0.8077 (ppp) REVERT: K 1127 ASP cc_start: 0.8786 (m-30) cc_final: 0.8459 (p0) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.9144 time to fit residues: 653.6529 Evaluate side-chains 433 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 0.2980 chunk 104 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN C 105 GLN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 964 ASN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 22501 Z= 0.218 Angle : 0.636 11.539 31656 Z= 0.379 Chirality : 0.057 1.663 3575 Planarity : 0.005 0.056 3041 Dihedral : 27.779 174.206 5404 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.74 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.18), residues: 1952 helix: 0.56 (0.20), residues: 653 sheet: -0.67 (0.24), residues: 431 loop : -1.16 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 344 HIS 0.005 0.001 HIS C 32 PHE 0.059 0.002 PHE E 68 TYR 0.021 0.001 TYR F 52 ARG 0.007 0.000 ARG L 276 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 491 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 491 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 182 ARG cc_start: 0.8968 (ptt-90) cc_final: 0.8720 (ptt90) REVERT: L 299 ASP cc_start: 0.9047 (t70) cc_final: 0.8842 (t0) REVERT: L 348 TYR cc_start: 0.8698 (m-80) cc_final: 0.8397 (m-80) REVERT: L 403 MET cc_start: 0.9441 (tpt) cc_final: 0.8837 (tpp) REVERT: A 57 LYS cc_start: 0.9513 (ttpt) cc_final: 0.9189 (tppt) REVERT: A 106 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8762 (tm-30) REVERT: B 68 ARG cc_start: 0.9577 (ttm-80) cc_final: 0.9214 (ttm-80) REVERT: C 88 ILE cc_start: 0.9153 (mt) cc_final: 0.8929 (tp) REVERT: C 103 ILE cc_start: 0.9377 (mm) cc_final: 0.9101 (tp) REVERT: C 116 LEU cc_start: 0.9112 (mm) cc_final: 0.8866 (mp) REVERT: D 68 ASN cc_start: 0.9008 (m-40) cc_final: 0.8271 (t0) REVERT: D 72 GLU cc_start: 0.8838 (pt0) cc_final: 0.8566 (pt0) REVERT: D 80 ARG cc_start: 0.9436 (mtp85) cc_final: 0.9109 (mtp85) REVERT: D 87 ARG cc_start: 0.8888 (mmt90) cc_final: 0.8422 (mmm160) REVERT: D 114 GLU cc_start: 0.9462 (mm-30) cc_final: 0.9166 (mm-30) REVERT: D 121 LYS cc_start: 0.9613 (mtpt) cc_final: 0.9162 (tppt) REVERT: E 74 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8656 (mt-10) REVERT: E 77 GLN cc_start: 0.8925 (tp40) cc_final: 0.8659 (mm110) REVERT: E 83 LEU cc_start: 0.8968 (mt) cc_final: 0.8748 (mt) REVERT: E 94 GLN cc_start: 0.9105 (tt0) cc_final: 0.8552 (tp40) REVERT: E 98 GLU cc_start: 0.9356 (mt-10) cc_final: 0.8828 (mt-10) REVERT: E 123 LYS cc_start: 0.9385 (pttt) cc_final: 0.9039 (pttt) REVERT: E 134 GLU cc_start: 0.6984 (tp30) cc_final: 0.6492 (tp30) REVERT: F 50 LEU cc_start: 0.9321 (mp) cc_final: 0.9092 (mp) REVERT: F 54 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8862 (mm-30) REVERT: F 65 ASN cc_start: 0.9567 (m-40) cc_final: 0.9314 (m110) REVERT: F 75 GLU cc_start: 0.9541 (tt0) cc_final: 0.8922 (tp30) REVERT: G 37 LYS cc_start: 0.9299 (tptp) cc_final: 0.9066 (tptp) REVERT: G 103 ILE cc_start: 0.9476 (mm) cc_final: 0.9016 (tp) REVERT: G 