Starting phenix.real_space_refine on Mon May 13 22:45:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unh_42402/05_2024/8unh_42402_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unh_42402/05_2024/8unh_42402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unh_42402/05_2024/8unh_42402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unh_42402/05_2024/8unh_42402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unh_42402/05_2024/8unh_42402_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unh_42402/05_2024/8unh_42402_trim_updated.pdb" } resolution = 3.21 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= 0.003 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12960 atoms to isotropic. 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 6 5.49 5 Mg 2 5.21 5 S 67 5.16 5 C 8409 2.51 5 N 2218 2.21 5 O 2542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 13244 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2509 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 307} Chain: "E" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2509 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 307} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "D" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "A" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1503 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain: "G" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1750 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "H" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1750 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "F" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.44, per 1000 atoms: 0.56 Number of scatterers: 13244 At special positions: 0 Unit cell: (96.416, 119.472, 124.712, 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 67 16.00 P 6 15.00 Mg 2 11.99 O 2542 8.00 N 2218 7.00 C 8409 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.36 Conformation dependent library (CDL) restraints added in 2.3 seconds 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3178 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 15 sheets defined 42.2% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 27 through 38 Processing helix chain 'B' and resid 57 through 66 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 163 through 183 Processing helix chain 'B' and resid 190 through 199 removed outlier: 4.057A pdb=" N ALA B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 215 Processing helix chain 'B' and resid 236 through 244 Processing helix chain 'B' and resid 248 through 275 Proline residue: B 255 - end of helix removed outlier: 4.126A pdb=" N ALA B 259 " --> pdb=" O PRO B 255 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N TRP B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 297 removed outlier: 3.615A pdb=" N TYR B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS B 295 " --> pdb=" O ASN B 291 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLY B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 315 Processing helix chain 'E' and resid 27 through 38 Processing helix chain 'E' and resid 57 through 66 Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'E' and resid 87 through 93 Processing helix chain 'E' and resid 115 through 128 removed outlier: 3.933A pdb=" N ARG E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 143 No H-bonds generated for 'chain 'E' and resid 141 through 143' Processing helix chain 'E' and resid 146 through 151 removed outlier: 3.700A pdb=" N SER E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG E 151 " --> pdb=" O PRO E 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 151' Processing helix chain 'E' and resid 162 through 182 Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.573A pdb=" N ALA E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 removed outlier: 4.588A pdb=" N SER E 216 " --> pdb=" O ASP E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 226 Processing helix chain 'E' and resid 236 through 244 Processing helix chain 'E' and resid 247 through 258 removed outlier: 3.882A pdb=" N ALA E 252 " --> pdb=" O LYS E 248 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 261 through 271 Processing helix chain 'E' and resid 278 through 294 removed outlier: 3.952A pdb=" N ILE E 282 " --> pdb=" O PRO E 278 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG E 283 " --> pdb=" O GLN E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 314 Processing helix chain 'C' and resid 236 through 244 Processing helix chain 'C' and resid 248 through 258 Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 261 through 275 removed outlier: 3.733A pdb=" N TYR C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 294 removed outlier: 4.188A pdb=" N ILE C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'D' and resid 236 through 244 Processing helix chain 'D' and resid 247 through 257 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 262 through 274 Processing helix chain 'D' and resid 278 through 293 removed outlier: 4.389A pdb=" N ILE D 282 " --> pdb=" O PRO D 278 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 Processing helix chain 'A' and resid 14 through 18 Processing helix chain 'A' and resid 22 through 32 removed outlier: 3.870A pdb=" N PHE A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 73 through 84 Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 111 through 131 removed outlier: 4.286A pdb=" N GLU A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.630A pdb=" N LYS A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 161 removed outlier: 3.944A pdb=" N GLU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLY A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.715A pdb=" N VAL A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 170' Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.627A pdb=" N LEU A 183 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 17 Processing helix chain 'G' and resid 57 through 66 removed outlier: 3.729A pdb=" N LEU G 66 " --> pdb=" O GLY