Starting phenix.real_space_refine on Sat Feb 24 01:13:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/02_2024/6r8z_4763_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/02_2024/6r8z_4763.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/02_2024/6r8z_4763_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/02_2024/6r8z_4763_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/02_2024/6r8z_4763_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/02_2024/6r8z_4763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/02_2024/6r8z_4763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/02_2024/6r8z_4763_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/02_2024/6r8z_4763_trim_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 12746 2.51 5 N 3909 2.21 5 O 4608 1.98 5 H 19198 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 78": "OD1" <-> "OD2" Residue "A ASP 82": "OD1" <-> "OD2" Residue "A ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ASP 82": "OD1" <-> "OD2" Residue "E ASP 107": "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 GLU 122": "OE1" <-> "OE2" Residue "H ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 52": "OD1" <-> "OD2" Residue "K TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K GLU 40": "OE1" <-> "OE2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "K GLU 65": "OE1" <-> "OE2" Residue "K ASP 75": "OD1" <-> "OD2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 96": "OE1" <-> "OE2" Residue "K ASP 99": "OD1" <-> "OD2" Residue "K ASP 110": "OD1" <-> "OD2" Residue "K GLU 127": "OE1" <-> "OE2" Residue "K ASP 137": "OD1" <-> "OD2" Residue "K ASP 146": "OD1" <-> "OD2" Residue "K GLU 160": "OE1" <-> "OE2" Residue "K ASP 166": "OD1" <-> "OD2" Residue "K GLU 199": "OE1" <-> "OE2" Residue "K GLU 213": "OE1" <-> "OE2" Residue "K GLU 224": "OE1" <-> "OE2" Residue "K ASP 243": "OD1" <-> "OD2" Residue "K ASP 275": "OD1" <-> "OD2" Residue "K GLU 277": "OE1" <-> "OE2" Residue "K PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 289": "OE1" <-> "OE2" Residue "K ASP 299": "OD1" <-> "OD2" Residue "K GLU 312": "OE1" <-> "OE2" Residue "K ASP 330": "OD1" <-> "OD2" Residue "K ASP 339": "OD1" <-> "OD2" Residue "K ASP 361": "OD1" <-> "OD2" Residue "K GLU 719": "OE1" <-> "OE2" Residue "K PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 784": "OE1" <-> "OE2" Residue "K PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 925": "OD1" <-> "OD2" Residue "K ASP 948": "OD1" <-> "OD2" Residue "K PHE 949": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 969": "OE1" <-> "OE2" Residue "K ASP 986": "OD1" <-> "OD2" Residue "K GLU 987": "OE1" <-> "OE2" Residue "K GLU 994": "OE1" <-> "OE2" Residue "K GLU 1019": "OE1" <-> "OE2" Residue "K GLU 1045": "OE1" <-> "OE2" Residue "K ASP 1053": "OD1" <-> "OD2" Residue "K PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 1092": "OD1" <-> "OD2" Residue "K GLU 1107": "OE1" <-> "OE2" Residue "K TYR 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 1115": "OD1" <-> "OD2" Residue "K ASP 1127": "OD1" <-> "OD2" Residue "K GLU 1134": "OE1" <-> "OE2" Residue "L PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 145": "OD1" <-> "OD2" 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 ASP 185": "OD1" <-> "OD2" Residue "L PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 255": "OD1" <-> "OD2" 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 TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 368": "OE1" <-> "OE2" Residue "L ASP 376": "OD1" <-> "OD2" Residue "L TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 426": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40815 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1708 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1434 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" 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: "D" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1559 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1708 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} 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: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1560 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} 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: "K" Number of atoms: 12900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 12900 Classifications: {'peptide': 825} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 797} Chain breaks: 1 Chain: "L" Number of atoms: 5666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 5666 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 340} Time building chain proxies: 18.91, per 1000 atoms: 0.46 Number of scatterers: 40815 At special positions: 0 Unit cell: (136.4, 183.7, 130.9, 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 4608 8.00 N 3909 7.00 C 12746 6.00 H 19198 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: 35.15 Conformation dependent library (CDL) restraints added in 3.7 seconds 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3690 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 23 sheets defined 29.4% alpha, 21.3% beta 141 base pairs and 218 stacking pairs defined. Time for finding SS restraints: 25.17 Creating SS restraints... Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.807A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 115 removed outlier: 3.701A pdb=" N ALA A 115 " --> pdb=" O CYS A 111 " (cutoff:3.500A) 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: 3.828A pdb=" N TYR B 52 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 3.747A 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 21 No H-bonds generated for 'chain 'C' and resid 18 through 21' Processing helix chain 'C' and resid 29 through 36 Processing helix chain 'C' and resid 48 through 74 Processing helix chain 'C' and resid 81 through 89 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 Processing helix chain 'E' and resid 87 through 115 removed outlier: 3.505A pdb=" N ALA E 115 " --> pdb=" O CYS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 131 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 51 through 76 Processing helix chain 'F' and resid 84 through 94 removed outlier: 3.727A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 21 No H-bonds generated for 'chain 'G' and resid 18 through 21' Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 48 through 73 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 85 removed outlier: 3.644A pdb=" N ASN H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'H' and resid 105 through 124 removed outlier: 3.514A pdb=" N SER H 124 " --> pdb=" O THR H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 255 removed outlier: 4.009A pdb=" N GLN K 255 " --> pdb=" O ILE K 252 " (cutoff:3.500A) 