116 LEU cc_start: 0.9492 (mt) cc_final: 0.9181 (pp) REVERT: H 114 GLU cc_start: 0.9579 (mm-30) cc_final: 0.9279 (mm-30) REVERT: H 117 LYS cc_start: 0.9776 (ttpt) cc_final: 0.9476 (tmtt) REVERT: K 130 MET cc_start: 0.7415 (ptp) cc_final: 0.6893 (pmm) REVERT: K 300 LEU cc_start: 0.9319 (mt) cc_final: 0.9081 (mt) REVERT: K 1055 GLN cc_start: 0.9155 (mm110) cc_final: 0.8814 (mm110) REVERT: K 1070 HIS cc_start: 0.9107 (t-90) cc_final: 0.8135 (t70) REVERT: K 1120 MET cc_start: 0.9041 (mmp) cc_final: 0.8075 (ppp) REVERT: K 1127 ASP cc_start: 0.8723 (m-30) cc_final: 0.8423 (p0) outliers start: 0 outliers final: 0 residues processed: 491 average time/residue: 0.8915 time to fit residues: 624.2046 Evaluate side-chains 429 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 190 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 964 ASN K 990 GLN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1034 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.129 22501 Z= 0.389 Angle : 0.755 11.869 31656 Z= 0.449 Chirality : 0.063 1.644 3575 Planarity : 0.006 0.057 3041 Dihedral : 28.055 172.665 5404 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 27.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.04 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.71 (0.18), residues: 1952 helix: -0.76 (0.18), residues: 644 sheet: -0.87 (0.25), residues: 418 loop : -1.45 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 270 HIS 0.008 0.002 HIS B 76 PHE 0.026 0.002 PHE K 975 TYR 0.053 0.002 TYR B 52 ARG 0.013 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 462 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 462 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 GLN cc_start: 0.9414 (tt0) cc_final: 0.8868 (tm-30) REVERT: L 172 PHE cc_start: 0.8111 (p90) cc_final: 0.7191 (p90) REVERT: L 311 GLU cc_start: 0.9089 (tp30) cc_final: 0.8879 (tp30) REVERT: L 348 TYR cc_start: 0.8529 (m-10) cc_final: 0.7936 (m-80) REVERT: L 403 MET cc_start: 0.9467 (tpt) cc_final: 0.8842 (tpp) REVERT: A 56 GLN cc_start: 0.9336 (mt0) cc_final: 0.8962 (mm-40) REVERT: A 57 LYS cc_start: 0.9571 (ttpt) cc_final: 0.9304 (tppt) REVERT: A 63 ILE cc_start: 0.7029 (mm) cc_final: 0.6390 (mm) REVERT: A 91 MET cc_start: 0.9634 (mtp) cc_final: 0.9379 (mtp) REVERT: B 68 ARG cc_start: 0.9642 (ttm-80) cc_final: 0.9404 (ttm-80) REVERT: B 89 TYR cc_start: 0.9172 (m-10) cc_final: 0.8819 (m-10) REVERT: D 68 ASN cc_start: 0.8997 (m-40) cc_final: 0.8239 (t0) REVERT: D 72 GLU cc_start: 0.8799 (pt0) cc_final: 0.8555 (pt0) REVERT: D 96 GLN cc_start: 0.9732 (tt0) cc_final: 0.9460 (tt0) REVERT: D 121 LYS cc_start: 0.9660 (mtpt) cc_final: 0.9286 (tppt) REVERT: E 74 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8795 (mt-10) REVERT: E 77 GLN cc_start: 0.9010 (tp40) cc_final: 0.8755 (mm110) REVERT: E 94 GLN cc_start: 0.9489 (tt0) cc_final: 0.8611 (tp-100) REVERT: E 98 GLU cc_start: 0.9469 (mt-10) cc_final: 0.9169 (mt-10) REVERT: E 134 GLU cc_start: 0.7362 (tp30) cc_final: 0.6701 (tp30) REVERT: F 50 LEU cc_start: 0.9374 (mp) cc_final: 