Starting phenix.real_space_refine on Tue Jul 23 05:15:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8e_31016/07_2024/7e8e_31016.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8e_31016/07_2024/7e8e_31016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8e_31016/07_2024/7e8e_31016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8e_31016/07_2024/7e8e_31016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8e_31016/07_2024/7e8e_31016.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8e_31016/07_2024/7e8e_31016.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 13764 2.51 5 N 3626 2.21 5 O 3870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 72": "OD1" <-> "OD2" Residue "G TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 203": "OD1" <-> "OD2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H ASP 99": "OD1" <-> "OD2" Residue "H ASP 193": "OD1" <-> "OD2" Residue "H PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 203": "OD1" <-> "OD2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 203": "OD1" <-> "OD2" Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 86": "OD1" <-> "OD2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 99": "OD1" <-> "OD2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "F ASP 203": "OD1" <-> "OD2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 21380 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "C" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3683 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 3 Chain: "K" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 211 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "H" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1459 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain breaks: 1 Chain: "D" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3675 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} Chain breaks: 3 Chain: "L" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 196 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "E" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "A" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3683 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 3 Chain: "I" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 211 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "F" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1459 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain breaks: 1 Chain: "B" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3675 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} Chain breaks: 3 Chain: "J" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 196 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Time building chain proxies: 11.26, per 1000 atoms: 0.53 Number of scatterers: 21380 At special positions: 0 Unit cell: (155.415, 151.405, 129.346, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3870 8.00 N 3626 7.00 C 13764 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: 8.58 Conformation dependent library (CDL) restraints added in 3.9 seconds 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 6 sheets defined 71.1% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'G' and resid 49 through 62 removed outlier: 3.635A pdb=" N VAL G 55 " --> pdb=" O ARG G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 80 removed outlier: 4.103A pdb=" N GLN G 76 " --> pdb=" O ASP G 72 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR G 78 " --> pdb=" O PHE G 74 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN G 80 " --> pdb=" O GLN G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 99 removed outlier: 3.577A pdb=" N ASN G 96 " --> pdb=" O HIS G 92 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA G 97 " --> pdb=" O TYR G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 103 removed outlier: 3.707A pdb=" N THR G 103 " --> pdb=" O THR G 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 100 through 103' Processing helix chain 'G' and resid 108 through 120 Processing helix chain 'G' and resid 122 through 135 removed outlier: 3.696A pdb=" N LEU G 127 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG G 128 " --> pdb=" O HIS G 124 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 156 removed outlier: 4.170A pdb=" N ASP G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 182 removed outlier: 4.408A pdb=" N ARG G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS G 181 " --> pdb=" O VAL G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 199 Processing helix chain 'G' and resid 202 through 215 removed outlier: 3.617A pdb=" N MET G 206 " --> pdb=" O ASP G 202 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN G 210 " --> pdb=" O MET G 206 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN G 214 " --> pdb=" O GLN G 210 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.562A pdb=" N VAL C 5 " --> pdb=" O ALA C 2 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA C 7 " --> pdb=" O GLY C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.710A pdb=" N ALA C 12 " --> pdb=" O TRP C 8 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 18 " --> pdb=" O ALA C 14 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 88 through 102 removed outlier: 4.058A pdb=" N HIS C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE C 95 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.513A pdb=" N ILE C 128 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE C 129 " --> pdb=" O PRO C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 129' Processing helix chain 'C' and resid 133 through 152 removed outlier: 3.897A pdb=" N ASP C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 177 removed outlier: 3.754A pdb=" N ARG C 173 " --> pdb=" O GLN C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 205 removed outlier: 3.770A pdb=" N LEU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 