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 1061 Processing helix chain 'K' and resid 1070 through 1074 Processing helix chain 'K' and resid 1091 through 1099 removed outlier: 3.854A pdb=" N PHE K1097 " --> pdb=" O LEU K1093 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU K1098 " --> pdb=" O ILE K1094 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP K1099 " --> pdb=" O GLU K1095 " (cutoff:3.500A) Processing helix chain 'K' and resid 1102 through 1109 Processing helix chain 'K' and resid 1126 through 1139 removed outlier: 3.527A pdb=" N ARG K1138 " --> pdb=" O GLU K1134 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE K1139 " --> pdb=" O GLU K1135 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 77 Processing helix chain 'L' and resid 83 through 100 removed outlier: 4.267A pdb=" N SER L 100 " --> pdb=" O HIS L 96 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 1088 through 1090 removed outlier: 6.890A pdb=" N ASN K 4 " --> pdb=" O ILE K1089 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE K1037 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL K1006 " --> pdb=" O GLY K1031 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 17 through 21 removed outlier: 6.374A pdb=" N VAL K 43 " --> pdb=" O PRO K 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 61 through 67 removed outlier: 6.542A pdb=" N LEU K 80 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N MET K 64 " --> pdb=" O PHE K 78 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE K 78 " --> pdb=" O MET K 64 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU K 66 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU K 76 " --> pdb=" O LEU K 66 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN K 85 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU K 90 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N THR K 102 " --> pdb=" O GLU K 90 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS K 92 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE K 100 " --> pdb=" O LYS K 92 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N SER K 94 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 121 through 124 Processing sheet with id= E, first strand: chain 'K' and resid 201 through 204 removed outlier: 3.659A pdb=" N ASP K 166 " --> pdb=" O VAL K 181 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN K 183 " --> pdb=" O VAL K 164 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL K 164 " --> pdb=" O GLN K 183 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 218 through 221 Processing sheet with id= G, first strand: chain 'K' and resid 258 through 263 removed outlier: 6.943A pdb=" N GLY K 274 " --> pdb=" O VAL K 259 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N HIS K 261 " --> pdb=" O LEU K 272 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU K 272 " --> pdb=" O HIS K 261 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG K 263 " --> pdb=" O ARG K 270 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ARG K 270 " --> pdb=" O ARG K 263 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG K 279 " --> pdb=" O ASP K 275 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET K 282 " --> pdb=" O LEU K 304 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU K 304 " --> pdb=" O MET K 282 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU K 284 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL K 302 " --> pdb=" O LEU K 284 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU K 286 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU K 300 " --> pdb=" O GLU K 286 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 287 through 289 Processing sheet with id= I, first strand: chain 'K' and resid 313 through 318 removed outlier: 6.636A pdb=" N VAL K 321 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS K 335 " --> pdb=" O ALA K 349 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA K 349 " --> pdb=" O LYS K 335 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 361 through 365 removed outlier: 3.983A pdb=" N ASP K 361 " --> pdb=" O CYS K 378 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 749 through 751 removed outlier: 6.853A pdb=" N ASP K 795 " --> pdb=" O VAL K 801 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL K 801 " --> pdb=" O ASP K 795 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 811 through 819 removed outlier: 6.666A pdb=" N GLY K 832 " --> pdb=" O LEU K 814 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU K 816 " --> pdb=" O ILE K 830 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE K 830 " --> pdb=" O LEU K 816 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER K 818 " --> pdb=" O TYR K 828 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TYR K 828 " --> pdb=" O SER K 818 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG K 847 " --> pdb=" O THR K 833 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLN K 852 " --> pdb=" O THR K 860 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR K 860 " --> pdb=" O GLN K 852 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER K 854 " --> pdb=" O LEU K 858 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU K 858 " --> pdb=" O SER K 854 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'K' and resid 872 through 876 removed outlier: 3.845A pdb=" N CYS K 903 " --> pdb=" O LEU K 890 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU K 892 " --> pdb=" O THR K 901 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N THR K 901 " --> pdb=" O GLU K 892 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'K' and resid 911 through 917 removed outlier: 6.897A pdb=" N GLY K 924 " --> pdb=" O LEU K 912 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU K 914 " --> pdb=" O LEU K 922 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU K 922 " --> pdb=" O LEU K 914 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR K 916 " --> pdb=" O PHE K 920 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE K 920 " --> pdb=" O THR K 916 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA K 934 " --> pdb=" O GLU K 944 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLU K 944 " --> pdb=" O ALA K 934 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS K 936 " --> pdb=" O PHE K 942 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE K 942 " --> pdb=" O LYS K 936 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 954 through 959 removed outlier: 6.848A pdb=" N ALA K 968 " --> pdb=" O SER K 955 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL K 957 " --> pdb=" O LEU K 966 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU K 966 " --> pdb=" O VAL K 957 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ILE K 959 " --> pdb=" O ASN K 964 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASN K 964 " --> pdb=" O ILE K 959 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN K 973 " --> pdb=" O GLU K 969 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN K 978 " --> pdb=" O GLU K 994 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU K 994 " --> pdb=" O GLN K 978 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'K' and resid 720 through 727 removed outlier: 6.626A pdb=" N LEU K 736 " --> pdb=" O ARG K 722 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE K 724 " --> pdb=" O GLY K 734 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY K 734 " --> pdb=" O ILE K 724 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TYR K 726 " --> pdb=" O CYS K 732 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N CYS K 732 " --> pdb=" O TYR K 726 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= R, first strand: chain 'L' and resid 148 through 150 Processing sheet with id= S, first strand: chain 'L' and resid 171 through 174 removed outlier: 6.680A pdb=" N ASP L 185 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE L 190 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 226 through 229 Processing sheet with id= U, first strand: chain 'L' and resid 248 through 250 Processing sheet with id= V, first strand: chain 'L' and resid 312 through 316 Processing sheet with id= W, first strand: chain 'L' and resid 350 through 354 removed outlier: 5.737A pdb=" N ASP L 376 " --> pdb=" O MET L 382 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET L 382 " --> pdb=" O ASP L 376 " (cutoff:3.500A) 639 hydrogen bonds defined for protein. 1725 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 339 hydrogen bonds 678 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 218 stacking parallelities Total time for adding SS restraints: 19.92 Time building geometry restraints manager: 36.40 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: 19172 1.03 - 1.22: 183 1.22 - 1.42: 9843 1.42 - 1.62: 12510 1.62 - 1.82: 108 Bond restraints: 41816 Sorted by residual: bond pdb=" C4' 3DR J 95 " pdb=" O4' 3DR J 95 " ideal model delta sigma weight residual 1.664 1.437 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C4' 3DR J 96 " pdb=" O4' 3DR J 96 " ideal model delta sigma weight residual 1.664 1.439 0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C4' 3DR J 95 " pdb=" C3' 3DR J 95 " ideal model delta sigma weight residual 1.336 1.533 -0.197 2.00e-02 2.50e+03 9.74e+01 bond pdb=" C4' 3DR J 96 " pdb=" C3' 3DR J 96 " ideal model delta sigma weight residual 1.336 1.530 -0.194 2.00e-02 2.50e+03 9.41e+01 bond pdb=" C2' 3DR J 95 " pdb=" C1' 3DR J 95 " ideal model delta sigma weight residual 1.600 1.473 0.127 2.00e-02 2.50e+03 4.04e+01 ... (remaining 41811 not shown) Histogram of bond angle deviations from ideal: 73.77 - 85.88: 3 85.88 - 98.00: 3 98.00 - 110.11: 36251 110.11 - 122.22: 32339 122.22 - 134.33: 7119 Bond angle restraints: 75715 Sorted by residual: angle pdb=" CB SER L 68 " pdb=" CA SER L 68 " pdb=" HA SER L 68 " ideal model delta sigma weight residual 109.00 73.77 35.23 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C SER L 68 " pdb=" CA SER L 68 " pdb=" HA SER L 68 " ideal model delta sigma weight residual 109.00 74.33 34.67 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N SER L 68 " pdb=" CA SER L 68 " pdb=" HA SER L 68 " ideal model delta sigma weight residual 110.00 82.76 27.24 3.00e+00 1.11e-01 8.24e+01 angle pdb=" C SER L 68 " pdb=" N ILE L 69 " pdb=" CA ILE L 69 " ideal model delta sigma weight residual 121.97 131.60 -9.63 1.80e+00 3.09e-01 2.87e+01 angle pdb=" N ILE K 884 " pdb=" CA ILE K 884 " pdb=" C ILE K 884 " ideal model delta sigma weight residual 108.99 101.39 7.60 1.56e+00 4.11e-01 2.37e+01 ... (remaining 75710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 16608 35.09 - 70.19: 1855 70.19 - 105.28: 45 105.28 - 140.38: 0 140.38 - 175.47: 2 Dihedral angle restraints: 18510 sinusoidal: 11967 harmonic: 6543 Sorted by residual: dihedral pdb=" CA ARG K 928 " pdb=" C ARG K 928 " pdb=" N SER K 929 " pdb=" CA SER K 929 " ideal model delta harmonic sigma weight residual -180.00 -133.27 -46.73 0 5.00e+00 4.00e-02 8.74e+01 dihedral pdb=" CA LYS B 21 " pdb=" C LYS B 21 " pdb=" N VAL B 22 " pdb=" CA VAL B 22 " ideal model delta harmonic sigma weight residual -180.00 -136.85 -43.15 0 5.00e+00 4.00e-02 7.45e+01 dihedral pdb=" CA LEU B 23 " pdb=" C LEU B 23 " pdb=" N ARG B 24 " pdb=" CA ARG B 24 " ideal model delta harmonic sigma weight residual 180.00 144.22 35.78 0 5.00e+00 4.00e-02 5.12e+01 ... (remaining 18507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 3433 0.116 - 0.231: 150 0.231 - 0.347: 2 0.347 - 0.462: 0 0.462 - 0.578: 1 Chirality restraints: 3586 Sorted by residual: chirality pdb=" CA SER L 68 " pdb=" N SER L 68 " pdb=" C SER L 68 " pdb=" CB SER L 68 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.35e+00 chirality pdb=" CB ILE L 69 " pdb=" CA ILE L 69 " pdb=" CG1 ILE L 69 " pdb=" CG2 ILE L 69 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C3' DC I 50 " pdb=" C4' DC I 50 " pdb=" O3' DC I 50 " pdb=" C2' DC I 50 " both_signs ideal model delta sigma weight residual False -2.66 -2.43 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 3583 not shown) Planarity restraints: 5162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 382 " -0.028 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C PHE K 382 " 0.094 2.00e-02 2.50e+03 pdb=" O PHE K 382 " -0.034 2.00e-02 2.50e+03 pdb=" N LYS K 383 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 381 " 0.026 2.00e-02 2.50e+03 5.25e-02 2.75e+01 pdb=" C ALA K 381 " -0.091 2.00e-02 2.50e+03 pdb=" O ALA K 381 " 0.034 2.00e-02 2.50e+03 pdb=" N PHE K 382 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS L 146 " 0.061 5.00e-02 4.00e+02 9.24e-02 1.37e+01 pdb=" N PRO L 147 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO L 147 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO L 147 " 0.050 5.00e-02 4.00e+02 ... (remaining 5159 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 3086 2.21 - 2.81: 81293 2.81 - 3.41: 102266 3.41 - 4.00: 145520 4.00 - 4.60: 215998 Nonbonded interactions: 548163 Sorted by model distance: nonbonded pdb=" H LYS K 335 " pdb=" O VAL K 348 " model vdw 1.616 1.850 nonbonded pdb=" H TYR K1114 " pdb=" O ARG K1122 " model vdw 1.626 1.850 nonbonded pdb=" O PHE K 67 " pdb=" H LEU K 76 " model vdw 1.632 1.850 nonbonded pdb=" HG1 THR L 371 " pdb=" O LEU L 386 " model vdw 1.634 1.850 nonbonded pdb=" OD1 ASN K 36 " pdb=" HZ2 LYS K 60 " model vdw 1.635 1.850 ... (remaining 548158 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' } ncs_group { reference = (chain 'B' and ((resid 22 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 23 through 103)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 30 