G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 133 Processing helix chain 'G' and resid 184 through 186 No H-bonds generated for 'chain 'G' and resid 184 through 186' Processing helix chain 'H' and resid 5 through 16 removed outlier: 3.847A pdb=" N THR H 16 " --> pdb=" O LYS H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 65 Processing helix chain 'H' and resid 120 through 133 Processing helix chain 'F' and resid 1005 through 1016 removed outlier: 3.772A pdb=" N THR F1016 " --> pdb=" O LYS F1012 " (cutoff:3.500A) Processing helix chain 'F' and resid 1057 through 1066 removed outlier: 3.538A pdb=" N LEU F1066 " --> pdb=" O GLY F1062 " (cutoff:3.500A) Processing helix chain 'F' and resid 1097 through 1099 No H-bonds generated for 'chain 'F' and resid 1097 through 1099' Processing helix chain 'F' and resid 1120 through 1133 removed outlier: 3.506A pdb=" N ARG F1131 " --> pdb=" O LEU F1127 " (cutoff:3.500A) Processing helix chain 'F' and resid 1184 through 1186 No H-bonds generated for 'chain 'F' and resid 1184 through 1186' Processing sheet with id= A, first strand: chain 'B' and resid 135 through 138 removed outlier: 6.027A pdb=" N ILE B 45 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ALA B 138 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU B 47 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG B 153 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N HIS B 48 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE B 155 " --> pdb=" O HIS B 48 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 70 through 75 Processing sheet with id= C, first strand: chain 'E' and resid 153 through 156 removed outlier: 6.612A pdb=" N LYS E 102 " --> pdb=" O SER E 133 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE E 135 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE E 104 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR E 137 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE E 106 " --> pdb=" O THR E 137 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 28 through 32 Processing sheet with id= E, first strand: chain 'G' and resid 181 through 183 removed outlier: 3.679A pdb=" N GLY G 170 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE G 149 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N THR G 168 " --> pdb=" O ILE G 149 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLY G 151 " --> pdb=" O SER G 166 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N SER G 166 " --> pdb=" O GLY G 151 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 197 through 201 Processing sheet with id= G, first strand: chain 'H' and resid 21 through 23 Processing sheet with id= H, first strand: chain 'H' and resid 28 through 32 removed outlier: 3.636A pdb=" N LYS H 208 " --> pdb=" O LEU H 197 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 73 through 75 Processing sheet with id= J, first strand: chain 'H' and resid 179 through 183 removed outlier: 3.696A pdb=" N PHE H 180 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY H 170 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE H 149 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR H 168 " --> pdb=" O ILE H 149 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 1021 through 1023 Processing sheet with id= L, first strand: chain 'F' and resid 1028 through 1032 Processing sheet with id= M, first strand: chain 'F' and resid 1072 through 1075 Processing sheet with id= N, first strand: chain 'F' and resid 1179 through 1183 removed outlier: 3.746A pdb=" N PHE F1180 " --> pdb=" O ILE F1140 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY F1170 " --> pdb=" O ILE F1147 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE F1149 " --> pdb=" O THR F1168 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N THR F1168 " --> pdb=" O ILE F1149 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLY F1151 " --> pdb=" O SER F1166 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N SER F1166 " --> pdb=" O GLY F1151 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 1194 through 1201 removed outlier: 3.778A pdb=" N GLU F1210 " --> pdb=" O LYS F1195 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 5.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 4386 1.37 - 1.51: 3754 1.51 - 1.66: 5225 1.66 - 1.80: 84 1.80 - 1.95: 30 Bond restraints: 13479 Sorted by residual: bond pdb=" N ASN A 48 " pdb=" CA ASN A 48 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.20e-02 6.94e+03 1.27e+01 bond pdb=" N ASN B 300 " pdb=" CA ASN B 300 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.17e-02 7.31e+03 7.50e+00 bond pdb=" N HIS C 304 " pdb=" CA HIS C 304 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.19e-02 7.06e+03 7.18e+00 bond pdb=" N TYR G 39 " pdb=" CA TYR G 39 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.21e-02 6.83e+03 6.55e+00 bond pdb=" N LEU H 126 " pdb=" CA LEU H 126 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.20e+00 ... (remaining 13474 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.98: 329 106.98 - 113.80: 7764 113.80 - 120.62: 5437 120.62 - 127.43: 4595 127.43 - 134.25: 110 Bond angle restraints: 18235 Sorted by residual: angle pdb=" N ALA A 56 " pdb=" CA ALA A 56 " pdb=" C ALA A 56 " ideal model delta sigma weight residual 113.43 108.71 4.72 1.26e+00 6.30e-01 1.40e+01 angle pdb=" N ASN A 48 " pdb=" CA ASN A 48 " pdb=" C ASN A 48 " ideal model delta sigma weight residual 111.14 115.01 -3.87 1.08e+00 8.57e-01 1.28e+01 angle pdb=" CA ASN A 48 " pdb=" C ASN A 48 " pdb=" O ASN A 48 " ideal model delta sigma weight residual 120.70 117.31 3.39 1.03e+00 9.43e-01 1.08e+01 angle pdb=" N ASN C 292 " pdb=" CA ASN C 292 " pdb=" C ASN C 292 " ideal model delta sigma weight residual 111.28 107.74 3.54 1.09e+00 8.42e-01 1.06e+01 angle pdb=" CA GLN C 317 " pdb=" C GLN C 317 " pdb=" O GLN C 317 " ideal model delta sigma weight residual 122.41 118.54 3.87 1.21e+00 6.83e-01 1.02e+01 ... (remaining 18230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7032 17.78 - 35.55: 902 35.55 - 53.33: 201 53.33 - 71.10: 34 71.10 - 88.88: 19 Dihedral angle restraints: 8188 