0.9138 (mp) REVERT: F 54 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8912 (mm-30) REVERT: G 18 ARG cc_start: 0.8813 (mtt180) cc_final: 0.8438 (mtp180) REVERT: G 103 ILE cc_start: 0.9507 (mm) cc_final: 0.9055 (tp) REVERT: H 58 LYS cc_start: 0.9327 (mtpt) cc_final: 0.8982 (mmmm) REVERT: H 117 LYS cc_start: 0.9822 (ttpt) cc_final: 0.9549 (tmtt) REVERT: K 130 MET cc_start: 0.7586 (ptp) cc_final: 0.7065 (pmm) REVERT: K 300 LEU cc_start: 0.9339 (mt) cc_final: 0.9119 (mt) REVERT: K 944 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8283 (tm-30) REVERT: K 1070 HIS cc_start: 0.9193 (t-90) cc_final: 0.8156 (t70) REVERT: K 1127 ASP cc_start: 0.8858 (m-30) cc_final: 0.8559 (p0) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.8624 time to fit residues: 571.0507 Evaluate side-chains 401 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 212 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 908 ASN K 964 ASN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22501 Z= 0.266 Angle : 0.669 11.609 31656 Z= 0.398 Chirality : 0.059 1.642 3575 Planarity : 0.005 0.057 3041 Dihedral : 28.164 174.673 5404 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.12 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.64 (0.18), residues: 1952 helix: -0.58 (0.19), residues: 647 sheet: -0.96 (0.24), residues: 445 loop : -1.44 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 320 HIS 0.007 0.001 HIS G 32 PHE 0.018 0.002 PHE F 101 TYR 0.026 0.002 TYR B 52 ARG 0.008 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 458 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 458 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 GLN cc_start: 0.9336 (tt0) cc_final: 0.8983 (tm-30) REVERT: L 172 PHE cc_start: 0.8069 (p90) cc_final: 0.7212 (p90) REVERT: L 182 ARG cc_start: 0.8972 (ptt-90) cc_final: 0.8757 (ptt90) REVERT: L 183 LEU cc_start: 0.8487 (tp) cc_final: 0.8275 (mt) REVERT: L 311 GLU cc_start: 0.9064 (tp30) cc_final: 0.8825 (tp30) REVERT: L 348 TYR cc_start: 0.8414 (m-10) cc_final: 0.7749 (m-80) REVERT: L 403 MET cc_start: 0.9428 (tpt) cc_final: 0.8612 (tpp) REVERT: A 56 GLN cc_start: 0.9279 (mt0) cc_final: 0.8864 (mm-40) REVERT: A 57 LYS cc_start: 0.9555 (ttpt) cc_final: 0.9275 (tppt) REVERT: A 63 ILE cc_start: 0.7111 (mm) cc_final: 0.6551 (mm) REVERT: A 91 MET cc_start: 0.9619 (mtp) cc_final: 0.9386 (mtp) REVERT: A 106 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8716 (tm-30) REVERT: B 68 ARG cc_start: 0.9657 (ttm-80) cc_final: 0.9370 (ttm-80) REVERT: B 75 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8560 (mm-30) REVERT: D 68 ASN cc_start: 0.8951 (m-40) cc_final: 0.8139 (t0) REVERT: D 72 GLU cc_start: 0.8764 (pt0) cc_final: 0.8465 (pt0) REVERT: D 121 LYS cc_start: 0.9650 (mtpt) cc_final: 0.9268 (tppt) REVERT: E 56 GLN cc_start: 0.9256 (mt0) cc_final: 0.8838 (mt0) REVERT: E 79 PHE cc_start: 0.9232 (m-80) cc_final: 0.8772 (m-80) REVERT: E 94 GLN cc_start: 0.9447 (tt0) cc_final: 0.8470 (tp40) REVERT: E 134 GLU cc_start: 0.6923 (tp30) cc_final: 0.6557 (tp30) REVERT: F 50 