191 " --> pdb=" O PHE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.556A pdb=" N SER C 212 " --> pdb=" O PRO C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 251 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.787A pdb=" N TYR C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.626A pdb=" N LEU C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 305 removed outlier: 3.798A pdb=" N ARG C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 318 removed outlier: 4.337A pdb=" N ARG C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 346 removed outlier: 4.068A pdb=" N GLY C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 326 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 367 removed outlier: 4.333A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 removed outlier: 3.555A pdb=" N ILE C 385 " --> pdb=" O ILE C 381 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 450 removed outlier: 3.819A pdb=" N ASN C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 489 Processing helix chain 'K' and resid 29 through 56 removed outlier: 3.526A pdb=" N ILE K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR K 56 " --> pdb=" O VAL K 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 64 removed outlier: 3.778A pdb=" N GLU H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 103 removed outlier: 3.629A pdb=" N THR H 103 " --> pdb=" O THR H 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 100 through 103' Processing helix chain 'H' and resid 107 through 120 Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 143 through 156 removed outlier: 3.847A pdb=" N MET H 147 " --> pdb=" O ASN H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 182 removed outlier: 4.335A pdb=" N ARG H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 200 Processing helix chain 'H' and resid 202 through 208 removed outlier: 3.560A pdb=" N MET H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 214 Processing helix chain 'D' and resid 5 through 7 No H-bonds generated for 'chain 'D' and resid 5 through 7' Processing helix chain 'D' and resid 8 through 17 removed outlier: 3.861A pdb=" N ILE D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.710A pdb=" N LEU D 59 " --> pdb=" O TRP D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.831A pdb=" N HIS D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 removed outlier: 3.670A pdb=" N PHE D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 130 through 153 removed outlier: 4.116A pdb=" N GLU D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU D 136 " --> pdb=" O CYS D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 177 removed outlier: 4.097A pdb=" N ALA D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 207 Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 228 through 250 removed outlier: 4.408A pdb=" N THR D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 235 " --> pdb=" O CYS D 231 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 Processing helix chain 'D' and resid 260 through 283 removed outlier: 3.761A pdb=" N ILE D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 307 through 320 removed outlier: 4.135A pdb=" N ARG D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 312 " --> pdb=" O GLN D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.473A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 removed outlier: 3.802A pdb=" N ILE D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE D 386 " --> pdb=" O ALA D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 450 Processing helix chain 'D' and resid 473 through 489 removed outlier: 3.905A pdb=" N GLN D 477 " --> pdb=" O SER D 473 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 56 Processing helix chain 'E' and resid 49 through 62 removed outlier: 3.635A pdb=" N VAL E 55 " --> pdb=" O ARG E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.102A pdb=" N GLN E 76 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR E 78 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 99 removed outlier: 3.577A pdb=" N ASN E 96 " --> pdb=" O HIS E 92 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA E 97 " --> pdb=" O TYR E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 103 removed outlier: 3.707A pdb=" N THR E 103 " --> pdb=" O THR E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 100 through 103' Processing helix chain 'E' and resid 108 through 120 Processing helix chain 'E' and resid 122 through 135 removed outlier: 3.697A pdb=" N LEU E 127 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG E 128 " --> pdb=" O HIS E 124 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR E 130 " --> pdb=" O LYS E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 156 removed outlier: 4.169A pdb=" N ASP E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 182 removed outlier: 4.408A pdb=" N ARG E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS E 181 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 199 Processing helix chain 'E' and resid 202 through 215 removed outlier: 3.617A pdb=" N MET E 206 " --> pdb=" O ASP E 202 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN E 210 " --> pdb=" O MET E 206 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU E 211 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN E 214 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.570A pdb=" N VAL A 5 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ALA A 7 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 19 removed outlier: 3.712A pdb=" N ALA A 12 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 88 through 102 removed outlier: 4.059A pdb=" N HIS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.514A pdb=" N ILE A 128 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 129 " --> pdb=" O PRO A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 129' Processing helix chain 'A' and