sinusoidal: 3280 harmonic: 4908 Sorted by residual: dihedral pdb=" CA LEU A 10 " pdb=" C LEU A 10 " pdb=" N ASN A 11 " pdb=" CA ASN A 11 " ideal model delta harmonic sigma weight residual 180.00 -163.05 -16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ASP G 157 " pdb=" CB ASP G 157 " pdb=" CG ASP G 157 " pdb=" OD1 ASP G 157 " ideal model delta sinusoidal sigma weight residual -30.00 -85.78 55.78 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU B 108 " pdb=" CG GLU B 108 " pdb=" CD GLU B 108 " pdb=" OE1 GLU B 108 " ideal model delta sinusoidal sigma weight residual 0.00 88.77 -88.77 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 8185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1421 0.035 - 0.069: 443 0.069 - 0.104: 145 0.104 - 0.138: 69 0.138 - 0.173: 3 Chirality restraints: 2081 Sorted by residual: chirality pdb=" CA MET C 316 " pdb=" N MET C 316 " pdb=" C MET C 316 " pdb=" CB MET C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CA ILE B 42 " pdb=" N ILE B 42 " pdb=" C ILE B 42 " pdb=" CB ILE B 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA GLN C 317 " pdb=" N GLN C 317 " pdb=" C GLN C 317 " pdb=" CB GLN C 317 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 2078 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 254 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.45e+00 pdb=" N PRO D 255 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 255 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 255 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 164 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C LYS H 164 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS H 164 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR H 165 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 47 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C ILE A 47 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 47 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN A 48 " -0.010 2.00e-02 2.50e+03 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 183 2.56 - 3.14: 11892 3.14 - 3.73: 20776 3.73 - 4.31: 29532 4.31 - 4.90: 50059 Nonbonded interactions: 112442 Sorted by model distance: nonbonded pdb=" O2B AGS E 401 " pdb="MG MG E 402 " model vdw 1.974 2.170 nonbonded pdb=" NZ LYS B 56 " pdb="MG MG B 402 " model vdw 2.102 2.250 nonbonded pdb=" O ASN B 300 " pdb=" OG1 THR B 301 " model vdw 2.148 2.440 nonbonded pdb=" N GLU F1175 " pdb=" OE1 GLU F1175 " model vdw 2.170 2.520 nonbonded pdb=" O2B AGS E 401 " pdb=" O2G AGS E 401 " model vdw 2.195 2.440 ... (remaining 112437 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 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 1 through 227 or (resid 228 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )))) selection = (chain 'H' and (resid 1 through 227 or (resid 228 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )))) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.000 Extract box with map and model: 2.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.520 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.004 0.043 13479 Z= 0.232 Angle : 0.480 5.604 18235 Z= 0.291 Chirality : 0.041 0.173 2081 Planarity : 0.003 0.077 2327 Dihedral : 16.689 88.879 5010 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 46.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.28 % Favored : 94.48 % Rotamer: Outliers : 0.49 % Allowed : 22.80 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.22), residues: 1667 helix: 1.56 (0.20), residues: 698 sheet: -1.52 (0.31), residues: 309 loop : -0.69 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 263 HIS 0.014 0.001 HIS D 304 PHE 0.027 0.001 PHE B 109 TYR 0.011 0.001 TYR D 261 ARG 0.002 0.000 ARG E 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 229 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 PHE cc_start: 0.7857 (t80) cc_final: 0.7652 (t80) REVERT: B 142 ASP cc_start: 0.8768 (m-30) cc_final: 0.8534 (p0) REVERT: B 168 MET cc_start: 0.9449 (ttp) cc_final: 0.9137 (ptm) REVERT: B 169 MET cc_start: 0.9077 (mmm) cc_final: 0.8784 (mmm) REVERT: B 172 MET cc_start: 0.9456 (tpt) cc_final: 0.8856 (tpt) REVERT: B 182 HIS cc_start: 0.8834 (m90) cc_final: 0.8550 (m90) REVERT: B 261 TYR cc_start: 0.7879 (t80) cc_final: 0.7637 (t80) REVERT: B 284 MET cc_start: 0.9677 (tmm) cc_final: 0.9388 (tmm) REVERT: B 294 TYR cc_start: 0.9300 (m-80) cc_final: 0.9044 (m-80) REVERT: B 307 TYR cc_start: 0.9052 (t80) cc_final: 0.8683 (t80) REVERT: E 169 MET cc_start: 0.9463 (mtt) cc_final: 0.9079 (mtp) REVERT: E 172 MET cc_start: 0.9331 (tpt) cc_final: 0.9109 (tpt) REVERT: E 284 MET cc_start: 0.9647 (tmm) cc_final: 0.9330 (tmm) REVERT: C 302 GLU cc_start: 0.9224 (pt0) cc_final: 0.8845 (pm20) REVERT: C 317 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.6946 (tp40) REVERT: D 244 ASN cc_start: 0.8730 (m110) cc_final: 0.8490 (m-40) REVERT: D 249 GLN cc_start: 0.9332 (tp40) cc_final: 0.9043 (tp-100) REVERT: D 291 ASN cc_start: 0.8666 (t0) cc_final: 0.8282 (t0) REVERT: A 4 PHE cc_start: 0.8107 (m-80) cc_final: 0.7808 (m-80) REVERT: A 21 ASP cc_start: 0.8466 (t0) cc_final: 0.7949 (t0) REVERT: A 30 ASP cc_start: 0.8947 (m-30) cc_final: 0.8716 (m-30) REVERT: A 156 LYS cc_start: 0.9599 (tmtt) cc_final: 0.9334 (tppt) REVERT: G 32 ARG cc_start: 0.8656 (ttp80) cc_final: 0.8327 (ptm-80) REVERT: H 126 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9240 (tp) REVERT: H 134 GLN cc_start: 0.9233 (mm-40) cc_final: 0.8884 (mm-40) REVERT: F 1055 TYR cc_start: 0.8109 (p90) cc_final: 0.7524 (p90) REVERT: F 1128 ARG cc_start: 0.9108 (mpp80) cc_final: 0.8859 (mtp85) REVERT: F 1134 GLN cc_start: 0.8878 (mp10) cc_final: 0.8674 (mp10) outliers start: 7 outliers final: 2 residues processed: 233 average time/residue: 0.2745 time to fit residues: 92.9936 Evaluate side-chains 184 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 180 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain H residue 126 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 0.0980 chunk 147 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 GLN H 13 ASN H 153 ASN H 176 