LEU cc_start: 0.9332 (mp) cc_final: 0.9047 (mp) REVERT: F 54 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8879 (mm-30) REVERT: G 18 ARG cc_start: 0.8812 (mtt180) cc_final: 0.8423 (mtp180) REVERT: G 103 ILE cc_start: 0.9515 (mm) cc_final: 0.9001 (tp) REVERT: H 58 LYS cc_start: 0.9299 (mtpt) cc_final: 0.8974 (mmmm) REVERT: H 85 ASN cc_start: 0.9083 (m110) cc_final: 0.8871 (m110) REVERT: H 117 LYS cc_start: 0.9786 (ttpt) cc_final: 0.9576 (tmtt) REVERT: K 130 MET cc_start: 0.7655 (ptp) cc_final: 0.7062 (pmm) REVERT: K 1070 HIS cc_start: 0.9148 (t-90) cc_final: 0.8431 (t70) REVERT: K 1127 ASP cc_start: 0.8850 (m-30) cc_final: 0.8550 (p0) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.9098 time to fit residues: 595.3184 Evaluate side-chains 403 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 91 GLN ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 964 ASN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 22501 Z= 0.275 Angle : 0.672 11.311 31656 Z= 0.401 Chirality : 0.059 1.618 3575 Planarity : 0.005 0.054 3041 Dihedral : 28.243 174.905 5404 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.68 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.72 (0.18), residues: 1952 helix: -0.58 (0.19), residues: 641 sheet: -1.16 (0.24), residues: 460 loop : -1.43 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 256 HIS 0.008 0.001 HIS C 32 PHE 0.032 0.002 PHE K 965 TYR 0.018 0.002 TYR B 52 ARG 0.010 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 455 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 455 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 GLN cc_start: 0.9396 (tt0) cc_final: 0.9080 (tm-30) REVERT: L 172 PHE cc_start: 0.8146 (p90) cc_final: 0.7378 (p90) REVERT: L 182 ARG cc_start: 0.8995 (ptt-90) cc_final: 0.8723 (ptt90) REVERT: L 255 ASP cc_start: 0.8936 (p0) cc_final: 0.8267 (p0) REVERT: L 311 GLU cc_start: 0.9094 (tp30) cc_final: 0.8850 (tp30) REVERT: L 348 TYR cc_start: 0.8445 (m-10) cc_final: 0.7761 (m-80) REVERT: L 403 MET cc_start: 0.9397 (tpt) cc_final: 0.8489 (tpp) REVERT: A 56 GLN cc_start: 0.9289 (mt0) cc_final: 0.9066 (mt0) REVERT: A 57 LYS cc_start: 0.9555 (ttpt) cc_final: 0.9305 (tppt) REVERT: A 63 ILE cc_start: 0.7201 (mm) cc_final: 0.6528 (mm) REVERT: A 91 MET cc_start: 0.9643 (mtp) cc_final: 0.9380 (mtp) REVERT: A 97 CYS cc_start: 0.9539 (m) cc_final: 0.9324 (m) REVERT: A 106 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8763 (tm-30) REVERT: B 52 TYR cc_start: 0.9193 (m-10) cc_final: 0.8991 (m-10) REVERT: D 68 ASN cc_start: 0.8901 (m-40) cc_final: 0.8012 (t0) REVERT: D 72 GLU cc_start: 0.8694 (pt0) cc_final: 0.8370 (pt0) REVERT: D 93 ARG cc_start: 0.9239 (ttp-170) cc_final: 0.8682 (ttp80) REVERT: D 114 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9128 (mm-30) REVERT: D 121 LYS cc_start: 0.9646 (mtpt) cc_final: 0.9246 (tppt) REVERT: E 49 LEU cc_start: 0.9352 (mt) cc_final: 0.8825 (mt) REVERT: E 56 GLN cc_start: 0.9268 (mt0) cc_final: 0.8877 (mt0) REVERT: E 71 LEU cc_start: 0.9591 (tp) cc_final: 0.9286 (mm) REVERT: E 98 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9215 (mt-10) REVERT: E 134 GLU cc_start: 0.7276 (tp30) cc_final: 0.6627 (tp30) REVERT: F 45 LYS cc_start: 0.9197 (tttt) cc_final: 0.8487 (tptm) REVERT: F 50 LEU cc_start: 0.9394 (mp) cc_final: 0.9160 (mp) REVERT: F 52 TYR cc_start: 0.9500 (m-10) cc_final: 0.9216 (m-10) REVERT: F 54 GLU cc_start: 0.9359 (mm-30) cc_final: 0.8957 (mm-30) REVERT: G 103 ILE cc_start: 0.9496 (mm) cc_final: 0.9014 (tp) REVERT: H 58 LYS cc_start: 0.9330 (mtpt) cc_final: 0.9070 (mmtm) REVERT: K 130 MET cc_start: 0.7618 (ptp) cc_final: 0.7050 (pmm) REVERT: K 1055 GLN cc_start: 0.9086 (mm110) cc_final: 0.8576 (mm110) REVERT: K 1058 LEU cc_start: 0.9163 (mt) cc_final: 0.8893 (mt) REVERT: K 1070 HIS cc_start: 0.9080 (t-90) cc_final: 0.8470 (t70) REVERT: K 1127 ASP cc_start: 0.8895 (m-30) cc_final: 0.8618 (p0) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.8547 time to fit residues: 564.5915 Evaluate side-chains 409 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 0.2980 chunk 134 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 192 optimal weight: 30.0000 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 332 GLN K 964 ASN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 22501 Z= 0.317 Angle : 0.701 11.350 31656 Z= 0.417 Chirality : 0.060 1.607 3575 Planarity : 0.006 0.092 3041 Dihedral : 28.370 174.542 5404 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.76 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.02 (0.18), residues: 1952 helix: -0.92 (0.18), residues: 635 sheet: -1.34 (0.24), residues: 457 loop : -1.52 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 344 HIS 0.007 0.002 HIS C 32 PHE 0.027 0.002 PHE F 101 TYR 0.020 0.002 TYR K 853 ARG 0.013 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 447 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 447 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 GLN cc_start: 0.9447 (tt0) cc_final: 0.8947 (tm-30) REVERT: L 172 PHE cc_start: 0.8156 (p90) cc_final: 0.7295 (p90) REVERT: L 182 ARG cc_start: 0.9003 (ptt-90) cc_final: 0.8767 (ptt90) REVERT: L 183 LEU cc_start: 0.8614 (tp) cc_final: 0.8412 (mt) REVERT: L 299 ASP cc_start: 0.8998 (t70) cc_final: 0.8775 (t70) REVERT: L 311 GLU cc_start: 0.9162 (tp30) cc_final: 0.8919 (tp30) REVERT: L 348 TYR cc_start: 0.8596 (m-10) cc_final: 0.7948 (m-10) REVERT: L 403 MET cc_start: 0.9421 (tpt) cc_final: 0.8509 (tpp) REVERT: A 56 GLN cc_start: 0.9269 (mt0) cc_final: 0.9055 (mt0) REVERT: A 57 LYS cc_start: 0.9554 (ttpt) cc_final: 0.9305 (tppt) REVERT: A 63 ILE cc_start: 0.7299 (mm) cc_final: 0.6662 (mm) REVERT: A 91 MET cc_start: 0.9634 (mtp) cc_final: 0.9393 (mtp) REVERT: A 106 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8798 (tm-30) REVERT: B 75 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8666 (mm-30) REVERT: B 80 LYS cc_start: 0.9417 (mmmm) cc_final: 0.9189 (mmmm) REVERT: D 68 ASN cc_start: 0.8913 (m-40) cc_final: 0.7940 (t0) REVERT: D 72 GLU cc_start: 0.8682 (pt0) cc_final: 0.8345 (pt0) REVERT: D 93 ARG