resid 133 through 152 removed outlier: 3.890A pdb=" N ASP A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.753A pdb=" N ARG A 173 " --> pdb=" O GLN A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 205 removed outlier: 3.769A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.556A pdb=" N SER A 212 " --> pdb=" O PRO A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 251 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.788A pdb=" N TYR A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 295 removed outlier: 3.626A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 removed outlier: 3.804A pdb=" N ARG A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 318 removed outlier: 4.333A pdb=" N ARG A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 346 removed outlier: 4.064A pdb=" N GLY A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 367 removed outlier: 4.328A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 removed outlier: 3.563A pdb=" N ILE A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 450 removed outlier: 3.819A pdb=" N ASN A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'I' and resid 29 through 55 removed outlier: 3.526A pdb=" N ILE I 34 " --> pdb=" O ALA I 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 64 removed outlier: 3.778A pdb=" N GLU F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 82 Processing helix chain 'F' and resid 87 through 99 Processing helix chain 'F' and resid 100 through 103 removed outlier: 3.628A pdb=" N THR F 103 " --> pdb=" O THR F 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 100 through 103' Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 143 through 156 removed outlier: 3.855A pdb=" N MET F 147 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 182 removed outlier: 4.353A pdb=" N ARG F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 200 Processing helix chain 'F' and resid 202 through 208 removed outlier: 3.569A pdb=" N MET F 206 " --> pdb=" O ASP F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 214 Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 8 through 17 removed outlier: 3.861A pdb=" N ILE B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.711A pdb=" N LEU B 59 " --> pdb=" O TRP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.831A pdb=" N HIS B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 removed outlier: 3.670A pdb=" N PHE B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 130 through 153 removed outlier: 4.116A pdb=" N GLU B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU B 136 " --> pdb=" O CYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 177 removed outlier: 4.096A pdb=" N ALA B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 207 Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 228 through 250 removed outlier: 4.409A pdb=" N THR B 234 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 235 " --> pdb=" O CYS B 231 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 260 through 283 removed outlier: 3.759A pdb=" N ILE B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 307 through 320 removed outlier: 4.135A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.477A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 369 " --> pdb=" O ILE B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.797A pdb=" N ILE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 450 Processing helix chain 'B' and resid 473 through 489 removed outlier: 3.905A pdb=" N GLN B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 56 Processing sheet with id=AA1, first strand: chain 'G' and resid 68 through 70 Processing sheet with id=AA2, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.871A pdb=" N LEU C 45 " --> pdb=" O PHE C 52 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR C 54 " --> pdb=" O ILE C 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.636A pdb=" N GLN D 82 " --> pdb=" O HIS D 77 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS D 77 " --> pdb=" O GLN D 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 68 through 70 Processing sheet with id=AA5, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.870A pdb=" N LEU A 45 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 54 " --> pdb=" O ILE A 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.635A pdb=" N GLN B 82 " --> pdb=" O HIS B 77 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS B 77 " --> pdb=" O GLN B 82 " (cutoff:3.500A) 1244 hydrogen bonds defined for protein. 3648 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: 6.70 Time building geometry restraints manager: 9.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6832 1.34 - 1.46: 5237 1.46 - 1.58: 9617 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 21878 Sorted by residual: bond pdb=" C THR J 56 " pdb=" N PRO J 57 " ideal model delta sigma weight residual 1.339 1.387 -0.048 3.40e-02 8.65e+02 1.99e+00 bond pdb=" C THR L 56 " pdb=" N PRO L 57 " ideal model delta sigma weight residual 1.339 1.387 -0.047 3.40e-02 8.65e+02 1.95e+00 bond pdb=" C SER F 208 " pdb=" N LEU F 209 " ideal model delta sigma weight residual 1.332 1.316 0.017 1.40e-02 5.10e+03 1.45e+00 bond pdb=" C SER H 208 " pdb=" N LEU H 209 " ideal model delta sigma weight residual 1.332 1.316 0.017 1.40e-02 5.10e+03 1.39e+00 bond pdb=" C LEU D 400 " pdb=" N PRO D 401 " ideal model delta sigma weight residual 1.336 1.347 -0.012 9.80e-03 1.04e+04 1.39e+00 ... (remaining 21873 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.63: 426 105.63 - 112.75: 11320 112.75 - 119.87: 7715 119.87 - 126.99: 9930 126.99 - 134.12: 215 Bond angle restraints: 29606 Sorted by residual: angle pdb=" N LEU G 39 " pdb=" CA LEU G 39 " pdb=" C LEU G 39 " ideal model delta sigma weight residual 114.56 108.33 6.23 1.27e+00 6.20e-01 2.40e+01 angle pdb=" N LEU E 39 " pdb=" CA LEU E 39 " pdb=" C LEU E 39 " ideal model delta