ASN F1179 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13479 Z= 0.259 Angle : 0.633 10.069 18235 Z= 0.323 Chirality : 0.044 0.168 2081 Planarity : 0.004 0.055 2327 Dihedral : 6.789 72.177 1840 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.20 % Favored : 95.56 % Rotamer: Outliers : 3.57 % Allowed : 21.05 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1667 helix: 1.20 (0.19), residues: 713 sheet: -1.52 (0.29), residues: 318 loop : -0.68 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 111 HIS 0.013 0.002 HIS D 304 PHE 0.025 0.002 PHE B 109 TYR 0.027 0.002 TYR C 307 ARG 0.004 0.001 ARG H 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 205 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7773 (ppp) cc_final: 0.7427 (ppp) REVERT: B 97 PHE cc_start: 0.7863 (t80) cc_final: 0.7647 (t80) REVERT: B 106 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9074 (mm) REVERT: B 120 HIS cc_start: 0.9077 (OUTLIER) cc_final: 0.8769 (m90) REVERT: B 142 ASP cc_start: 0.8766 (m-30) cc_final: 0.8496 (p0) REVERT: B 169 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8977 (mmt) REVERT: B 172 MET cc_start: 0.9434 (tpt) cc_final: 0.8915 (tpt) REVERT: B 182 HIS cc_start: 0.8823 (m90) cc_final: 0.8487 (m90) REVERT: B 284 MET cc_start: 0.9666 (tmm) cc_final: 0.9299 (tmm) REVERT: B 307 TYR cc_start: 0.9127 (t80) cc_final: 0.8746 (t80) REVERT: E 98 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8501 (p0) REVERT: E 169 MET cc_start: 0.9463 (mtt) cc_final: 0.9237 (mtp) REVERT: E 284 MET cc_start: 0.9598 (tmm) cc_final: 0.9250 (tmm) REVERT: E 316 MET cc_start: 0.9167 (mmp) cc_final: 0.8838 (mmm) REVERT: C 302 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8829 (pm20) REVERT: C 305 LEU cc_start: 0.9425 (mm) cc_final: 0.9109 (mp) REVERT: D 244 ASN cc_start: 0.8792 (m110) cc_final: 0.8501 (m-40) REVERT: D 250 LEU cc_start: 0.9301 (mp) cc_final: 0.9062 (mp) REVERT: D 291 ASN cc_start: 0.8737 (t0) cc_final: 0.8422 (t0) REVERT: D 315 GLU cc_start: 0.8222 (tp30) cc_final: 0.7987 (tp30) REVERT: A 4 PHE cc_start: 0.8333 (m-80) cc_final: 0.8005 (m-80) REVERT: A 21 ASP cc_start: 0.8665 (t0) cc_final: 0.8226 (t0) REVERT: A 30 ASP cc_start: 0.9015 (m-30) cc_final: 0.8786 (m-30) REVERT: A 99 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8152 (tpt) REVERT: A 156 LYS cc_start: 0.9611 (tmtt) cc_final: 0.9343 (tppt) REVERT: G 32 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8433 (ptm-80) REVERT: H 172 TYR cc_start: 0.8964 (t80) cc_final: 0.8744 (t80) REVERT: F 1055 TYR cc_start: 0.8015 (p90) cc_final: 0.7578 (p90) outliers start: 51 outliers final: 17 residues processed: 243 average time/residue: 0.2545 time to fit residues: 91.1236 Evaluate side-chains 200 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1223 ASP Chi-restraints excluded: chain F residue 1224 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 ASN ** F1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13479 Z= 0.331 Angle : 0.612 7.917 18235 Z= 0.314 Chirality : 0.044 0.180 2081 Planarity : 0.004 0.047 2327 Dihedral : 6.506 68.764 1832 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.44 % Favored : 95.32 % Rotamer: Outliers : 3.71 % Allowed : 22.10 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1667 helix: 1.20 (0.19), residues: 709 sheet: -1.47 (0.28), residues: 335 loop : -0.69 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 111 HIS 0.010 0.001 HIS D 304 PHE 0.017 0.002 PHE E 264 TYR 0.016 0.002 TYR C 273 ARG 0.004 0.000 ARG H 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 188 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7959 (ppp) cc_final: 0.7587 (ppp) REVERT: B 120 HIS cc_start: 0.9200 (OUTLIER) cc_final: 0.8758 (m90) REVERT: B 142 ASP cc_start: 0.8776 (m-30) cc_final: 0.8518 (p0) REVERT: B 169 MET cc_start: 0.9293 (mmm) cc_final: 0.9085 (mmt) REVERT: B 172 MET cc_start: 0.9467 (tpt) cc_final: 0.8878 (tpt) REVERT: B 182 HIS cc_start: 0.8821 (m90) cc_final: 0.8459 (m90) REVERT: B 261 TYR cc_start: 0.7088 (t80) cc_final: 0.6833 (t80) REVERT: B 284 MET cc_start: 0.9651 (tmm) cc_final: 0.9252 (tmm) REVERT: B 285 TYR cc_start: 0.9415 (m-80) cc_final: 0.8998 (m-80) REVERT: B 307 TYR cc_start: 0.9097 (t80) cc_final: 0.8805 (t80) REVERT: E 98 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8481 (p0) REVERT: E 120 HIS cc_start: 0.8738 (m170) cc_final: 0.8477 (m170) REVERT: E 137 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8452 (p) REVERT: E 169 MET cc_start: 0.9492 (mtt) cc_final: 0.9289 (mtp) REVERT: E 284 MET cc_start: 0.9630 (tmm) cc_final: 0.9259 (tmm) REVERT: E 316 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8925 (mmm) REVERT: C 286 GLU cc_start: 0.9229 (pt0) cc_final: 0.8844 (pp20) REVERT: C 302 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8931 (pm20) REVERT: C 305 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9155 (mp) REVERT: D 244 ASN cc_start: 0.8769 (m110) cc_final: 0.8419 (m-40) REVERT: D 250 LEU cc_start: 0.9291 (mp) cc_final: 0.9065 (mp) REVERT: D 270 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8747 (pt0) REVERT: D 271 GLU cc_start: 0.9434 (OUTLIER) cc_final: 0.8702 (mp0) REVERT: D 284 MET cc_start: 0.9374 (tmm) cc_final: 0.8781 (tmm) REVERT: A 4 PHE cc_start: 0.8424 (m-80) cc_final: 0.8032 (m-80) REVERT: A 21 ASP cc_start: 0.8772 (t0) cc_final: 0.8344 (t0) REVERT: A 30 ASP cc_start: 0.9061 (m-30) cc_final: 0.8854 (m-30) REVERT: A 99 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8199 (tpt) REVERT: A 156 LYS cc_start: 0.9628 (tmtt) cc_final: 0.9353 (tppt) REVERT: A 171 THR cc_start: 0.9185 (m) cc_final: 0.8691 (p) REVERT: A 172 LYS cc_start: 0.9271 (mppt) cc_final: 0.8985 (mmtm) REVERT: A 179 GLN cc_start: 0.9314 (pm20) cc_final: 0.9098 (pm20) REVERT: G 51 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8601 (m-30) REVERT: F 1055 TYR cc_start: 0.8112 (p90) cc_final: 0.7656 (p90) outliers start: 53 outliers final: 25 residues processed: 223 average time/residue: 0.2389 time to fit residues: 78.9519 Evaluate side-chains 208 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 174 