Starting phenix.real_space_refine (version: dev) on Tue May 17 14:23:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/05_2022/6r8z_4763_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/05_2022/6r8z_4763.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/05_2022/6r8z_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_4763/05_2022/6r8z_4763_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/05_2022/6r8z_4763_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/05_2022/6r8z_4763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/05_2022/6r8z_4763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/05_2022/6r8z_4763_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8z_4763/05_2022/6r8z_4763_trim_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'5*END': 1, '3*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: {'5*END': 1, '3*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: {'PTRANS': 25, 'TRANS': 797, 'PCIS': 2} 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: 18.25, per 1000 atoms: 0.45 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: 32.48 Conformation dependent library (CDL) restraints added in 3.0 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: 18.07 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: 19.75 Time building geometry restraints manager: 33.39 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 1.669 1.437 0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C4' 3DR J 96 " pdb=" O4' 3DR J 96 " ideal model delta sigma weight residual 1.669 1.439 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C4' 3DR J 95 " pdb=" C3' 3DR J 95 " ideal model delta sigma weight residual 1.333 1.533 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C4' 3DR J 96 " pdb=" C3' 3DR J 96 " ideal model delta sigma weight residual 1.333 1.530 -0.197 2.00e-02 2.50e+03 9.70e+01 bond pdb=" C2' 3DR J 95 " pdb=" C1' 3DR J 95 " ideal model delta sigma weight residual 1.598 1.473 0.125 2.00e-02 2.50e+03 3.92e+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: 14318 35.09 - 70.19: 1519 70.19 - 105.28: 45 105.28 - 140.38: 0 140.38 - 175.47: 2 Dihedral angle restraints: 15884 sinusoidal: 9341 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 15881 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 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. 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: 1.120 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: 1.010 Extract box with map and model: 8.180 Check model and map are aligned: 0.570 Convert atoms to be neutral: 0.320 Process input model: 135.940 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 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 0.232 22618 Z= 0.733 Angle : 0.939 12.510 31802 Z= 0.548 Chirality : 0.056 0.578 3586 Planarity : 0.007 0.092 3059 Dihedral : 22.757 175.472 8929 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.64 % Favored : 95.01 % Rotamer Outliers : 0.18 % 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 *********************** 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 : 2.836 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 outliers start: 3 outliers final: 1 residues processed: 445 average time/residue: 0.9470 time to fit residues: 598.9855 Evaluate side-chains 309 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 308 time to evaluate : 2.687 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.5272 time to fit residues: 4.1111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 129 optimal weight: 0.2980 chunk 201 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 859 GLN ** 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** ** K 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1059 ASN ** L 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 22618 Z= 0.194 Angle : 0.640 6.421 31802 Z= 0.376 Chirality : 0.042 0.436 3586 Planarity : 0.005 0.084 3059 Dihedral : 26.431 174.174 5079 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.38 % Favored : 95.36 % Rotamer Outliers : 1.41 % 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: -0.48 (0.18), residues: 1962 helix: 1.64 (0.20), residues: 615 sheet: -0.32 (0.23), residues: 454 loop : -1.77 (0.18), residues: 893 *********************** 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 354 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 330 time to evaluate : 2.851 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 outliers start: 24 outliers final: 18 residues processed: 342 average time/residue: 0.9196 time to fit residues: 453.4758 Evaluate side-chains 324 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 306 time to evaluate : 2.804 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.5115 time to fit residues: 19.9069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 167 optimal weight: 0.0970 chunk 137 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 990 GLN ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 22618 Z= 0.255 Angle : 0.651 7.260 31802 Z= 0.381 Chirality : 0.043 0.419 3586 Planarity : 0.005 0.101 3059 Dihedral : 26.339 173.019 5079 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.45 % Favored : 94.29 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 1962 helix: 1.63 (0.21), residues: 617 sheet: -0.29 (0.24), residues: 475 loop : -1.67 (0.19), residues: 870 *********************** 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 344 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 328 time to evaluate : 2.865 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 outliers start: 16 outliers final: 12 residues processed: 336 average time/residue: 0.8607 time to fit residues: 421.8503 Evaluate side-chains 322 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 310 time to evaluate : 2.807 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4445 time to fit residues: 13.3796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 156 ASN K 727 GLN ** K 964 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** ** L 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 22618 Z= 0.291 Angle : 0.670 9.916 31802 Z= 0.391 Chirality : 0.044 0.422 3586 Planarity : 0.004 0.072 3059 Dihedral : 26.323 171.222 5079 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.96 % Favored : 93.83 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.62 (0.18), residues: 1962 helix: 1.21 (0.21), residues: 614 sheet: -0.27 (0.24), residues: 464 loop : -1.69 (0.19), residues: 884 *********************** 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 339 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 326 time to evaluate : 2.853 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 outliers start: 13 outliers final: 10 residues processed: 331 average time/residue: 0.8416 time to fit residues: 408.6829 Evaluate side-chains 316 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 306 time to evaluate : 2.778 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.4438 time to fit residues: 11.4755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 3 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 0.0770 chunk 192 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.5942 ------------------------------------------------------------------------------- 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 287 HIS ** 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: 0.7509 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 22618 Z= 0.234 Angle : 0.626 6.140 31802 Z= 0.368 Chirality : 0.043 0.411 3586 Planarity : 0.005 0.114 3059 Dihedral : 26.309 171.702 5079 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.32 % Favored : 93.48 % Rotamer Outliers : 0.88 % 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: -0.49 (0.19), residues: 1962 helix: 1.37 (0.21), residues: 614 sheet: -0.28 (0.24), residues: 467 loop : -1.60 (0.19), residues: 881 *********************** 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 329 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 314 time to evaluate : 2.754 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 outliers start: 15 outliers final: 12 residues processed: 319 average time/residue: 0.8241 time to fit residues: 385.3600 Evaluate side-chains 313 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 301 time to evaluate : 2.751 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4135 time to fit residues: 12.6724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** 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: 0.7515 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 22618 Z= 0.232 Angle : 0.627 10.264 31802 Z= 0.366 Chirality : 0.043 0.418 3586 Planarity : 0.005 0.130 3059 Dihedral : 26.311 171.926 5079 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.37 % Favored : 93.43 % Rotamer Outliers : 0.47 % 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: -0.43 (0.19), residues: 1962 helix: 1.44 (0.21), residues: 614 sheet: -0.27 (0.24), residues: 463 loop : -1.57 (0.19), residues: 885 *********************** 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 325 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 317 time to evaluate : 2.842 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 outliers start: 8 outliers final: 7 residues processed: 319 average time/residue: 0.8478 time to fit residues: 399.2031 Evaluate side-chains 307 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 300 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4758 time to fit residues: 9.8952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 156 optimal weight: 0.0170 chunk 121 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- 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: 0.7489 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.111 22618 Z= 0.209 Angle : 0.607 6.716 31802 Z= 0.357 Chirality : 0.042 0.405 3586 Planarity : 0.004 0.083 3059 Dihedral : 26.294 172.807 5079 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.07 % Favored : 93.73 % Rotamer Outliers : 0.24 % 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: -0.31 (0.19), residues: 1962 helix: 1.65 (0.21), residues: 614 sheet: -0.22 (0.24), residues: 458 loop : -1.56 (0.20), residues: 890 *********************** 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 307 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 303 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 306 average time/residue: 0.8271 time to fit residues: 369.6611 Evaluate side-chains 304 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 300 time to evaluate : 2.787 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4020 time to fit residues: 6.4564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 136 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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** ** L 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.099 22618 Z= 0.278 Angle : 0.637 9.845 31802 Z= 0.374 Chirality : 0.043 0.412 3586 Planarity : 0.005 0.131 3059 Dihedral : 26.310 173.041 5079 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.34 % Favored : 92.46 % Rotamer Outliers : 0.77 % 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: -0.49 (0.19), residues: 1962 helix: 1.33 (0.21), residues: 614 sheet: -0.24 (0.24), residues: 456 loop : -1.59 (0.20), residues: 892 *********************** 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 320 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 307 time to evaluate : 2.967 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 outliers start: 13 outliers final: 9 residues processed: 310 average time/residue: 0.8487 time to fit residues: 381.5273 Evaluate side-chains 306 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 297 time to evaluate : 2.753 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4174 time to fit residues: 10.4151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 120 optimal weight: 0.0030 chunk 86 optimal weight: 4.9990 chunk 156 optimal weight: 0.0030 chunk 61 optimal weight: 2.9990 chunk 180 optimal weight: 0.0020 chunk 188 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 overall best weight: 0.3608 ------------------------------------------------------------------------------- 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 ** L 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.092 22618 Z= 0.178 Angle : 0.609 9.689 31802 Z= 0.353 Chirality : 0.041 0.406 3586 Planarity : 0.005 0.101 3059 Dihedral : 26.300 173.709 5079 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.94 % Favored : 94.90 % Rotamer Outliers : 0.47 % 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: -0.04 (0.19), residues: 1962 helix: 1.96 (0.21), residues: 607 sheet: -0.17 (0.24), residues: 463 loop : -1.39 (0.20), residues: 892 *********************** 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 321 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 313 time to evaluate : 2.902 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 outliers start: 8 outliers final: 5 residues processed: 315 average time/residue: 0.8324 time to fit residues: 385.6804 Evaluate side-chains 300 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 295 time to evaluate : 2.832 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4677 time to fit residues: 7.4863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.102 22618 Z= 0.290 Angle : 0.652 12.955 31802 Z= 0.379 Chirality : 0.044 0.411 3586 Planarity : 0.006 0.161 3059 Dihedral : 26.298 172.759 5079 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.03 % Favored : 92.81 % Rotamer Outliers : 0.29 % 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: -0.37 (0.19), residues: 1962 helix: 1.48 (0.21), residues: 607 sheet: -0.27 (0.24), residues: 465 loop : -1.47 (0.20), residues: 890 ********************** 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 309 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 304 time to evaluate : 2.822 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 outliers start: 5 outliers final: 4 residues processed: 305 average time/residue: 0.8516 time to fit residues: 376.9758 Evaluate side-chains 304 residues out of total 1699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 300 time to evaluate : 2.770 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4322 time to fit residues: 6.5618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.8980 chunk 187 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 162 optimal weight: 0.0070 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 176 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 907 ASN ** L 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.181364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.139775 restraints weight = 123320.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.145904 restraints weight = 48705.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.149564 restraints weight = 27364.594| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.089 22618 Z= 0.186 Angle : 0.610 7.704 31802 Z= 0.353 Chirality : 0.041 0.408 3586 Planarity : 0.004 0.102 3059 Dihedral : 26.304 173.405 5079 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.20 % Favored : 94.65 % Rotamer Outliers : 0.12 % 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: -0.10 (0.19), residues: 1962 helix: 1.81 (0.21), residues: 610 sheet: -0.12 (0.24), residues: 464 loop : -1.40 (0.20), residues: 888 =============================================================================== Job complete usr+sys time: 9969.82 seconds wall clock time: 177 minutes 11.55 seconds (10631.55 seconds total)