sigma weight residual 114.56 108.35 6.21 1.27e+00 6.20e-01 2.39e+01 angle pdb=" CA ARG H 172 " pdb=" CB ARG H 172 " pdb=" CG ARG H 172 " ideal model delta sigma weight residual 114.10 122.76 -8.66 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA ARG F 172 " pdb=" CB ARG F 172 " pdb=" CG ARG F 172 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.84e+01 angle pdb=" C MET G 206 " pdb=" N ARG G 207 " pdb=" CA ARG G 207 " ideal model delta sigma weight residual 122.56 115.51 7.05 1.72e+00 3.38e-01 1.68e+01 ... (remaining 29601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 11632 17.79 - 35.58: 1079 35.58 - 53.37: 241 53.37 - 71.16: 28 71.16 - 88.95: 24 Dihedral angle restraints: 13004 sinusoidal: 5182 harmonic: 7822 Sorted by residual: dihedral pdb=" CA ARG C 108 " pdb=" C ARG C 108 " pdb=" N HIS C 109 " pdb=" CA HIS C 109 " ideal model delta harmonic sigma weight residual -180.00 -150.52 -29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA ARG A 108 " pdb=" C ARG A 108 " pdb=" N HIS A 109 " pdb=" CA HIS A 109 " ideal model delta harmonic sigma weight residual -180.00 -150.59 -29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ARG F 172 " pdb=" C ARG F 172 " pdb=" N GLN F 173 " pdb=" CA GLN F 173 " ideal model delta harmonic sigma weight residual 180.00 153.72 26.28 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 13001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2589 0.051 - 0.102: 587 0.102 - 0.153: 116 0.153 - 0.205: 2 0.205 - 0.256: 2 Chirality restraints: 3296 Sorted by residual: chirality pdb=" CA ARG H 172 " pdb=" N ARG H 172 " pdb=" C ARG H 172 " pdb=" CB ARG H 172 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ARG F 172 " pdb=" N ARG F 172 " pdb=" C ARG F 172 " pdb=" CB ARG F 172 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA THR J 56 " pdb=" N THR J 56 " pdb=" C THR J 56 " pdb=" CB THR J 56 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 3293 not shown) Planarity restraints: 3766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 129 " -0.021 2.00e-02 2.50e+03 1.97e-02 9.72e+00 pdb=" CG TRP G 129 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP G 129 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP G 129 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 129 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 129 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 129 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 129 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 129 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP G 129 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 129 " 0.021 2.00e-02 2.50e+03 1.96e-02 9.62e+00 pdb=" CG TRP E 129 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP E 129 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 129 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 129 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 129 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 129 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 129 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 129 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 129 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 30 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO A 31 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " 0.040 5.00e-02 4.00e+02 ... (remaining 3763 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 495 2.68 - 3.24: 23872 3.24 - 3.79: 34703 3.79 - 4.35: 44092 4.35 - 4.90: 69574 Nonbonded interactions: 172736 Sorted by model distance: nonbonded pdb=" NH1 ARG H 172 " pdb=" OE1 GLN H 173 " model vdw 2.130 2.520 nonbonded pdb=" NH1 ARG F 172 " pdb=" OE1 GLN F 173 " model vdw 2.134 2.520 nonbonded pdb=" OG1 THR B 65 " pdb=" OH TYR B 99 " model vdw 2.139 2.440 nonbonded pdb=" OG1 THR D 65 " pdb=" OH TYR D 99 " model vdw 2.142 2.440 nonbonded pdb=" O MET B 238 " pdb=" OG1 THR B 241 " model vdw 2.152 2.440 ... (remaining 172731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 218 or resid 224 through 495)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 218 or resid 224 through 495)) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 37 through 216) selection = chain 'F' selection = (chain 'G' and resid 37 through 216) selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 31 through 58) selection = chain 'J' selection = (chain 'K' and resid 31 through 58) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 56.250 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 0.048 21878 Z= 0.256 Angle : 0.683 8.660 29606 Z= 0.367 Chirality : 0.044 0.256 3296 Planarity : 0.005 0.073 3766 Dihedral : 14.763 88.953 7936 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.98 % Favored : 92.86 % Rotamer: Outliers : 0.04 % Allowed : 0.39 % Favored : 99.57 % 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: -0.20 (0.17), residues: 2606 helix: 0.66 (0.13), residues: 1680 sheet: -1.51 (1.18), residues: 20 loop : -1.57 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP G 129 HIS 0.007 0.001 HIS D 77 PHE 0.027 0.002 PHE A 194 TYR 0.015 0.001 TYR F 57 ARG 0.008 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 634 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 204 ASN cc_start: 0.6693 (OUTLIER) cc_final: 0.6446 (t0) REVERT: C 224 ARG cc_start: 0.4852 (mmt-90) cc_final: 0.4307 (mtp85) REVERT: C 238 MET cc_start: 0.5759 (mtt) cc_final: 0.5478 (ttm) REVERT: C 299 ARG cc_start: 0.7413 (mmt-90) cc_final: 0.7060 (mtm-85) REVERT: C 318 LYS cc_start: 0.7382 (mmpt) cc_final: 0.7143 (tppt) REVERT: C 485 LEU cc_start: 0.8635 (mm) cc_final: 0.8424 (tp) REVERT: H 76 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7532 (tp-100) REVERT: H 77 ILE cc_start: 0.8304 (mm) cc_final: 0.7917 (mm) REVERT: H 107 LYS cc_start: 0.7783 (tttt) cc_final: 0.7419 (tttt) REVERT: H 110 ASP cc_start: 0.7438 (m-30) cc_final: 0.7160 (t0) REVERT: H 