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1184 MET Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1223 ASP Chi-restraints excluded: chain F residue 1224 SER Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13479 Z= 0.274 Angle : 0.596 8.739 18235 Z= 0.302 Chirality : 0.043 0.294 2081 Planarity : 0.003 0.044 2327 Dihedral : 6.437 65.138 1832 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.50 % Favored : 95.26 % Rotamer: Outliers : 3.57 % Allowed : 23.22 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1667 helix: 1.18 (0.19), residues: 711 sheet: -1.44 (0.29), residues: 325 loop : -0.73 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 318 HIS 0.006 0.001 HIS D 304 PHE 0.016 0.001 PHE E 264 TYR 0.018 0.002 TYR C 307 ARG 0.006 0.000 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 186 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7974 (ppp) cc_final: 0.7591 (ppp) REVERT: B 120 HIS cc_start: 0.9193 (OUTLIER) cc_final: 0.8709 (m90) REVERT: B 142 ASP cc_start: 0.8769 (m-30) cc_final: 0.8509 (p0) REVERT: B 172 MET cc_start: 0.9457 (tpt) cc_final: 0.8883 (tpt) REVERT: B 182 HIS cc_start: 0.8782 (m90) cc_final: 0.8388 (m90) REVERT: B 261 TYR cc_start: 0.7188 (t80) cc_final: 0.6874 (t80) REVERT: B 284 MET cc_start: 0.9656 (tmm) cc_final: 0.9175 (tmm) REVERT: B 285 TYR cc_start: 0.9390 (m-80) cc_final: 0.8908 (m-80) REVERT: B 307 TYR cc_start: 0.9101 (t80) cc_final: 0.8736 (t80) REVERT: E 98 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8482 (p0) REVERT: E 120 HIS cc_start: 0.8727 (m170) cc_final: 0.8443 (m170) REVERT: E 137 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8407 (p) REVERT: E 172 MET cc_start: 0.9494 (tpt) cc_final: 0.9279 (tpt) REVERT: E 176 LEU cc_start: 0.9766 (OUTLIER) cc_final: 0.9497 (mm) REVERT: E 284 MET cc_start: 0.9638 (tmm) cc_final: 0.9323 (tmm) REVERT: E 316 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8958 (mmm) REVERT: C 286 GLU cc_start: 0.9271 (pt0) cc_final: 0.8839 (pp20) REVERT: C 302 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8941 (pm20) REVERT: C 305 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9196 (mp) REVERT: D 270 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8811 (pt0) REVERT: D 284 MET cc_start: 0.9459 (tmm) cc_final: 0.8870 (tmm) REVERT: A 4 PHE cc_start: 0.8442 (m-80) cc_final: 0.8071 (m-80) REVERT: A 21 ASP cc_start: 0.8763 (t0) cc_final: 0.8334 (t0) REVERT: A 30 ASP cc_start: 0.9071 (m-30) cc_final: 0.8845 (m-30) REVERT: A 99 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8248 (tpt) REVERT: A 168 LYS cc_start: 0.9254 (mmmt) cc_final: 0.8657 (mmmt) REVERT: A 171 THR cc_start: 0.9264 (m) cc_final: 0.8676 (p) REVERT: A 172 LYS cc_start: 0.9300 (mppt) cc_final: 0.9006 (mmtm) REVERT: G 32 ARG cc_start: 0.8777 (ttp80) cc_final: 0.8548 (ptm-80) REVERT: F 1055 TYR cc_start: 0.8104 (p90) cc_final: 0.7598 (p90) outliers start: 51 outliers final: 32 residues processed: 220 average time/residue: 0.2489 time to fit residues: 80.6146 Evaluate side-chains 209 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1184 MET Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1223 ASP Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 2 optimal weight: 0.1980 chunk 116 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 79 optimal weight: 0.0970 chunk 140 optimal weight: 9.9990 chunk 39 optimal weight: 0.0970 overall best weight: 2.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13479 Z= 0.252 Angle : 0.598 10.311 18235 Z= 0.298 Chirality : 0.044 0.304 2081 Planarity : 0.003 0.042 2327 Dihedral : 6.388 60.594 1832 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.26 % Favored : 95.50 % Rotamer: Outliers : 3.92 % Allowed : 24.20 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1667 helix: 1.20 (0.20), residues: 711 sheet: -1.35 (0.29), residues: 329 loop : -0.74 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 111 HIS 0.005 0.001 HIS D 304 PHE 0.015 0.001 PHE E 264 TYR 0.025 0.002 TYR H 172 ARG 0.007 0.001 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 188 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.9820 (OUTLIER) cc_final: 0.9243 (mp10) REVERT: B 120 HIS cc_start: 0.9167 (OUTLIER) cc_final: 0.8743 (m90) REVERT: B 125 MET cc_start: 0.9181 (mtm) cc_final: 0.8979 (mtp) REVERT: B 142 ASP cc_start: 0.8758 (m-30) cc_final: 0.8503 (p0) REVERT: B 169 MET cc_start: 0.9217 (mmt) cc_final: 0.8925 (mmt) REVERT: B 172 MET cc_start: 0.9462 (tpt) cc_final: 0.8878 (tpt) REVERT: B 182 HIS cc_start: 0.8774 (m90) cc_final: 0.8362 (m90) REVERT: B 284 MET cc_start: 0.9669 (tmm) cc_final: 0.9180 (tmm) REVERT: B 307 TYR cc_start: 0.9131 (t80) cc_final: 0.8755 (t80) REVERT: E 98 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8486 (p0) REVERT: E 120 HIS cc_start: 0.8725 (m170) cc_final: 0.8435 (m170) REVERT: E 137 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8261 (p) REVERT: E 172 MET cc_start: 0.9491 (tpt) cc_final: 0.9233 (tpt) REVERT: E 284 MET cc_start: 0.9645 (tmm) cc_final: 0.9366 (tmm) REVERT: E 316 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.9005 (mmm) REVERT: C 286 GLU cc_start: 0.9294 (pt0) cc_final: 0.8860 (pp20) REVERT: C 302 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8940 (pm20) REVERT: C 305 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9258 (mp) REVERT: D 240 GLU cc_start: 0.9132 (tp30) cc_final: 0.8534 (tp30) REVERT: D 244 ASN cc_start: 0.8975 (m-40) cc_final: 0.8032 (m-40) REVERT: D 270 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8848 (pt0) REVERT: D 284 MET cc_start: 0.9528 (tmm) cc_final: 0.8927 (tmm) REVERT: A 4 PHE cc_start: 0.8449 (m-80) cc_final: 0.8026 (m-80) REVERT: A 21 ASP cc_start: 0.8774 (t0) cc_final: 0.8354 (t0) REVERT: A 99 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8250 (tpt) REVERT: A 168 LYS cc_start: 0.9303 (mmmt) cc_final: 0.8704 (mmmt) REVERT: A 171 THR cc_start: 0.9325 (m) cc_final: 0.8810 (p) REVERT: A 172 LYS cc_start: 0.9334 (mppt) cc_final: 0.9055 (mmtm) REVERT: G 32 ARG cc_start: 0.8834 (ttp80) cc_final: 0.8598 (ptm-80) REVERT: H 117 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8550 (tm-30) REVERT: F 1055 TYR cc_start: 0.8104 (p90) cc_final: 0.7597 (p90) outliers start: 56 outliers final: 35 residues processed: 228 average time/residue: 0.2524 time to fit residues: 84.5435 Evaluate side-chains 221 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 177 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 9.9990 chunk 141 optimal weight: 0.0040 chunk 30 optimal weight: 9.9990 chunk 91 optimal weight: 0.0000 chunk 38 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13479 Z= 0.164 Angle : 0.599 12.426 18235 Z= 0.294 Chirality : 0.043 0.329 2081 Planarity : 0.003 0.040 2327 Dihedral : 6.259 59.478 1832 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.84 % Favored : 95.98 % Rotamer: Outliers : 3.29 % Allowed : 25.59 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1667 helix: 1.24 (0.19), residues: 712 sheet: -1.22 (0.29), residues: 314 loop : -0.82 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 263 HIS 0.004 0.001 HIS D 304 PHE 0.020 0.001 PHE A 63 TYR 0.029 0.002 TYR C 307 ARG 0.007 0.001 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 201 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.9817 (OUTLIER) cc_final: 0.9266 (mp10) REVERT: B 120 HIS cc_start: 0.9057 (OUTLIER) cc_final: 0.8753 (m90) REVERT: B 142 ASP cc_start: 0.8774 (m-30) cc_final: 0.8478 (p0) REVERT: B 172 MET cc_start: 0.9455 (tpt) cc_final: 0.8885 (tpt) REVERT: B 182 HIS cc_start: 0.8730 (m90) cc_final: 0.8365 (m-70) REVERT: B 284 MET cc_start: 0.9659 (tmm) cc_final: 0.9283 (tmm) REVERT: B 307 TYR cc_start: 0.9108 (t80) cc_final: 0.8720 (t80) REVERT: E 98 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8535 (p0) REVERT: E 120 HIS cc_start: 0.8692 (m170) cc_final: 0.8377 (m170) REVERT: E 284 MET cc_start: 0.9641 (tmm) cc_final: 0.9408 (tmm) REVERT: E 316 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.8981 (mmm) REVERT: C 286 GLU cc_start: 0.9316 (pt0) cc_final: 0.8780 (pp20) REVERT: C 287 ILE cc_start: 0.9616 (mt) cc_final: 0.9391 (mm) REVERT: C 302 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8942 (pm20) REVERT: C 305 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9192 (mt) REVERT: D 240 GLU cc_start: 0.9088 (tp30) cc_final: 0.8290 (tp30) REVERT: D 244 ASN cc_start: 0.8938 (m-40) cc_final: 0.7804 (m-40) REVERT: D 270 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8828 (pt0) REVERT: D 284 MET cc_start: 0.9551 (tmm) cc_final: 0.8939 (tmm) REVERT: A 4 PHE cc_start: 0.8392 (m-80) cc_final: 0.7938 (m-80) REVERT: A 21 ASP cc_start: 0.8732 (t0) cc_final: 0.8364 (t0) REVERT: A 63 PHE cc_start: 0.8871 (t80) cc_final: 0.8584 (t80) REVERT: A 64 MET cc_start: 0.8755 (tpp) cc_final: 0.8548 (mpp) REVERT: A 99 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8205 (tpt) REVERT: A 168 LYS cc_start: 0.9332 (mmmt) cc_final: 0.8721 (mmmt) REVERT: A 171 THR cc_start: 0.9358 (m) cc_final: 0.8876 (p) REVERT: A 172 LYS cc_start: 0.9333 (mppt) cc_final: 0.9017 (mmtm) REVERT: G 137 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8851 (p) REVERT: H 117 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: H 162 ARG cc_start: 0.8641 (ttm110) cc_final: 0.7887 (ptp-110) REVERT: H 172 TYR cc_start: 0.8881 (t80) cc_final: 0.8437 (t80) REVERT: F 1027 GLN cc_start: 0.8980 (mt0) cc_final: 0.8637 (mt0) REVERT: F 1055 TYR cc_start: 0.7992 (p90) cc_final: 0.7461 (p90) outliers start: 47 outliers final: 26 residues processed: 231 average time/residue: 0.2401 time to fit residues: 82.5238 Evaluate side-chains 212 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 177 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13479 Z= 0.407 Angle : 0.655 9.077 18235 Z= 0.330 Chirality : 0.044 0.279 2081 Planarity : 0.003 0.037 2327 Dihedral : 6.367 59.355 1832 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.40 % Favored : 94.36 % Rotamer: Outliers : 3.78 % Allowed : 25.94 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1667 helix: 1.19 (0.20), residues: 713 sheet: -1.22 (0.30), residues: 314 loop : -0.78 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 318 HIS 0.005 0.001 HIS A 94 PHE 0.019 0.002 PHE E 264 TYR 0.025 0.002 TYR B 261 ARG 0.006 0.001 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 173 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.9828 (OUTLIER) cc_final: 0.9248 (mp10) REVERT: B 106 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8964 (mm) REVERT: B 142 ASP cc_start: 0.8830 (m-30) cc_final: 0.8577 (p0) REVERT: B 182 HIS cc_start: 0.8751 (m90) cc_final: 0.8443 (m-70) REVERT: B 284 MET cc_start: 0.9675 (tmm) cc_final: 0.9244 (tmm) REVERT: B 307 TYR cc_start: 0.9198 (t80) cc_final: 0.8834 (t80) REVERT: E 98 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8469 (p0) REVERT: E 137 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8385 (p) REVERT: E 284 MET cc_start: 0.9663 (tmm) cc_final: 0.9349 (tmm) REVERT: E 316 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.9078 (mmm) REVERT: C 279 GLN cc_start: 0.8859 (pp30) cc_final: 0.8575 (pp30) REVERT: C 286 GLU cc_start: 0.9373 (pt0) cc_final: 0.8869 (pp20) REVERT: C 302 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8914 (pm20) REVERT: C 305 LEU cc_start: 0.9595 (mm) cc_final: 0.9318 (mt) REVERT: D 240 GLU cc_start: 0.9151 (tp30) cc_final: 0.8330 (tp30) REVERT: D 244 ASN cc_start: 0.9034 (m-40) cc_final: 0.7831 (m-40) REVERT: D 270 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8963 (mt-10) REVERT: D 284 MET cc_start: 0.9559 (tmm) cc_final: 0.8963 (tmm) REVERT: A 4 PHE cc_start: 0.8516 (m-80) cc_final: 0.8099 (m-80) REVERT: A 21 ASP cc_start: 0.8890 (t0) cc_final: 0.8439 (t0) REVERT: A 99 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8260 (tpt) REVERT: A 168 LYS cc_start: 0.9370 (mmmt) cc_final: 0.8793 (mmmt) REVERT: A 171 THR cc_start: 0.9364 (m) cc_final: 0.8851 (p) REVERT: A 172 LYS cc_start: 0.9368 (mppt) cc_final: 0.9070 (mmtm) REVERT: G 32 ARG cc_start: 0.8651 (ptm-80) cc_final: 0.8111 (ptm-80) REVERT: G 137 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8824 (p) REVERT: H 117 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8511 (tm-30) REVERT: H 162 ARG cc_start: 0.8697 (ttm110) cc_final: 0.8225 (ptp-110) REVERT: H 172 TYR cc_start: 0.8984 (t80) cc_final: 0.8448 (t80) REVERT: F 1055 TYR cc_start: 0.8170 (p90) cc_final: 0.7641 (p90) outliers start: 54 outliers final: 37 residues processed: 210 average time/residue: 0.2590 time to fit residues: 79.8215 Evaluate side-chains 215 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 169 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1196 LEU Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1223 ASP Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 142 optimal weight: 0.0770 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13479 Z= 0.195 Angle : 0.629 10.980 18235 Z= 0.303 Chirality : 0.044 0.298 2081 Planarity : 0.003 0.040 2327 Dihedral : 6.344 59.748 1832 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.14 % Favored : 95.62 % Rotamer: Outliers : 3.50 % Allowed : 25.94 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1667 helix: 1.31 (0.20), residues: 712 sheet: -1.14 (0.30), residues: 316 loop : -0.80 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 263 HIS 0.006 0.001 HIS C 304 PHE 0.025 0.001 PHE C 264 TYR 0.025 0.002 TYR B 261 ARG 0.007 0.001 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 186 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.9819 (OUTLIER) cc_final: 0.9242 (mp10) REVERT: B 106 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8989 (mm) REVERT: B 142 ASP cc_start: 0.8786 (m-30) cc_final: 0.8513 (p0) REVERT: B 168 MET cc_start: 0.9130 (ptp) cc_final: 0.8650 (mtp) REVERT: B 182 HIS cc_start: 0.8744 (m90) cc_final: 0.8405 (m-70) REVERT: B 284 MET cc_start: 0.9691 (tmm) cc_final: 0.9286 (tmm) REVERT: B 307 TYR cc_start: 0.9122 (t80) cc_final: 0.8754 (t80) REVERT: E 98 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8541 (p0) REVERT: E 120 HIS cc_start: 0.8746 (m170) cc_final: 0.8405 (m170) REVERT: E 137 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8265 (p) REVERT: E 168 MET cc_start: 0.9333 (mmt) cc_final: 0.8931 (mmt) REVERT: E 284 MET cc_start: 0.9646 (tmm) cc_final: 0.9391 (tmm) REVERT: C 276 VAL cc_start: 0.8855 (t) cc_final: 0.8592 (t) REVERT: C 279 GLN cc_start: 0.8870 (pp30) cc_final: 0.8611 (pp30) REVERT: C 286 GLU cc_start: 0.9380 (pt0) cc_final: 0.8857 (pp20) REVERT: C 302 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8954 (pm20) REVERT: C 305 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9265 (mt) REVERT: D 240 GLU cc_start: 0.9144 (tp30) cc_final: 0.8237 (tp30) REVERT: D 244 ASN cc_start: 0.9020 (m-40) cc_final: 0.7769 (m-40) REVERT: D 249 GLN cc_start: 0.9412 (tp40) cc_final: 0.9203 (tp-100) REVERT: D 270 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8818 (pt0) REVERT: D 284 MET cc_start: 0.9561 (tmm) cc_final: 0.8947 (tmm) REVERT: A 4 PHE cc_start: 0.8487 (m-80) cc_final: 0.7994 (m-80) REVERT: A 21 ASP cc_start: 0.8828 (t0) cc_final: 0.8398 (t0) REVERT: A 82 MET cc_start: 0.9572 (mmp) cc_final: 0.9218 (mmm) REVERT: A 99 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8207 (tpt) REVERT: A 168 LYS cc_start: 0.9341 (mmmt) cc_final: 0.8563 (mmmt) REVERT: A 171 THR cc_start: 0.9394 (m) cc_final: 0.8675 (p) REVERT: A 172 LYS cc_start: 0.9371 (mppt) cc_final: 0.9005 (mmtm) REVERT: G 32 ARG cc_start: 0.8582 (ptm-80) cc_final: 0.8381 (ptm-80) REVERT: G 137 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8844 (p) REVERT: H 162 ARG cc_start: 0.8577 (ttm110) cc_final: 0.8149 (ptp-110) REVERT: H 172 TYR cc_start: 0.8975 (t80) cc_final: 0.8461 (t80) REVERT: F 1027 GLN cc_start: 0.8937 (mt0) cc_final: 0.8609 (mt0) REVERT: F 1055 TYR cc_start: 0.8051 (p90) cc_final: 0.7481 (p90) REVERT: F 1163 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8945 (t) outliers start: 50 outliers final: 35 residues processed: 219 average time/residue: 0.2527 time to fit residues: 81.5176 Evaluate side-chains 222 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 178 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1163 VAL Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13479 Z= 0.229 Angle : 0.632 10.255 18235 Z= 0.306 Chirality : 0.044 0.296 2081 Planarity : 0.003 0.039 2327 Dihedral : 6.295 58.871 1832 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.98 % Favored : 94.84 % Rotamer: Outliers : 3.57 % Allowed : 25.45 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1667 helix: 1.31 (0.20), residues: 718 sheet: -1.06 (0.30), residues: 314 loop : -0.69 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 318 HIS 0.005 0.001 HIS D 295 PHE 0.023 0.001 PHE B 97 TYR 0.030 0.002 TYR D 261 ARG 0.007 0.001 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 183 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.9825 (OUTLIER) cc_final: 0.9238 (mp10) REVERT: B 106 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8994 (mm) REVERT: B 142 ASP cc_start: 0.8809 (m-30) cc_final: 0.8526 (p0) REVERT: B 168 MET cc_start: 0.9120 (ptp) cc_final: 0.8639 (mtp) REVERT: B 182 HIS cc_start: 0.8735 (m90) cc_final: 0.8394 (m-70) REVERT: B 284 MET cc_start: 0.9687 (tmm) cc_final: 0.9280 (tmm) REVERT: B 307 TYR cc_start: 0.9149 (t80) cc_final: 0.8799 (t80) REVERT: E 98 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8501 (p0) REVERT: E 120 HIS cc_start: 0.8780 (m170) cc_final: 0.8459 (m170) REVERT: E 137 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8273 (p) REVERT: E 168 MET cc_start: 0.9337 (mmt) cc_final: 0.8898 (mmt) REVERT: E 172 MET cc_start: 0.9457 (tpt) cc_final: 0.9211 (tpt) REVERT: E 190 MET cc_start: 0.9503 (tpp) cc_final: 0.9254 (tpp) REVERT: E 284 MET cc_start: 0.9677 (tmm) cc_final: 0.9458 (tmm) REVERT: C 276 VAL cc_start: 0.8791 (t) cc_final: 0.8538 (t) REVERT: C 279 GLN cc_start: 0.8937 (pp30) cc_final: 0.8641 (pp30) REVERT: C 286 GLU cc_start: 0.9420 (pt0) cc_final: 0.8939 (pp20) REVERT: C 305 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9270 (mt) REVERT: D 240 GLU cc_start: 0.9148 (tp30) cc_final: 0.8309 (tp30) REVERT: D 244 ASN cc_start: 0.9047 (m-40) cc_final: 0.7840 (m-40) REVERT: D 249 GLN cc_start: 