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB o \ r name HG21 or name HG22 or name HG23)) or resid 90 through 126)) } ncs_group { reference = (chain 'I' and (resid 1 through 71 or resid 75 through 94 or resid 97 through 14 \ 5)) selection = (chain 'J' and (resid 1 through 71 or resid 75 through 94 or resid 97 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: 1.060 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: 0.540 Extract box with map and model: 6.950 Check model and map are aligned: 0.580 Set scattering table: 0.340 Process input model: 151.940 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 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 : 0.012 0.227 22618 Z= 0.732 Angle : 0.939 12.510 31802 Z= 0.549 Chirality : 0.056 0.578 3586 Planarity : 0.007 0.092 3059 Dihedral : 22.887 175.472 9275 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.64 % Favored : 95.01 % Rotamer: Outliers : 0.18 % Allowed : 3.35 % Favored : 96.47 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.37 (0.17), residues: 1962 helix: 0.53 (0.19), residues: 616 sheet: -0.68 (0.23), residues: 451 loop : -2.09 (0.17), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP K 207 HIS 0.014 0.002 HIS L 333 PHE 0.023 0.003 PHE K 382 TYR 0.030 0.003 TYR G 51 ARG 0.011 0.001 ARG L 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 445 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 442 time to evaluate : 2.688 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: A 58 SER cc_start: 0.9013 (t) cc_final: 0.8695 (m) REVERT: B 80 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7706 (mttm) REVERT: C 57 GLU cc_start: 0.7632 (tt0) cc_final: 0.7416 (tm-30) REVERT: D 35 LYS cc_start: 0.8602 (tppt) cc_final: 0.8341 (tptm) REVERT: D 121 LYS cc_start: 0.8986 (tttm) cc_final: 0.8753 (ttpp) REVERT: E 56 GLN cc_start: 0.8385 (mt0) cc_final: 0.7885 (mt0) REVERT: E 121 MET cc_start: 0.7994 (mtp) cc_final: 0.7711 (mtp) REVERT: F 45 LYS cc_start: 0.7824 (tttt) cc_final: 0.7591 (tttp) REVERT: H 44 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7540 (ttmm) REVERT: K 6 VAL cc_start: 0.8274 (t) cc_final: 0.7965 (m) REVERT: K 15 VAL cc_start: 0.8567 (t) cc_final: 0.8298 (t) REVERT: K 215 GLU cc_start: 0.8747 (tp30) cc_final: 0.7873 (tm-30) REVERT: K 271 TYR cc_start: 0.7223 (m-80) cc_final: 0.6382 (m-80) REVERT: K 277 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7653 (tt0) REVERT: K 933 LEU cc_start: 0.7622 (mt) cc_final: 0.7273 (tt) REVERT: K 1072 PHE cc_start: 0.7404 (t80) cc_final: 0.6971 (t80) REVERT: L 88 GLN cc_start: 0.7882 (tp40) cc_final: 0.7499 (tm-30) REVERT: L 243 LYS cc_start: 0.8716 (mttt) cc_final: 0.8403 (mttm) REVERT: L 356 TYR cc_start: 0.8778 (t80) cc_final: 0.8473 (t80) outliers start: 3 outliers final: 1 residues processed: 445 average time/residue: 1.0018 time to fit residues: 621.1171 Evaluate side-chains 317 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 421 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN K 93 GLN ** K 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 990 GLN K1059 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22618 Z= 0.213 Angle : 0.647 6.385 31802 Z= 0.381 Chirality : 0.042 0.437 3586 Planarity : 0.005 0.081 3059 Dihedral : 26.144 174.060 5428 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.54 % Favored : 95.21 % Rotamer: Outliers : 1.47 % Allowed : 9.71 % Favored : 88.82 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.52 (0.18), residues: 1962 helix: 1.56 (0.20), residues: 615 sheet: -0.33 (0.23), residues: 454 loop : -1.76 (0.18), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 418 HIS 0.015 0.001 HIS L 96 PHE 0.017 0.001 PHE K 965 TYR 0.017 0.002 TYR H 84 ARG 0.004 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 365 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 340 time to evaluate : 2.714 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: A 58 SER cc_start: 0.8873 (t) cc_final: 0.8599 (m) REVERT: B 80 LYS cc_start: 0.8037 (mtpp) cc_final: 0.7793 (mttp) REVERT: B 89 TYR cc_start: 0.7939 (m-80) cc_final: 0.7513 (m-80) REVERT: C 57 GLU cc_start: 0.7473 (tt0) cc_final: 0.7205 (tm-30) REVERT: D 121 LYS cc_start: 0.9000 (tttm) cc_final: 0.8774 (ttpp) REVERT: E 56 GLN cc_start: 0.8361 (mt0) cc_final: 0.7881 (mt0) REVERT: E 121 MET cc_start: 0.8228 (mtp) cc_final: 0.8024 (mtp) REVERT: G 20 SER cc_start: 0.8211 (m) cc_final: 0.7463 (t) REVERT: G 51 TYR cc_start: 0.8644 (t80) cc_final: 0.8136 (t80) REVERT: H 37 SER cc_start: 0.8204 (t) cc_final: 0.7719 (m) REVERT: H 84 TYR cc_start: 0.7833 (m-80) cc_final: 0.7547 (m-80) REVERT: K 6 VAL cc_start: 0.8340 (t) cc_final: 0.8046 (m) REVERT: K 36 ASN cc_start: 0.8326 (p0) cc_final: 0.8084 (p0) REVERT: K 215 GLU cc_start: 0.8760 (tp30) cc_final: 0.7858 (tm-30) REVERT: K 271 TYR cc_start: 0.7296 (m-80) cc_final: 0.6532 (m-80) REVERT: K 277 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7604 (tt0) REVERT: K 285 LEU cc_start: 0.8138 (mp) cc_final: 0.7840 (mp) REVERT: K 814 LEU cc_start: 0.9150 (mt) cc_final: 0.8946 (mt) REVERT: K 933 LEU cc_start: 0.7644 (mt) cc_final: 0.7292 (tt) REVERT: K 938 MET cc_start: 0.6644 (tpt) cc_final: 0.6369 (tmm) REVERT: K 1072 PHE cc_start: 0.7224 (t80) cc_final: 0.6928 (t80) REVERT: L 88 GLN cc_start: 0.7795 (tp40) cc_final: 0.7456 (tm-30) REVERT: L 172 PHE cc_start: 0.6013 (p90) cc_final: 0.5401 (p90) REVERT: L 184 GLN cc_start: 0.7124 (tt0) cc_final: 0.6913 (tt0) REVERT: L 221 ASN cc_start: 0.7240 (p0) cc_final: 0.6950 (p0) REVERT: L 356 TYR cc_start: 0.8716 (t80) cc_final: 0.8461 (t80) outliers start: 25 outliers final: 20 residues processed: 352 average time/residue: 0.9358 time to fit residues: 463.0090 Evaluate side-chains 335 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 315 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 382 PHE Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain K residue 1037 ILE Chi-restraints excluded: chain L residue 170 ASN Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 318 SER Chi-restraints excluded: chain L residue 398 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 167 optimal weight: 0.5980 chunk 137 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 162 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 ASN K 727 GLN ** K 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 22618 Z= 0.277 Angle : 0.666 6.527 31802 Z= 0.390 Chirality : 0.044 0.420 3586 Planarity : 0.005 0.062 3059 Dihedral : 25.981 172.416 5425 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.86 % Favored : 93.93 % Rotamer: Outliers : 1.82 % Allowed : 11.01 % Favored : 87.17 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.46 (0.18), residues: 1962 helix: 1.48 (0.21), residues: 618 sheet: -0.31 (0.24), residues: 464 loop : -1.63 