186 LYS cc_start: 0.6338 (tptt) cc_final: 0.5774 (mmmt) REVERT: H 204 ASN cc_start: 0.7459 (m-40) cc_final: 0.7214 (m-40) REVERT: H 214 ASN cc_start: 0.7203 (p0) cc_final: 0.6886 (p0) REVERT: H 216 MET cc_start: 0.7319 (tpp) cc_final: 0.7077 (mtt) REVERT: D 83 TYR cc_start: 0.8390 (m-80) cc_final: 0.8002 (m-80) REVERT: D 243 GLU cc_start: 0.7204 (pm20) cc_final: 0.6534 (tt0) REVERT: D 368 MET cc_start: 0.8257 (mmm) cc_final: 0.8021 (mmm) REVERT: D 406 VAL cc_start: 0.8413 (p) cc_final: 0.8123 (t) REVERT: E 211 LEU cc_start: 0.7107 (mt) cc_final: 0.4675 (mt) REVERT: A 224 ARG cc_start: 0.4891 (mmt-90) cc_final: 0.4330 (mtp85) REVERT: A 238 MET cc_start: 0.5747 (mtt) cc_final: 0.5455 (ttm) REVERT: A 299 ARG cc_start: 0.7390 (mmt-90) cc_final: 0.7019 (mtm-85) REVERT: A 318 LYS cc_start: 0.7410 (mmpt) cc_final: 0.7157 (tppt) REVERT: A 484 CYS cc_start: 0.8712 (t) cc_final: 0.8509 (t) REVERT: F 76 GLN cc_start: 0.7967 (tp-100) cc_final: 0.7541 (tp-100) REVERT: F 77 ILE cc_start: 0.8285 (mm) cc_final: 0.7897 (mm) REVERT: F 107 LYS cc_start: 0.7804 (tttt) cc_final: 0.7424 (tttt) REVERT: F 110 ASP cc_start: 0.7444 (m-30) cc_final: 0.7147 (t0) REVERT: F 186 LYS cc_start: 0.6323 (tptt) cc_final: 0.5759 (mmmt) REVERT: F 191 THR cc_start: 0.6496 (m) cc_final: 0.6193 (m) REVERT: F 204 ASN cc_start: 0.7470 (m-40) cc_final: 0.7229 (m-40) REVERT: F 214 ASN cc_start: 0.7230 (p0) cc_final: 0.6918 (p0) REVERT: F 216 MET cc_start: 0.7317 (tpp) cc_final: 0.7081 (mtt) REVERT: B 83 TYR cc_start: 0.8364 (m-80) cc_final: 0.7993 (m-80) REVERT: B 243 GLU cc_start: 0.7242 (pm20) cc_final: 0.6679 (tt0) REVERT: B 406 VAL cc_start: 0.8417 (p) cc_final: 0.8138 (t) outliers start: 1 outliers final: 0 residues processed: 635 average time/residue: 0.3543 time to fit residues: 335.1440 Evaluate side-chains 397 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 396 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 204 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 1.9990 chunk 197 optimal weight: 0.1980 chunk 109 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 132 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 78 optimal weight: 0.0470 chunk 123 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 236 optimal weight: 0.0020 overall best weight: 0.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 124 HIS G 174 HIS ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS H 96 ASN ** H 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 124 HIS E 174 HIS ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS F 96 ASN F 124 HIS ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21878 Z= 0.198 Angle : 0.656 9.813 29606 Z= 0.339 Chirality : 0.043 0.242 3296 Planarity : 0.005 0.058 3766 Dihedral : 4.475 26.221 2924 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.91 % Favored : 93.94 % Rotamer: Outliers : 2.13 % Allowed : 13.22 % Favored : 84.65 % 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: -0.22 (0.17), residues: 2606 helix: 0.65 (0.13), residues: 1718 sheet: -1.10 (1.27), residues: 20 loop : -1.70 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 19 HIS 0.006 0.001 HIS E 174 PHE 0.025 0.002 PHE C 329 TYR 0.021 0.001 TYR D 137 ARG 0.019 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 475 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 129 TRP cc_start: 0.6970 (t60) cc_final: 0.6617 (t60) REVERT: G 132 ASN cc_start: 0.7855 (m110) cc_final: 0.7181 (t0) REVERT: C 224 ARG cc_start: 0.4822 (mmt-90) cc_final: 0.4282 (mtp85) REVERT: C 238 MET cc_start: 0.5665 (mtt) cc_final: 0.5454 (ttm) REVERT: C 299 ARG cc_start: 0.7485 (mmt-90) cc_final: 0.7159 (mtm-85) REVERT: C 318 LYS cc_start: 0.7440 (mmpt) cc_final: 0.7236 (tppt) REVERT: C 404 VAL cc_start: 0.8717 (p) cc_final: 0.8485 (t) REVERT: H 76 GLN cc_start: 0.7898 (tp-100) cc_final: 0.7518 (tp-100) REVERT: H 77 ILE cc_start: 0.8288 (mm) cc_final: 0.7987 (mm) REVERT: H 84 HIS cc_start: 0.6189 (OUTLIER) cc_final: 0.5558 (p-80) REVERT: H 107 LYS cc_start: 0.7896 (tttt) cc_final: 0.7439 (ttpt) REVERT: H 186 LYS cc_start: 0.6247 (tptt) cc_final: 0.6029 (tptt) REVERT: H 214 ASN cc_start: 0.7280 (p0) cc_final: 0.7068 (p0) REVERT: D 83 TYR cc_start: 0.8323 (m-80) cc_final: 0.8049 (m-80) REVERT: D 368 MET cc_start: 0.8185 (mmm) cc_final: 0.7971 (mmm) REVERT: D 406 VAL cc_start: 0.8380 (p) cc_final: 0.8097 (t) REVERT: D 429 ARG cc_start: 0.7985 (mmp-170) cc_final: 0.6757 (tpp-160) REVERT: E 129 TRP cc_start: 0.6948 (t60) cc_final: 0.6589 (t60) REVERT: E 132 ASN cc_start: 0.7857 (m110) cc_final: 0.7199 (t0) REVERT: A 224 ARG cc_start: 0.4870 (mmt-90) cc_final: 0.4300 (mtp85) REVERT: A 238 MET cc_start: 0.5642 (mtt) cc_final: 0.5425 (ttm) REVERT: A 299 ARG cc_start: 0.7485 (mmt-90) cc_final: 0.7088 (mtm-85) REVERT: A 318 LYS cc_start: 0.7459 (mmpt) cc_final: 0.7254 (tppt) REVERT: A 404 VAL cc_start: 0.8716 (p) cc_final: 0.8479 (t) REVERT: F 76 GLN cc_start: 0.7929 (tp-100) cc_final: 0.7520 (tp-100) REVERT: F 77 ILE cc_start: 0.8279 (mm) cc_final: 0.7996 (mm) REVERT: F 80 GLN cc_start: 0.7873 (tt0) cc_final: 0.7576 (tt0) REVERT: F 84 HIS cc_start: 0.6262 (OUTLIER) cc_final: 0.5639 (p-80) REVERT: F 107 LYS cc_start: 0.7909 (tttt) cc_final: 0.7439 (ttpt) REVERT: F 214 ASN cc_start: 0.7310 (p0) cc_final: 0.7099 (p0) REVERT: B 83 TYR cc_start: 0.8310 (m-80) cc_final: 0.8038 (m-80) REVERT: B 406 VAL cc_start: 0.8398 (p) cc_final: 0.8111 (t) REVERT: B 429 ARG cc_start: 0.7998 (mmp-170) cc_final: 0.6744 (tpp-160) outliers start: 49 outliers final: 29 residues processed: 490 average time/residue: 0.3459 time to fit residues: 262.6677 Evaluate side-chains 442 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 411 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 124 HIS Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 161 TYR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 161 TYR Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain J residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 ASN G 204 ASN ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS C 416 ASN H 41 GLN H 80 GLN ** H 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 62 ASN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS A 416 ASN F 41 GLN ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 202 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 21878 Z= 0.515 Angle : 0.769 10.360 29606 Z= 0.409 Chirality : 0.048 0.174 3296 Planarity : 0.006 0.068 3766 Dihedral : 4.851 28.078 2922 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.18 % Favored : 92.75 % Rotamer: Outliers : 3.65 % Allowed : 18.17 % Favored : 78.17 % 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: -0.65 (0.16), residues: 2606 helix: 0.29 (0.12), residues: 1722 sheet: None (None), residues: 0 loop : -1.79 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP C 19 HIS 0.006 0.002 HIS F 84 PHE 0.028 0.003 PHE A 194 TYR 0.029 0.003 TYR D 137 ARG 0.013 0.001 ARG D 299 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 399 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: C 224 ARG cc_start: 0.5402 (mmt-90) cc_final: 0.4878 (mtp85) REVERT: C 238 MET cc_start: 0.5722 (mtt) cc_final: 0.5516 (ttm) REVERT: C 299 ARG cc_start: 0.7497 (mmt-90) cc_final: 0.7109 (mtm-85) REVERT: H 76 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7599 (tp-100) REVERT: H 77 ILE cc_start: 0.8362 (mm) cc_final: 0.8078 (mm) REVERT: H 80 GLN cc_start: 0.8086 (tt0) cc_final: 0.7781 (tt0) REVERT: H 107 LYS cc_start: 0.8111 (tttt) cc_final: 0.7531 (tttt) REVERT: H 148 MET cc_start: 0.6518 (mmm) cc_final: 0.6139 (mmm) REVERT: D 83 TYR cc_start: 0.8363 (m-80) cc_final: 0.8101 (m-80) REVERT: D 136 GLU cc_start: 0.7282 (tm-30) cc_final: 0.7048 (tm-30) REVERT: D 406 VAL cc_start: 0.8424 (p) cc_final: 0.8171 (t) REVERT: A 60 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8027 (pm20) REVERT: A 224 ARG cc_start: 0.5435 (mmt-90) cc_final: 0.4985 (mtp85) REVERT: A 238 MET cc_start: 0.5729 (mtt) cc_final: 0.5524 (ttm) REVERT: A 299 ARG cc_start: 0.7551 (mmt-90) cc_final: 0.7153 (mtm-85) REVERT: F 76 GLN cc_start: 0.7954 (tp-100) cc_final: 0.7597 (tp-100) REVERT: F 77 ILE cc_start: 0.8351 (mm) cc_final: 0.8068 (mm) REVERT: F 107 LYS cc_start: 0.8120 (tttt) cc_final: 0.7534 (tttt) REVERT: F 148 MET cc_start: 0.6584 (mmm) cc_final: 0.6212 (mmm) REVERT: B 83 TYR cc_start: 0.8357 (m-80) cc_final: 0.8098 (m-80) REVERT: B 136 GLU cc_start: 0.7268 (tm-30) cc_final: 0.7023 (tm-30) REVERT: B 406 VAL cc_start: 0.8430 (p) cc_final: 0.8173 (t) outliers start: 84 outliers final: 50 residues processed: 455 average time/residue: 0.3397 time to fit residues: 234.9030 Evaluate side-chains 419 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 367 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 181 LYS Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain H residue 124 HIS Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 161 TYR Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 161 TYR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain J residue 38 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 9.9990 chunk 177 optimal weight: 0.0170 chunk 122 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 251 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 224 optimal weight: 0.0050 chunk 67 optimal weight: 6.9990 overall best weight: 0.5234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 ASN G 204 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS H 41 GLN H 70 ASN ** H 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 62 ASN E 70 ASN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS F 70 ASN F 124 HIS ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 202 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21878 Z= 0.188 Angle : 0.625 9.374 29606 Z= 0.323 Chirality : 0.043 0.328 3296 Planarity : 0.004 0.049 3766 Dihedral : 4.479 24.007 2922 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.14 % Favored : 93.78 % Rotamer: Outliers : 2.87 % Allowed : 19.39 % Favored : 77.74 % 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: -0.24 (0.17), residues: 2606 helix: 0.60 (0.13), residues: 1742 sheet: None (None), residues: 0 loop : -1.67 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 19 HIS 0.005 0.001 HIS D 109 PHE 0.023 0.002 PHE A 194 TYR 0.015 0.001 TYR H 90 ARG 0.016 0.001 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 435 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 208 SER cc_start: 0.7338 (p) cc_final: 0.7007 (p) REVERT: C 60 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7892 (pm20) REVERT: C 224 ARG cc_start: 0.4942 (mmt-90) cc_final: 0.4499 (mtp85) REVERT: C 238 MET cc_start: 0.5664 (mtt) cc_final: 0.5457 (ttm) REVERT: C 299 ARG cc_start: 0.7513 (mmt-90) cc_final: 0.7066 (mtm-85) REVERT: C 311 ARG cc_start: 0.6798 (mtm180) cc_final: 0.6442 (mpp80) REVERT: H 76 GLN cc_start: 0.7889 (tp-100) cc_final: 0.7472 (tp-100) REVERT: H 80 GLN cc_start: 0.7960 (tt0) cc_final: 0.7748 (tt0) REVERT: H 84 HIS cc_start: 0.6020 (p-80) cc_final: 0.5465 (p-80) REVERT: H 90 TYR cc_start: 0.6722 (t80) cc_final: 0.6408 (t80) REVERT: H 107 LYS cc_start: 0.8019 (tttt) cc_final: 0.7543 (ttpt) REVERT: H 148 MET cc_start: 0.6635 (mmm) cc_final: 0.6395 (mmm) REVERT: D 83 TYR cc_start: 0.8268 (m-80) cc_final: 0.8057 (m-80) REVERT: D 187 PHE cc_start: 0.5578 (OUTLIER) cc_final: 0.4625 (t80) REVERT: D 271 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8737 (tt) REVERT: D 406 VAL cc_start: 0.8378 (p) cc_final: 0.8130 (t) REVERT: D 429 ARG cc_start: 0.8085 (mmp-170) cc_final: 0.7011 (ttm170) REVERT: A 60 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: A 224 ARG cc_start: 0.4973 (mmt-90) cc_final: 0.4510 (mtp85) REVERT: A 238 MET cc_start: 0.5631 (mtt) cc_final: 0.5419 (ttm) REVERT: A 299 ARG cc_start: 0.7602 (mmt-90) cc_final: 