0.9451 (tp40) cc_final: 0.9201 (tp-100) REVERT: D 270 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8802 (pt0) REVERT: D 284 MET cc_start: 0.9610 (tmm) cc_final: 0.9084 (tmm) REVERT: D 316 MET cc_start: 0.8958 (ptp) cc_final: 0.8608 (ptp) REVERT: A 4 PHE cc_start: 0.8499 (m-80) cc_final: 0.7999 (m-80) REVERT: A 21 ASP cc_start: 0.8883 (t0) cc_final: 0.8444 (t0) REVERT: A 99 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8206 (tpt) REVERT: A 104 ARG cc_start: 0.8623 (mtt-85) cc_final: 0.8209 (mtp85) REVERT: A 168 LYS cc_start: 0.9346 (mmmt) cc_final: 0.8560 (mmmt) REVERT: A 171 THR cc_start: 0.9405 (m) cc_final: 0.8725 (p) REVERT: A 172 LYS cc_start: 0.9381 (mppt) cc_final: 0.9007 (mmtm) REVERT: G 32 ARG cc_start: 0.8626 (ptm-80) cc_final: 0.8381 (ptm-80) REVERT: G 37 THR cc_start: 0.9648 (OUTLIER) cc_final: 0.9398 (p) REVERT: G 137 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8834 (p) REVERT: H 162 ARG cc_start: 0.8566 (ttm110) cc_final: 0.8137 (ptp-110) REVERT: H 172 TYR cc_start: 0.9003 (t80) cc_final: 0.8473 (t80) REVERT: F 1055 TYR cc_start: 0.8039 (p90) cc_final: 0.7515 (p90) REVERT: F 1163 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8954 (t) outliers start: 51 outliers final: 33 residues processed: 219 average time/residue: 0.2635 time to fit residues: 83.9659 Evaluate side-chains 219 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 177 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1163 VAL Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1223 ASP Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 106 optimal weight: 0.4980 chunk 161 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 0.1980 chunk 102 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13479 Z= 0.173 Angle : 0.641 11.426 18235 Z= 0.307 Chirality : 0.044 0.312 2081 Planarity : 0.003 0.041 2327 Dihedral : 6.263 58.346 1832 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.32 % Favored : 95.50 % Rotamer: Outliers : 2.80 % Allowed : 26.36 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.21), residues: 1667 helix: 1.32 (0.20), residues: 717 sheet: -0.97 (0.30), residues: 316 loop : -0.72 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 263 HIS 0.006 0.001 HIS D 295 PHE 0.043 0.001 PHE C 264 TYR 0.032 0.002 TYR C 273 ARG 0.008 0.001 ARG F1131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.9825 (OUTLIER) cc_final: 0.9223 (mp10) REVERT: B 106 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.9001 (mm) REVERT: B 142 ASP cc_start: 0.8778 (m-30) cc_final: 0.8485 (p0) REVERT: B 168 MET cc_start: 0.9144 (ptp) cc_final: 0.8630 (mtp) REVERT: B 182 HIS cc_start: 0.8702 (m90) cc_final: 0.8337 (m-70) REVERT: B 284 MET cc_start: 0.9694 (tmm) cc_final: 0.9305 (tmm) REVERT: B 307 TYR cc_start: 0.9134 (t80) cc_final: 0.8748 (t80) REVERT: E 98 ASP cc_start: 0.9038 (OUTLIER) cc_final: 0.8533 (p0) REVERT: E 112 SER cc_start: 0.8314 (m) cc_final: 0.7907 (p) REVERT: E 120 HIS cc_start: 0.8714 (m170) cc_final: 0.8380 (m170) REVERT: E 137 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8191 (p) REVERT: E 168 MET cc_start: 0.9326 (mmt) cc_final: 0.8901 (mmt) REVERT: E 172 MET cc_start: 0.9438 (tpt) cc_final: 0.9216 (tpt) REVERT: E 284 MET cc_start: 0.9661 (tmm) cc_final: 0.9430 (tmm) REVERT: C 279 GLN cc_start: 0.8895 (pp30) cc_final: 0.8641 (pp30) REVERT: C 286 GLU cc_start: 0.9421 (pt0) cc_final: 0.8973 (pp20) REVERT: C 305 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9191 (mt) REVERT: D 240 GLU cc_start: 0.9142 (tp30) cc_final: 0.8293 (tp30) REVERT: D 244 ASN cc_start: 0.9054 (m-40) cc_final: 0.7846 (m-40) REVERT: D 270 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8774 (pt0) REVERT: D 284 MET cc_start: 0.9607 (tmm) cc_final: 0.9067 (tmm) REVERT: D 316 MET cc_start: 0.8899 (ptp) cc_final: 0.8503 (ptp) REVERT: A 4 PHE cc_start: 0.8475 (m-80) cc_final: 0.7962 (m-80) REVERT: A 21 ASP cc_start: 0.8854 (t0) cc_final: 0.8434 (t0) REVERT: A 99 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8111 (tpt) REVERT: A 168 LYS cc_start: 0.9345 (mmmt) cc_final: 0.8555 (mmmt) REVERT: A 171 THR cc_start: 0.9411 (m) cc_final: 0.8796 (p) REVERT: A 172 LYS cc_start: 0.9385 (mppt) cc_final: 0.9018 (mmtm) REVERT: G 16 THR cc_start: 0.9427 (m) cc_final: 0.9160 (p) REVERT: G 32 ARG cc_start: 0.8580 (ptm-80) cc_final: 0.8338 (ptm-80) REVERT: G 37 THR cc_start: 0.9631 (OUTLIER) cc_final: 0.9381 (p) REVERT: G 137 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8808 (p) REVERT: H 162 ARG cc_start: 0.8522 (ttm110) cc_final: 0.8111 (ptp-110) REVERT: H 172 TYR cc_start: 0.8996 (t80) cc_final: 0.8489 (t80) REVERT: F 1055 TYR cc_start: 0.8004 (p90) cc_final: 0.7484 (p90) REVERT: F 1163 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8972 (t) outliers start: 40 outliers final: 28 residues processed: 217 average time/residue: 0.2857 time to fit residues: 91.7488 Evaluate side-chains 215 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 178 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain F residue 1163 VAL Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 18 optimal weight: 40.0000 chunk 35 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 0.0980 chunk 113 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.039929 restraints weight = 51466.913| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 4.41 r_work: 0.2500 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13479 Z= 0.226 Angle : 0.648 12.395 18235 Z= 0.312 Chirality : 0.044 0.305 2081 Planarity : 0.003 0.040 2327 Dihedral : 6.278 59.665 1832 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.38 % Favored : 95.38 % Rotamer: Outliers : 2.66 % Allowed : 26.57 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1667 helix: 1.30 (0.20), residues: 723 sheet: -0.95 (0.30), residues: 317 loop : -0.66 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 263 HIS 0.008 0.001 HIS D 295 PHE 0.026 0.001 PHE C 264 TYR 0.038 0.002 TYR D 261 ARG 0.010 0.001 ARG D 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2847.04 seconds wall clock time: 53 minutes 0.42 seconds (3180.42 seconds total)