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 418 HIS 0.008 0.001 HIS K1070 PHE 0.018 0.002 PHE L 141 TYR 0.020 0.002 TYR K 891 ARG 0.005 0.001 ARG K 889 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 376 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 345 time to evaluate : 2.903 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: A 58 SER cc_start: 0.9001 (t) cc_final: 0.8694 (m) REVERT: A 60 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6799 (tm-30) REVERT: A 98 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6388 (mm-30) REVERT: B 80 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7893 (mttp) REVERT: B 85 MET cc_start: 0.7710 (mmm) cc_final: 0.7233 (tpp) REVERT: B 89 TYR cc_start: 0.8213 (m-80) cc_final: 0.7782 (m-80) REVERT: C 37 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7624 (mtmt) REVERT: C 57 GLU cc_start: 0.7743 (tt0) cc_final: 0.6904 (tt0) REVERT: E 56 GLN cc_start: 0.8459 (mt0) cc_final: 0.7916 (mt0) REVERT: E 74 GLU cc_start: 0.7605 (tp30) cc_final: 0.7311 (tp30) REVERT: F 80 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7616 (mtmt) REVERT: G 20 SER cc_start: 0.8258 (m) cc_final: 0.7573 (t) REVERT: G 51 TYR cc_start: 0.8892 (t80) cc_final: 0.8059 (t80) REVERT: H 44 LYS cc_start: 0.8077 (mtpt) cc_final: 0.7813 (ttmm) REVERT: K 6 VAL cc_start: 0.8535 (t) cc_final: 0.8258 (m) REVERT: K 36 ASN cc_start: 0.8169 (p0) cc_final: 0.7931 (p0) REVERT: K 54 GLU cc_start: 0.6449 (pm20) cc_final: 0.6134 (pm20) REVERT: K 148 ASP cc_start: 0.8105 (m-30) cc_final: 0.7788 (t0) REVERT: K 165 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7785 (tt) REVERT: K 215 GLU cc_start: 0.8832 (tp30) cc_final: 0.7548 (tm-30) REVERT: K 271 TYR cc_start: 0.7450 (m-80) cc_final: 0.6569 (m-80) REVERT: K 938 MET cc_start: 0.6576 (tpt) cc_final: 0.6264 (tmm) REVERT: K 1072 PHE cc_start: 0.7201 (t80) cc_final: 0.6919 (t80) REVERT: L 221 ASN cc_start: 0.7446 (p0) cc_final: 0.6902 (p0) REVERT: L 356 TYR cc_start: 0.8839 (t80) cc_final: 0.8574 (t80) REVERT: L 403 MET cc_start: 0.8784 (tpt) cc_final: 0.8450 (tpp) REVERT: L 405 ASP cc_start: 0.8664 (p0) cc_final: 0.8221 (p0) outliers start: 31 outliers final: 27 residues processed: 360 average time/residue: 0.9067 time to fit residues: 466.9819 Evaluate side-chains 349 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 320 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 382 PHE Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain K residue 1054 MET Chi-restraints excluded: chain L residue 170 ASN Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 371 THR Chi-restraints excluded: chain L residue 398 ASN Chi-restraints excluded: chain L residue 411 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 105 optimal weight: 0.2980 chunk 192 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22618 Z= 0.219 Angle : 0.620 6.460 31802 Z= 0.365 Chirality : 0.042 0.418 3586 Planarity : 0.004 0.059 3059 Dihedral : 25.904 171.517 5425 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.35 % Favored : 94.44 % Rotamer: Outliers : 1.82 % Allowed : 13.24 % Favored : 84.93 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 1962 helix: 1.59 (0.21), residues: 614 sheet: -0.23 (0.25), residues: 455 loop : -1.58 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 418 HIS 0.008 0.001 HIS L 336 PHE 0.017 0.001 PHE L 172 TYR 0.026 0.001 TYR H 84 ARG 0.006 0.000 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 361 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 330 time to evaluate : 2.796 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: A 58 SER cc_start: 0.8955 (t) cc_final: 0.8688 (m) REVERT: A 62 LEU cc_start: 0.8524 (mt) cc_final: 0.8224 (mp) REVERT: A 74 GLU cc_start: 0.7938 (tt0) cc_final: 0.7340 (tt0) REVERT: B 26 ASN cc_start: 0.6913 (m-40) cc_final: 0.6408 (t0) REVERT: B 80 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7902 (mttp) REVERT: B 85 MET cc_start: 0.7670 (mmm) cc_final: 0.7256 (tpp) REVERT: B 89 TYR cc_start: 0.8183 (m-10) cc_final: 0.7763 (m-80) REVERT: C 57 GLU cc_start: 0.7636 (tt0) cc_final: 0.7258 (tm-30) REVERT: E 56 GLN cc_start: 0.8299 (mt0) cc_final: 0.7865 (mt0) REVERT: F 93 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6813 (ttp80) REVERT: G 20 SER cc_start: 0.8341 (m) cc_final: 0.7700 (t) REVERT: G 51 TYR cc_start: 0.8884 (t80) cc_final: 0.7995 (t80) REVERT: H 44 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7862 (ttmm) REVERT: K 6 VAL cc_start: 0.8467 (t) cc_final: 0.8166 (m) REVERT: K 36 ASN cc_start: 0.8056 (p0) cc_final: 0.7849 (p0) REVERT: K 148 ASP cc_start: 0.8033 (m-30) cc_final: 0.7489 (p0) REVERT: K 215 GLU cc_start: 0.8630 (tp30) cc_final: 0.7450 (tm-30) REVERT: K 271 TYR cc_start: 0.7291 (m-80) cc_final: 0.6282 (m-80) REVERT: K 277 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7634 (tt0) REVERT: K 713 ARG cc_start: 0.7675 (ttt-90) cc_final: 0.7412 (ttt-90) REVERT: K 1072 PHE cc_start: 0.7187 (t80) cc_final: 0.6911 (t80) REVERT: L 177 MET cc_start: 0.4990 (mmm) cc_final: 0.4762 (mmm) REVERT: L 405 ASP cc_start: 0.8580 (p0) cc_final: 0.8148 (p0) outliers start: 31 outliers final: 27 residues processed: 340 average time/residue: 0.8822 time to fit residues: 434.2514 Evaluate side-chains 346 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 318 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain K residue 382 PHE Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 170 ASN Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 371 THR Chi-restraints excluded: chain L residue 398 ASN Chi-restraints excluded: chain L residue 411 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 950 ASN ** K 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 22618 Z= 0.348 Angle : 0.690 6.760 31802 Z= 0.407 Chirality : 0.046 0.411 3586 Planarity : 0.005 0.052 3059 Dihedral : 25.992 171.599 5425 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.63 % Favored : 93.17 % Rotamer: Outliers : 2.35 % Allowed : 13.89 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 1962 helix: 0.83 (0.21), residues: 614 sheet: -0.35 (0.24), residues: 469 loop : -1.67 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 418 HIS 0.013 0.001 HIS L 333 PHE 0.018 0.002 PHE K 323 TYR 0.019 0.002 TYR H 84 ARG 0.006 0.001 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 366 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 326 time to evaluate : 2.551 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: A 58 SER cc_start: 0.9030 (t) cc_final: 0.8745 (m) REVERT: A 62 LEU cc_start: 0.8567 (mt) cc_final: 0.8330 (mp) REVERT: A 98 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6623 (mm-30) REVERT: B 85 MET cc_start: 0.7852 (mmm) cc_final: 0.7473 (tpp) REVERT: C 37 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7655 (mtmt) REVERT: C 