0.7164 (mtm-85) REVERT: F 76 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7494 (tp-100) REVERT: F 80 GLN cc_start: 0.8022 (tt0) cc_final: 0.7818 (tt0) REVERT: F 84 HIS cc_start: 0.6035 (p-80) cc_final: 0.5488 (p-80) REVERT: F 90 TYR cc_start: 0.6743 (t80) cc_final: 0.6417 (t80) REVERT: F 107 LYS cc_start: 0.8029 (tttt) cc_final: 0.7543 (ttpt) REVERT: F 148 MET cc_start: 0.6624 (mmm) cc_final: 0.6385 (mmm) REVERT: F 207 ARG cc_start: 0.7889 (ptm160) cc_final: 0.7659 (tmm-80) REVERT: B 83 TYR cc_start: 0.8259 (m-80) cc_final: 0.8053 (m-80) REVERT: B 187 PHE cc_start: 0.5639 (OUTLIER) cc_final: 0.4684 (t80) REVERT: B 271 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8655 (tt) REVERT: B 406 VAL cc_start: 0.8384 (p) cc_final: 0.8124 (t) REVERT: B 429 ARG cc_start: 0.8103 (mmp-170) cc_final: 0.6988 (ttm170) outliers start: 66 outliers final: 36 residues processed: 474 average time/residue: 0.3273 time to fit residues: 236.8155 Evaluate side-chains 442 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 400 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 181 LYS Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 124 HIS Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 161 TYR Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 161 TYR Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain J residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 9.9990 chunk 142 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 187 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS H 70 ASN H 80 GLN ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 45 GLN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS F 70 ASN ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21878 Z= 0.225 Angle : 0.628 10.319 29606 Z= 0.326 Chirality : 0.042 0.214 3296 Planarity : 0.004 0.054 3766 Dihedral : 4.381 22.446 2922 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.64 % Favored : 93.28 % Rotamer: Outliers : 3.61 % Allowed : 21.04 % Favored : 75.35 % 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: -0.24 (0.17), residues: 2606 helix: 0.59 (0.12), residues: 1740 sheet: None (None), residues: 0 loop : -1.65 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP C 19 HIS 0.004 0.001 HIS C 491 PHE 0.022 0.002 PHE A 194 TYR 0.015 0.001 TYR H 90 ARG 0.011 0.000 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 441 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLN cc_start: 0.8225 (pm20) cc_final: 0.7989 (pm20) REVERT: G 80 GLN cc_start: 0.8257 (pt0) cc_final: 0.7971 (pm20) REVERT: G 208 SER cc_start: 0.7221 (p) cc_final: 0.6904 (p) REVERT: C 60 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7882 (pm20) REVERT: C 224 ARG cc_start: 0.5032 (mmt-90) cc_final: 0.4693 (mtp85) REVERT: C 238 MET cc_start: 0.5555 (mtt) cc_final: 0.5332 (ttm) REVERT: C 299 ARG cc_start: 0.7540 (mmt-90) cc_final: 0.7019 (mtm-85) REVERT: C 311 ARG cc_start: 0.6745 (mtm180) cc_final: 0.6434 (mpp80) REVERT: C 400 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7019 (tp) REVERT: C 404 VAL cc_start: 0.8563 (p) cc_final: 0.8207 (t) REVERT: H 107 LYS cc_start: 0.8030 (tttt) cc_final: 0.7536 (ttpt) REVERT: H 148 MET cc_start: 0.6822 (mmm) cc_final: 0.6419 (mmm) REVERT: D 83 TYR cc_start: 0.8286 (m-80) cc_final: 0.8071 (m-80) REVERT: D 187 PHE cc_start: 0.5703 (OUTLIER) cc_final: 0.4716 (t80) REVERT: D 406 VAL cc_start: 0.8403 (p) cc_final: 0.8156 (t) REVERT: D 429 ARG cc_start: 0.8156 (mmp-170) cc_final: 0.7071 (ttm170) REVERT: D 445 MET cc_start: 0.8275 (mmm) cc_final: 0.7710 (mmt) REVERT: E 181 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7660 (mtmt) REVERT: A 60 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: A 224 ARG cc_start: 0.5060 (mmt-90) cc_final: 0.4705 (mtp85) REVERT: A 238 MET cc_start: 0.5595 (mtt) cc_final: 0.5387 (ttm) REVERT: A 299 ARG cc_start: 0.7577 (mmt-90) cc_final: 0.7114 (mtm-85) REVERT: A 400 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7050 (tp) REVERT: F 107 LYS cc_start: 0.8039 (tttt) cc_final: 0.7534 (ttpt) REVERT: F 148 MET cc_start: 0.6791 (mmm) cc_final: 0.6374 (mmm) REVERT: F 172 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6873 (pmt-80) REVERT: F 207 ARG cc_start: 0.7975 (ptm160) cc_final: 0.7666 (tmm-80) REVERT: B 83 TYR cc_start: 0.8277 (m-80) cc_final: 0.8062 (m-80) REVERT: B 187 PHE cc_start: 0.5726 (OUTLIER) cc_final: 0.4742 (t80) REVERT: B 406 VAL cc_start: 0.8396 (p) cc_final: 0.8156 (t) REVERT: B 429 ARG cc_start: 0.8154 (mmp-170) cc_final: 0.6907 (ttm170) REVERT: B 445 MET cc_start: 0.8268 (mmm) cc_final: 0.7695 (mmt) outliers start: 83 outliers final: 50 residues processed: 496 average time/residue: 0.3536 time to fit residues: 270.5130 Evaluate side-chains 461 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 403 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 181 LYS Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain H residue 124 HIS Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 161 TYR Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 161 TYR Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 42 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 251 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS C 416 ASN H 70 ASN ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS A 416 ASN F 70 ASN ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21878 Z= 0.199 Angle : 0.635 10.008 29606 Z= 0.324 Chirality : 0.042 0.364 3296 Planarity : 0.004 0.056 3766 Dihedral : 4.284 21.265 2922 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.49 % Favored : 93.44 % Rotamer: Outliers : 3.13 % Allowed : 22.04 % Favored : 74.83 % 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 (0.17), residues: 2606 helix: 0.74 (0.13), residues: 1732 sheet: None (None), residues: 0 loop : -1.65 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 19 HIS 0.003 0.001 HIS D 109 PHE 0.021 0.001 PHE A 194 