cc_start: 0.9290 (ttp-170) cc_final: 0.9040 (ttp80) REVERT: D 114 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9116 (mm-30) REVERT: D 117 LYS cc_start: 0.9615 (ptpp) cc_final: 0.9303 (ptpp) REVERT: D 121 LYS cc_start: 0.9661 (mtpt) cc_final: 0.9265 (tppt) REVERT: E 56 GLN cc_start: 0.9276 (mt0) cc_final: 0.8896 (mt0) REVERT: E 71 LEU cc_start: 0.9607 (tp) cc_final: 0.9278 (mm) REVERT: E 79 PHE cc_start: 0.9341 (m-80) cc_final: 0.8921 (m-80) REVERT: E 98 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9207 (tm-30) REVERT: E 134 GLU cc_start: 0.7427 (tp30) cc_final: 0.6878 (tp30) REVERT: F 50 LEU cc_start: 0.9477 (mp) cc_final: 0.9266 (mp) REVERT: F 52 TYR cc_start: 0.9528 (m-10) cc_final: 0.9270 (m-10) REVERT: F 54 GLU cc_start: 0.9370 (mm-30) cc_final: 0.9005 (mm-30) REVERT: G 18 ARG cc_start: 0.8771 (mtt180) cc_final: 0.8314 (mtp180) REVERT: G 103 ILE cc_start: 0.9531 (mm) cc_final: 0.9041 (tp) REVERT: H 58 LYS cc_start: 0.9349 (mtpt) cc_final: 0.9055 (mmmm) REVERT: K 130 MET cc_start: 0.7688 (ptp) cc_final: 0.7085 (pmm) REVERT: K 1036 MET cc_start: 0.8520 (tmm) cc_final: 0.8299 (tmm) REVERT: K 1127 ASP cc_start: 0.8986 (m-30) cc_final: 0.8720 (p0) outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.8568 time to fit residues: 555.9052 Evaluate side-chains 395 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 9.9990 chunk 185 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 GLN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 964 ASN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 22501 Z= 0.260 Angle : 0.664 11.216 31656 Z= 0.395 Chirality : 0.058 1.616 3575 Planarity : 0.005 0.054 3041 Dihedral : 28.395 175.546 5404 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.30 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.87 (0.18), residues: 1952 helix: -0.71 (0.19), residues: 639 sheet: -1.33 (0.24), residues: 453 loop : -1.46 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 320 HIS 0.006 0.001 HIS G 32 PHE 0.018 0.002 PHE F 101 TYR 0.017 0.002 TYR K 853 ARG 0.011 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 443 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 GLN cc_start: 0.9428 (tt0) cc_final: 0.9037 (tm-30) REVERT: L 172 PHE cc_start: 0.8196 (p90) cc_final: 0.7440 (p90) REVERT: L 182 ARG cc_start: 0.8990 (ptt-90) cc_final: 0.8714 (ptt90) REVERT: L 255 ASP cc_start: 0.7785 (p0) cc_final: 0.7309 (p0) REVERT: L 311 GLU cc_start: 0.9129 (tp30) cc_final: 0.8869 (tp30) REVERT: L 348 TYR cc_start: 0.8505 (m-10) cc_final: 0.7884 (m-10) REVERT: L 403 MET cc_start: 0.9393 (tpt) cc_final: 0.8348 (tpp) REVERT: A 56 GLN cc_start: 0.9270 (mt0) cc_final: 0.9048 (mt0) REVERT: A 57 LYS cc_start: 0.9544 (ttpt) cc_final: 0.9293 (tppt) REVERT: A 63 ILE cc_start: 0.7341 (mm) cc_final: 0.6707 (mm) REVERT: A 91 MET cc_start: 0.9673 (mtp) cc_final: 0.9383 (mtp) REVERT: A 106 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8767 (tm-30) REVERT: A 130 ARG cc_start: 0.9264 (tmt-80) cc_final: 0.8755 (tmt-80) REVERT: B 52 TYR cc_start: 0.9171 (m-10) cc_final: 