115 VAL cc_start: 0.9032 (m) cc_final: 0.8778 (t) REVERT: D 43 TYR cc_start: 0.7908 (t80) cc_final: 0.7293 (t80) REVERT: D 52 ASP cc_start: 0.8093 (m-30) cc_final: 0.7815 (m-30) REVERT: D 109 LYS cc_start: 0.8457 (tmtt) cc_final: 0.8243 (tptp) REVERT: E 56 GLN cc_start: 0.8431 (mt0) cc_final: 0.7936 (mt0) REVERT: E 74 GLU cc_start: 0.7653 (tp30) cc_final: 0.7368 (tp30) REVERT: F 80 LYS cc_start: 0.8011 (mtpp) cc_final: 0.7670 (mtmt) REVERT: F 85 MET cc_start: 0.7066 (mmm) cc_final: 0.6680 (tpt) REVERT: F 93 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6936 (ttp80) REVERT: G 20 SER cc_start: 0.8383 (m) cc_final: 0.7840 (t) REVERT: H 44 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7854 (ttmm) REVERT: K 6 VAL cc_start: 0.8462 (t) cc_final: 0.8182 (m) REVERT: K 148 ASP cc_start: 0.8243 (m-30) cc_final: 0.7738 (p0) REVERT: K 215 GLU cc_start: 0.8721 (tp30) cc_final: 0.7934 (tm-30) REVERT: K 271 TYR cc_start: 0.7364 (m-80) cc_final: 0.6281 (m-80) REVERT: K 713 ARG cc_start: 0.7738 (ttt-90) cc_final: 0.7496 (ttt-90) REVERT: K 1036 MET cc_start: 0.7091 (tmm) cc_final: 0.6860 (tmm) REVERT: K 1072 PHE cc_start: 0.7316 (t80) cc_final: 0.7104 (t80) REVERT: L 163 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7721 (mmtt) REVERT: L 177 MET cc_start: 0.5266 (mmm) cc_final: 0.4964 (mmm) REVERT: L 331 HIS cc_start: 0.8343 (OUTLIER) cc_final: 0.7976 (p90) REVERT: L 405 ASP cc_start: 0.8687 (p0) cc_final: 0.8204 (p0) outliers start: 40 outliers final: 34 residues processed: 348 average time/residue: 0.9127 time to fit residues: 455.7437 Evaluate side-chains 344 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 307 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 296 THR Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 749 THR Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 985 THR Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 170 ASN Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 398 ASN Chi-restraints excluded: chain L residue 411 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** K 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22618 Z= 0.213 Angle : 0.619 6.145 31802 Z= 0.365 Chirality : 0.042 0.411 3586 Planarity : 0.004 0.099 3059 Dihedral : 25.904 172.735 5425 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.01 % Favored : 93.78 % Rotamer: Outliers : 2.18 % Allowed : 15.01 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.55 (0.19), residues: 1962 helix: 1.24 (0.21), residues: 614 sheet: -0.28 (0.24), residues: 468 loop : -1.59 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 418 HIS 0.005 0.001 HIS F 76 PHE 0.024 0.001 PHE K 67 TYR 0.023 0.001 TYR K 891 ARG 0.006 0.000 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 366 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 329 time to evaluate : 2.691 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: A 58 SER cc_start: 0.8989 (t) cc_final: 0.8708 (m) REVERT: A 130 ARG cc_start: 0.7949 (tpt90) cc_final: 0.7555 (tpm170) REVERT: C 37 LYS cc_start: 0.7706 (mtpt) cc_final: 0.7463 (mtmt) REVERT: C 57 GLU cc_start: 0.7609 (tt0) cc_final: 0.7153 (tm-30) REVERT: C 115 VAL cc_start: 0.8965 (m) cc_final: 0.8704 (t) REVERT: D 43 TYR cc_start: 0.7690 (t80) cc_final: 0.7333 (t80) REVERT: D 52 ASP cc_start: 0.8180 (m-30) cc_final: 0.7915 (m-30) REVERT: E 74 GLU cc_start: 0.7592 (tp30) cc_final: 0.7264 (tp30) REVERT: F 80 LYS cc_start: 0.7967 (mtpp) cc_final: 0.7615 (mtmt) REVERT: F 93 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6968 (ttp80) REVERT: G 20 SER cc_start: 0.8348 (m) cc_final: 0.7778 (t) REVERT: G 51 TYR cc_start: 0.8993 (t80) cc_final: 0.8424 (t80) REVERT: H 44 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7836 (ttmm) REVERT: K 6 VAL cc_start: 0.8454 (t) cc_final: 0.8179 (m) REVERT: K 36 ASN cc_start: 0.8346 (p0) cc_final: 0.7256 (p0) REVERT: K 148 ASP cc_start: 0.8160 (m-30) cc_final: 0.7631 (p0) REVERT: K 215 GLU cc_start: 0.8722 (tp30) cc_final: 0.7933 (tm-30) REVERT: K 271 TYR cc_start: 0.7319 (m-80) cc_final: 0.6208 (m-80) REVERT: K 277 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7658 (tt0) REVERT: K 713 ARG cc_start: 0.7704 (ttt-90) cc_final: 0.7408 (ttt-90) REVERT: K 1034 ASN cc_start: 0.7334 (m-40) cc_final: 0.6923 (t0) REVERT: K 1072 PHE cc_start: 0.7278 (t80) cc_final: 0.7077 (t80) REVERT: L 177 MET cc_start: 0.5366 (mmm) cc_final: 0.5032 (mmm) REVERT: L 184 GLN cc_start: 0.7099 (pt0) cc_final: 0.6663 (pt0) REVERT: L 331 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.7968 (p90) REVERT: L 403 MET cc_start: 0.8931 (tpp) cc_final: 0.8725 (tpp) REVERT: L 405 ASP cc_start: 0.8593 (p0) cc_final: 0.8162 (p0) outliers start: 37 outliers final: 33 residues processed: 346 average time/residue: 0.9020 time to fit residues: 445.2615 Evaluate side-chains 347 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 312 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 296 THR Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 749 THR Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 985 THR Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 170 ASN Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 398 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 121 optimal weight: 0.0170 chunk 180 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 22618 Z= 0.343 Angle : 0.687 8.554 31802 Z= 0.404 Chirality : 0.045 0.408 3586 Planarity : 0.005 0.099 3059 Dihedral : 25.994 173.538 5425 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.46 % Favored : 91.34 % Rotamer: Outliers : 2.71 % Allowed : 15.30 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.18), residues: 1962 helix: 0.69 (0.21), residues: 610 sheet: -0.40 (0.24), residues: 463 loop : -1.73 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 418 HIS 0.011 0.001 HIS L 333 PHE 0.029 0.002 PHE K 67 TYR 0.022 0.002 TYR D 84 ARG 0.006 0.001 ARG E 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 367 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 321 time to evaluate : 2.927 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: A 58 SER cc_start: 0.8987 (t) cc_final: 0.8667 (m) REVERT: A 98 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6971 (mm-30) REVERT: C 115 VAL cc_start: 0.9036 (m) cc_final: 0.8806 (t) REVERT: D 43 TYR cc_start: 0.7949 (t80) cc_final: 0.7287 (t80) REVERT: D 52 ASP cc_start: 0.8217 (m-30) cc_final: 0.7988 (m-30) REVERT: E 74 GLU cc_start: 0.7497 (tp30) cc_final: 0.7268 (tp30) REVERT: F 45 LYS cc_start: 0.7858 (tttp) cc_final: 0.7573 (tppt) REVERT: F 80 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7668 (mtmt) REVERT: F 93 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7148 (ttp80) REVERT: G 20 SER cc_start: 0.8492 (m) cc_final: 0.7946 (t) REVERT: K 6 VAL cc_start: 0.8456 (t) cc_final: 0.8183 (m) REVERT: K 36 ASN cc_start: 0.8386 (p0) cc_final: 0.7259 (p0) REVERT: K 117 GLU cc_start: 0.7586 (tt0) cc_final: 0.7211 (tt0) REVERT: K 148 ASP cc_start: 0.8268 (m-30) cc_final: 0.7777 (p0) REVERT: K 215 GLU cc_start: 0.8704 (tp30) cc_final: 0.7856 (tm-30) REVERT: K 218 MET cc_start: 0.7899 (mpp) cc_final: 0.7050 (mpp) REVERT: K 713 ARG cc_start: 0.7727 (ttt-90) cc_final: 0.7329 (ttt-90) REVERT: K 987 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7291 (tm-30) REVERT: K 1014 MET cc_start: 0.4929 (mtt) cc_final: 0.4286 (mmt) REVERT: K 1034 ASN cc_start: 0.7258 (m-40) cc_final: 0.6802 (t0) REVERT: K 1068 ILE cc_start: 0.8676 (mt) cc_final: 0.8401 (tp) REVERT: K 1070 HIS cc_start: 0.8375 (t70) cc_final: 0.7703 (t70) REVERT: L 177 MET cc_start: 0.5715 (mmm) cc_final: 0.5433 (mmm) REVERT: L 405 ASP cc_start: 0.8721 (p0) cc_final: 0.8338 (p0) outliers start: 46 outliers final: 41 residues processed: 346 average time/residue: 0.8908 time to fit residues: 443.1036 Evaluate side-chains 352 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 309 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 296 THR Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 749 THR Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 985 THR Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 170 ASN Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 376 ASP Chi-restraints excluded: chain L residue 398 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 136 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 168 optimal weight: 0.0570 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22618 Z= 0.175 Angle : 0.608 6.344 31802 Z= 0.356 Chirality : 0.041 0.411 3586 Planarity : 0.004 0.083 3059 Dihedral : 25.894 174.378 5425 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.56 % Favored : 94.24 % Rotamer: Outliers : 2.00 % Allowed : 16.72 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.43 (0.19), residues: 1962 helix: 1.46 (0.21), residues: 610 sheet: -0.32 (0.24), residues: 472 loop : -1.54 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 203 HIS 0.003 0.001 HIS H 83 PHE 0.026 0.001 PHE K 67 TYR 0.013 0.001 TYR K 891 ARG 0.007 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 365 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 331 time to evaluate : 2.783 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: A 43 ARG cc_start: 0.7849 (tpp80) cc_final: 0.7614 (tpp-160) REVERT: A 58 SER cc_start: 0.8966 (t) cc_final: 0.8666 (m) REVERT: A 130 ARG cc_start: 0.8048 (tpt90) cc_final: 0.7661 (tpm170) REVERT: C 57 GLU cc_start: 0.7348 (tt0) cc_final: 0.7090 (tm-30) REVERT: C 115 VAL cc_start: 0.8927 (m) cc_final: 0.8687 (t) REVERT: D 52 ASP cc_start: 0.8161 (m-30) cc_final: 0.7899 (m-30) REVERT: E 74 GLU cc_start: 0.7594 (tp30) cc_final: 0.7330 (tp30) REVERT: F 80 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7598 (mtmt) REVERT: F 92 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7779 (tptt) REVERT: G 20 SER cc_start: 0.8283 (m) cc_final: 0.7729 (t) REVERT: G 51 TYR cc_start: 0.8923 (t80) cc_final: 0.8294 (t80) REVERT: K 6 VAL cc_start: 0.8469 (t) cc_final: 0.8183 (m) REVERT: K 36 ASN cc_start: 0.8182 (p0) cc_final: 0.7912 (p0) REVERT: K 117 GLU cc_start: 0.7381 (tt0) cc_final: 0.6970 (tt0) REVERT: K 148 ASP cc_start: 0.8209 (m-30) cc_final: 0.7717 (p0) REVERT: K 215 GLU cc_start: 0.8686 (tp30) cc_final: 0.7941 (tm-30) REVERT: K 277 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7767 (tt0) REVERT: K 313 CYS cc_start: 0.6138 (OUTLIER) cc_final: 0.5724 (p) REVERT: K 713 ARG cc_start: 0.7686 (ttt-90) cc_final: 0.7307 (ttt-90) REVERT: K 987 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7328 (tm-30) REVERT: K 1014 MET cc_start: 0.4957 (mtt) cc_final: 0.4349 (mmt) REVERT: K 1055 GLN cc_start: 0.7481 (mt0) cc_final: 0.6635 (mt0) REVERT: K 1068 ILE cc_start: 0.8579 (mt) cc_final: 0.8322 (tp) REVERT: K 1070 HIS cc_start: 0.8294 (t70) cc_final: 0.7467 (t70) REVERT: L 177 MET cc_start: 0.5645 (mmm) cc_final: 0.5432 (mmm) REVERT: L 403 MET cc_start: 0.8966 (tpp) cc_final: 0.8673 (tpp) REVERT: L 405 ASP cc_start: 0.8586 (p0) cc_final: 0.8247 (p0) outliers start: 34 outliers final: 32 residues processed: 348 average time/residue: 0.9003 time to fit residues: 448.5951 Evaluate side-chains 353 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 320 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 296 THR Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 749 THR Chi-restraints excluded: chain K residue 794 ILE Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 985 THR Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 170 ASN Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 360 ASN Chi-restraints excluded: chain L residue 398 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 156 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 198 optimal weight: 0.4980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 ASN K 908 ASN K 964 ASN K 978 GLN ** L 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22618 Z= 0.198 Angle : 0.610 6.907 31802 Z= 0.356 Chirality : 0.042 0.408 3586 Planarity : 0.004 0.080 3059 Dihedral : 25.870 173.928 5425 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.98 % Favored : 92.86 % Rotamer: Outliers : 2.00 % Allowed : 17.07 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 1962 helix: 1.57 (0.21), residues: 610 sheet: -0.25 (0.24), residues: 464 loop : -1.53 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 203 HIS 0.006 0.001 HIS L 333 PHE 0.028 0.001 PHE K 67 TYR 0.011 0.001 TYR K 891 ARG 0.005 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 357 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 323 time to evaluate : 2.522 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: A 43 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7631 (tpp-160) REVERT: A 58 SER cc_start: 0.8972 (t) cc_final: 0.8696 (m) REVERT: A 130 ARG cc_start: 0.8061 (tpt90) cc_final: 0.7660 (tpm170) REVERT: B 86 ASP cc_start: 0.7606 (m-30) cc_final: 0.7211 (t0) REVERT: C 57 GLU cc_start: 0.7416 (tt0) cc_final: 0.7124 (tm-30) REVERT: C 115 VAL cc_start: 0.8946 (m) cc_final: 0.8728 (t) REVERT: D 43 TYR cc_start: 0.7720 (t80) cc_final: 0.7322 (t80) REVERT: D 52 ASP cc_start: 0.8162 (m-30) cc_final: 0.7902 (m-30) REVERT: E 74 GLU cc_start: 0.7523 (tp30) cc_final: 0.7243 (tp30) REVERT: F 80 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7617 (mtmt) REVERT: G 20 SER cc_start: 0.8303 (m) cc_final: 0.7749 (t) REVERT: G 51 TYR cc_start: 0.8919 (t80) cc_final: 0.8278 (t80) REVERT: K 6 VAL cc_start: 0.8371 (t) cc_final: 0.8074 (m) REVERT: K 36 ASN cc_start: 0.8176 (p0) cc_final: 0.7926 (p0) REVERT: K 117 GLU cc_start: 0.7436 (tt0) cc_final: 0.7042 (tt0) REVERT: K 148 ASP cc_start: 0.8230 (m-30) cc_final: 0.7744 (p0) REVERT: K 215 GLU cc_start: 0.8690 (tp30) cc_final: 0.7989 (tm-30) REVERT: K 277 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7718 (tt0) REVERT: K 313 CYS cc_start: 0.6153 (OUTLIER) cc_final: 0.5753 (p) REVERT: K 383 LYS cc_start: 0.8775 (ptmm) cc_final: 0.8506 (ptpt) REVERT: K 964 ASN cc_start: 0.7134 (OUTLIER) cc_final: 0.6784 (m-40) REVERT: K 987 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7329 (tm-30) REVERT: K 1014 MET cc_start: 0.4937 (mtt) cc_final: 0.4363 (mmt) REVERT: K 1055 GLN cc_start: 0.7535 (mt0) cc_final: 0.6681 (mt0) REVERT: K 1068 ILE cc_start: 0.8592 (mt) cc_final: 0.8335 (tp) REVERT: K 1070 HIS cc_start: 0.8325 (t70) cc_final: 0.7512 (t70) REVERT: L 177 MET cc_start: 0.5680 (mmm) cc_final: 0.5425 (mmm) REVERT: L 403 MET cc_start: 0.8993 (tpp) cc_final: 0.8673 (tpp) REVERT: L 405 ASP cc_start: 0.8608 (p0) cc_final: 0.8294 (p0) outliers start: 34 outliers final: 29 residues processed: 339 average time/residue: 0.9345 time to fit residues: 456.1204 Evaluate side-chains 346 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 315 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 749 THR Chi-restraints excluded: chain K residue 794 ILE Chi-restraints excluded: chain K residue 908 ASN Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 955 SER Chi-restraints excluded: chain K residue 964 ASN Chi-restraints excluded: chain K residue 985 THR Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 170 ASN Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 360 ASN Chi-restraints excluded: chain L residue 398 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 9.9990 chunk 210 optimal weight: 0.7980 chunk 128 optimal weight: 0.1980 chunk 100 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 221 optimal weight: 0.2980 chunk 203 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 39 ASN ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 22618 Z= 0.293 Angle : 0.786 59.199 31802 Z= 0.483 Chirality : 0.043 0.405 3586 Planarity : 0.005 0.169 3059 Dihedral : 25.867 173.907 5425 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.83 % Favored : 93.02 % Rotamer: Outliers : 1.94 % Allowed : 17.19 % Favored : 80.87 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 1962 helix: 1.58 (0.21), residues: 610 sheet: -0.17 (0.25), residues: 449 loop : -1.59 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 203 HIS 0.006 0.001 HIS L 333 PHE 0.026 0.001 PHE K 67 TYR 0.016 0.001 TYR H 84 ARG 0.010 0.000 ARG F 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 89 is missing expected H atoms. Skipping. Evaluate side-chains 346 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 313 time to evaluate : 2.808 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: A 43 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7567 (tpp-160) REVERT: A 58 SER cc_start: 0.8967 (t) cc_final: 0.8697 (m) REVERT: A 130 ARG cc_start: 0.8068 (tpt90) cc_final: 0.7665 (tpm170) REVERT: B 86 ASP cc_start: 0.7630 (m-30) cc_final: 0.7230 (t0) REVERT: C 57 GLU cc_start: 0.7421 (tt0) cc_final: 0.7131 (tm-30) REVERT: C 115 VAL cc_start: 0.8944 (m) cc_final: 0.8729 (t) REVERT: D 43 TYR cc_start: 0.7729 (t80) cc_final: 0.7329 (t80) REVERT: D 52 ASP cc_start: 0.8166 (m-30) cc_final: 0.7907 (m-30) REVERT: E 74 GLU cc_start: 0.7529 (tp30) cc_final: 0.7250 (tp30) REVERT: F 45 LYS cc_start: 0.8020 (tttp) cc_final: 0.7766 (tppt) REVERT: F 80 LYS cc_start: 0.7961 (mtpp) cc_final: 0.7613 (mtmt) REVERT: G 20 SER cc_start: 0.8310 (m) cc_final: 0.7756 (t) REVERT: G 51 TYR cc_start: 0.8923 (t80) cc_final: 0.8287 (t80) REVERT: K 6 VAL cc_start: 0.8376 (t) cc_final: 0.8077 (m) REVERT: K 36 ASN cc_start: 0.8179 (p0) cc_final: 0.7928 (p0) REVERT: K 117 GLU cc_start: 0.7439 (tt0) cc_final: 0.7045 (tt0) REVERT: K 148 ASP cc_start: 0.8232 (m-30) cc_final: 0.7744 (p0) REVERT: K 215 GLU cc_start: 0.8689 (tp30) cc_final: 0.7990 (tm-30) REVERT: K 277 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7720 (tt0) REVERT: K 313 CYS cc_start: 0.6151 (OUTLIER) cc_final: 0.5753 (p) REVERT: K 383 LYS cc_start: 0.8776 (ptmm) cc_final: 0.8507 (ptpt) REVERT: K 987 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7330 (tm-30) REVERT: K 1014 MET cc_start: 0.4943 (mtt) cc_final: 0.4362 (mmt) REVERT: K 1055 GLN cc_start: 0.7550 (mt0) cc_final: 0.6686 (mt0) REVERT: K 1068 ILE cc_start: 0.8598 (mt) cc_final: 0.8336 (tp) REVERT: K 1070 HIS cc_start: 0.8325 (t70) cc_final: 0.7515 (t70) REVERT: L 177 MET cc_start: 0.5662 (mmm) cc_final: 0.5401 (mmm) REVERT: L 184 GLN cc_start: 0.7084 (pt0) cc_final: 0.6682 (pt0) REVERT: L 403 MET cc_start: 0.8995 (tpp) cc_final: 0.8666 (tpp) REVERT: L 405 ASP cc_start: 0.8597 (p0) cc_final: 0.8392 (p0) outliers start: 33 outliers final: 30 residues processed: 329 average time/residue: 0.8871 time to fit residues: 417.4456 Evaluate side-chains 344 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 313 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain K residue 313 CYS Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 749 THR Chi-restraints excluded: chain K residue 794 ILE Chi-restraints excluded: chain K residue 952 ASN Chi-restraints excluded: chain K residue 955 SER Chi-restraints excluded: chain K residue 985 THR Chi-restraints excluded: chain K residue 1009 HIS Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 170 ASN Chi-restraints excluded: chain L residue 189 ASN Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 360 ASN Chi-restraints excluded: chain L residue 398 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 162 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 181 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 237 ASN ** 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 = 0.4512 r_free = 0.4512 target = 0.178181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.137256 restraints weight = 123289.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.144885 restraints weight = 48050.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.145108 restraints weight = 23473.648| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 22618 Z= 0.293 Angle : 0.786 59.199 31802 Z= 0.483 Chirality : 0.043 0.405 3586 Planarity : 0.005 0.169 3059 Dihedral : 25.867 173.907 5425 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.83 % Favored : 93.02 % Rotamer: Outliers : 1.82 % Allowed : 17.42 % Favored : 80.75 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 1962 helix: 1.58 (0.21), residues: 610 sheet: -0.17 (0.25), residues: 449 loop : -1.59 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 203 HIS 0.006 0.001 HIS L 333 PHE 0.026 0.001 PHE K 67 TYR 0.016 0.001 TYR H 84 ARG 0.010 0.000 ARG F 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10597.71 seconds wall clock time: 187 minutes 46.32 seconds (11266.32 seconds total)