0.8960 (m-10) REVERT: B 75 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8644 (mm-30) REVERT: B 80 LYS cc_start: 0.9419 (mmmm) cc_final: 0.9186 (mmmm) REVERT: D 68 ASN cc_start: 0.8847 (m-40) cc_final: 0.7947 (t0) REVERT: D 72 GLU cc_start: 0.8681 (pt0) cc_final: 0.8358 (pt0) REVERT: D 93 ARG cc_start: 0.9263 (ttp-170) cc_final: 0.8881 (ttp80) REVERT: D 114 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9159 (mm-30) REVERT: E 46 THR cc_start: 0.9055 (m) cc_final: 0.8761 (p) REVERT: E 56 GLN cc_start: 0.9233 (mt0) cc_final: 0.8893 (mt0) REVERT: E 71 LEU cc_start: 0.9605 (tp) cc_final: 0.9307 (mm) REVERT: E 94 GLN cc_start: 0.9440 (tt0) cc_final: 0.8715 (tp40) REVERT: E 98 GLU cc_start: 0.9455 (mt-10) cc_final: 0.9132 (tm-30) REVERT: E 134 GLU cc_start: 0.7403 (tp30) cc_final: 0.6834 (tp30) REVERT: F 50 LEU cc_start: 0.9473 (mp) cc_final: 0.9260 (mp) REVERT: F 52 TYR cc_start: 0.9518 (m-10) cc_final: 0.9252 (m-10) REVERT: F 54 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8992 (mm-30) REVERT: G 18 ARG cc_start: 0.8775 (mtt180) cc_final: 0.8296 (mtp180) REVERT: H 58 LYS cc_start: 0.9335 (mtpt) cc_final: 0.9096 (mmtm) REVERT: H 114 GLU cc_start: 0.9631 (mm-30) cc_final: 0.9417 (mm-30) REVERT: H 117 LYS cc_start: 0.9836 (ttpt) cc_final: 0.9542 (tmtt) REVERT: K 130 MET cc_start: 0.7646 (ptp) cc_final: 0.7093 (pmm) REVERT: K 1036 MET cc_start: 0.8504 (tmm) cc_final: 0.8277 (tmm) REVERT: K 1127 ASP cc_start: 0.8922 (m-30) cc_final: 0.8666 (p0) outliers start: 0 outliers final: 0 residues processed: 443 average time/residue: 0.8563 time to fit residues: 550.3214 Evaluate side-chains 397 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 145 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 87 GLN ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.6689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 22501 Z= 0.353 Angle : 0.732 12.256 31656 Z= 0.434 Chirality : 0.061 1.575 3575 Planarity : 0.006 0.067 3041 Dihedral : 28.555 174.639 5404 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 29.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.04 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.26 (0.18), residues: 1952 helix: -1.14 (0.18), residues: 629 sheet: -1.56 (0.24), residues: 436 loop : -1.61 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 203 HIS 0.008 0.002 HIS G 32 PHE 0.030 0.002 PHE F 101 TYR 0.022 0.002 TYR C 40 ARG 0.013 0.001 ARG E 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 435 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 GLN cc_start: 0.9442 (tt0) cc_final: 0.9020 (tm-30) REVERT: L 172 PHE cc_start: 0.8217 (p90) cc_final: 0.7214 (p90) REVERT: L 255 ASP cc_start: 0.7723 (p0) cc_final: 0.7053 (p0) REVERT: L 311 GLU cc_start: 0.9171 (tp30) cc_final: 0.8941 (tp30) REVERT: L 348 TYR cc_start: 0.8528 (m-10) cc_final: 0.7936 (m-10) REVERT: L 403 MET cc_start: 0.9395 (tpt) cc_final: 0.8402 (tpp) REVERT: A 56 GLN cc_start: 0.9269 (mt0) cc_final: 0.8914 (mm-40) REVERT: A 63 ILE cc_start: 0.7552 (mm) cc_final: 0.6849 (mm) REVERT: A 91 MET cc_start: 0.9673 (mtp) cc_final: 0.9385 (mtp) REVERT: A 106 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8809 (tm-30) REVERT: B 35 ILE cc_start: 0.9735 (mm) cc_final: 0.9451 (tt) REVERT: B 52 TYR cc_start: 0.9189 (m-10) cc_final: 0.8964 (m-10) REVERT: B 80 LYS cc_start: 0.9466 (mmmm) cc_final: 0.9235 (mmmm) REVERT: D 68 ASN cc_start: 0.8808 (m-40) cc_final: 0.8132 (t0) REVERT: D 72 GLU cc_start: 0.8686 (pt0) cc_final: 0.8470 (pt0) REVERT: D 93 ARG cc_start: 0.9305 (ttp-170) cc_final: 0.8926 (ttt180) REVERT: D 114 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9171 (mm-30) REVERT: D 121 LYS cc_start: 0.9653 (mtpt) cc_final: 0.9270 (tppt) REVERT: E 46 THR cc_start: 0.9091 (m) cc_final: 0.8809 (p) REVERT: E 71 LEU cc_start: 0.9649 (tp) cc_final: 0.9309 (mm) REVERT: E 79 PHE cc_start: 0.9408 (m-80) cc_final: 0.8988 (m-80) REVERT: E 94 GLN cc_start: 0.9437 (tt0) cc_final: 0.8625 (tp40) REVERT: E 98 GLU cc_start: 0.9432 (mt-10) cc_final: 0.9100 (tm-30) REVERT: E 134 GLU cc_start: 0.7588 (tp30) cc_final: 0.7038 (tp30) REVERT: F 50 LEU cc_start: 0.9509 (mp) cc_final: 0.9282 (mp) REVERT: F 54 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9045 (mm-30) REVERT: G 18 ARG cc_start: 0.8821 (mtt180) cc_final: 0.8260 (mtp180) REVERT: G 42 GLU cc_start: 0.8927 (mp0) cc_final: 0.8727 (mp0) REVERT: H 58 LYS cc_start: 0.9384 (mtpt) cc_final: 0.9124 (mmmm) REVERT: H 85 ASN cc_start: 0.9062 (m110) cc_final: 0.8846 (m110) REVERT: H 117 LYS cc_start: 0.9835 (ttpt) cc_final: 0.9587 (tmtt) REVERT: K 376 VAL cc_start: 0.8691 (t) cc_final: 0.8324 (p) REVERT: K 1036 MET cc_start: 0.8570 (tmm) cc_final: 0.8296 (tmm) REVERT: K 1127 ASP cc_start: 0.9021 (m-30) cc_final: 0.8774 (p0) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.8421 time to fit residues: 536.9562 Evaluate side-chains 394 residues out of total 1689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 991 HIS ** 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 = 0.3264 r_free = 0.3264 target = 0.058909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.041656 restraints weight = 288969.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.044881 restraints weight = 123837.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046993 restraints weight = 67034.086| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.6781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22501 Z= 0.267 Angle : 0.677 11.202 31656 Z= 0.401 Chirality : 0.058 1.589 3575 Planarity : 0.005 0.055 3041 Dihedral : 28.580 175.664 5404 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.56 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.09 (0.18), residues: 1952 helix: -0.83 (0.19), residues: 639 sheet: -1.55 (0.23), residues: 456 loop : -1.59 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 344 HIS 0.008 0.001 HIS C 32 PHE 0.021 0.002 PHE F 101 TYR 0.021 0.002 TYR F 99 ARG 0.011 0.001 ARG E 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11948.35 seconds wall clock time: 211 minutes 45.88 seconds (12705.88 seconds total)