TYR 0.013 0.001 TYR B 188 ARG 0.016 0.000 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 436 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 42 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5941 (mp) REVERT: G 181 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7555 (mtmt) REVERT: C 19 TRP cc_start: 0.7442 (p90) cc_final: 0.6889 (p90) REVERT: C 60 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: C 193 PHE cc_start: 0.7967 (t80) cc_final: 0.7676 (t80) REVERT: C 224 ARG cc_start: 0.5039 (mmt-90) cc_final: 0.4670 (mtp85) REVERT: C 238 MET cc_start: 0.5530 (mtt) cc_final: 0.5319 (ttm) REVERT: C 299 ARG cc_start: 0.7545 (mmt-90) cc_final: 0.7005 (mtm-85) REVERT: C 311 ARG cc_start: 0.6784 (mtm180) cc_final: 0.6434 (mpp80) REVERT: C 400 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7014 (tp) REVERT: C 404 VAL cc_start: 0.8569 (p) cc_final: 0.8260 (t) REVERT: H 84 HIS cc_start: 0.5645 (p-80) cc_final: 0.5198 (p-80) REVERT: H 107 LYS cc_start: 0.8014 (tttt) cc_final: 0.7516 (ttpt) REVERT: D 83 TYR cc_start: 0.8253 (m-80) cc_final: 0.8046 (m-80) REVERT: D 187 PHE cc_start: 0.5803 (OUTLIER) cc_final: 0.4756 (t80) REVERT: D 406 VAL cc_start: 0.8376 (p) cc_final: 0.8141 (t) REVERT: D 429 ARG cc_start: 0.7893 (mmp-170) cc_final: 0.6815 (ttm170) REVERT: D 437 LYS cc_start: 0.8447 (tppt) cc_final: 0.8187 (tptp) REVERT: D 445 MET cc_start: 0.8332 (mmm) cc_final: 0.7738 (mmt) REVERT: A 19 TRP cc_start: 0.7412 (p90) cc_final: 0.7024 (p90) REVERT: A 60 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: A 193 PHE cc_start: 0.7987 (t80) cc_final: 0.7712 (t80) REVERT: A 224 ARG cc_start: 0.5075 (mmt-90) cc_final: 0.4705 (mtp85) REVERT: A 238 MET cc_start: 0.5492 (mtt) cc_final: 0.5270 (ttm) REVERT: A 299 ARG cc_start: 0.7560 (mmt-90) cc_final: 0.7074 (mtm-85) REVERT: A 318 LYS cc_start: 0.7718 (mmpt) cc_final: 0.7213 (tppt) REVERT: A 400 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7046 (tp) REVERT: A 404 VAL cc_start: 0.8568 (p) cc_final: 0.8254 (t) REVERT: F 84 HIS cc_start: 0.5747 (p-80) cc_final: 0.5286 (p-80) REVERT: F 107 LYS cc_start: 0.8019 (tttt) cc_final: 0.7507 (ttpt) REVERT: F 148 MET cc_start: 0.6862 (mmm) cc_final: 0.6660 (mmm) REVERT: F 172 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6907 (pmt-80) REVERT: F 207 ARG cc_start: 0.7967 (ptm160) cc_final: 0.7694 (tmm-80) REVERT: B 83 TYR cc_start: 0.8242 (m-80) cc_final: 0.8042 (m-80) REVERT: B 187 PHE cc_start: 0.5771 (OUTLIER) cc_final: 0.4751 (t80) REVERT: B 406 VAL cc_start: 0.8386 (p) cc_final: 0.8151 (t) REVERT: B 429 ARG cc_start: 0.7909 (mmp-170) cc_final: 0.6813 (ttm170) REVERT: B 437 LYS cc_start: 0.8480 (tppt) cc_final: 0.8197 (tptp) REVERT: B 445 MET cc_start: 0.8301 (mmm) cc_final: 0.7702 (mmt) outliers start: 72 outliers final: 44 residues processed: 482 average time/residue: 0.3352 time to fit residues: 246.2328 Evaluate side-chains 466 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 413 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 181 LYS Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 161 TYR Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 161 TYR Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain J residue 38 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 140 optimal weight: 0.1980 chunk 250 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS C 416 ASN ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 45 GLN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS A 416 ASN ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21878 Z= 0.185 Angle : 0.634 11.064 29606 Z= 0.322 Chirality : 0.042 0.259 3296 Planarity : 0.004 0.055 3766 Dihedral : 4.209 20.354 2922 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.37 % Favored : 93.55 % Rotamer: Outliers : 3.48 % Allowed : 22.48 % Favored : 74.04 % 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: -0.03 (0.17), residues: 2606 helix: 0.80 (0.13), residues: 1742 sheet: None (None), residues: 0 loop : -1.67 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 129 HIS 0.003 0.001 HIS C 491 PHE 0.019 0.001 PHE A 194 TYR 0.030 0.001 TYR C 444 ARG 0.012 0.000 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 439 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7622 (mtmt) REVERT: C 19 TRP cc_start: 0.7325 (p90) cc_final: 0.7107 (p90) REVERT: C 60 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: C 146 GLU cc_start: 0.7901 (pp20) cc_final: 0.7353 (pt0) REVERT: C 193 PHE cc_start: 0.7915 (t80) cc_final: 0.7655 (t80) REVERT: C 224 ARG cc_start: 0.5056 (mmt-90) cc_final: 0.4744 (mtp85) REVERT: C 238 MET cc_start: 0.5517 (mtt) cc_final: 0.5294 (ttm) REVERT: C 299 ARG cc_start: 0.7535 (mmt-90) cc_final: 0.7155 (mtm-85) REVERT: C 318 LYS cc_start: 0.7682 (mmpt) cc_final: 0.7153 (tppt) REVERT: C 400 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6943 (tp) REVERT: C 404 VAL cc_start: 0.8550 (p) cc_final: 0.8280 (t) REVERT: H 84 HIS cc_start: 0.5670 (p-80) cc_final: 0.5250 (p-80) REVERT: H 107 LYS cc_start: 0.8031 (tttt) cc_final: 0.7521 (ttpt) REVERT: H 181 LYS cc_start: 0.6238 (OUTLIER) cc_final: 0.5728 (tptp) REVERT: D 83 TYR cc_start: 0.8230 (m-80) cc_final: 0.8023 (m-80) REVERT: D 187 PHE cc_start: 0.5774 (OUTLIER) cc_final: 0.4704 (t80) REVERT: D 406 VAL cc_start: 0.8378 (p) cc_final: 0.8162 (t) REVERT: D 429 ARG cc_start: 0.7882 (mmp-170) cc_final: 0.6974 (ttm170) REVERT: D 445 MET cc_start: 0.8289 (mmm) cc_final: 0.7368 (tpt) REVERT: A 19 TRP cc_start: 0.7348 (p90) cc_final: 0.6991 (p90) REVERT: A 60 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: A 146 GLU cc_start: 0.7888 (pp20) cc_final: 0.7353 (pt0) REVERT: A 193 PHE cc_start: 0.7915 (t80) cc_final: 0.7654 (t80) REVERT: A 224 ARG cc_start: 0.5092 (mmt-90) cc_final: 0.4758 (mtp85) REVERT: A 238 MET cc_start: 0.5484 (mtt) cc_final: 0.5259 (ttm) REVERT: A 299 ARG cc_start: 0.7554 (mmt-90) cc_final: 0.7050 (mtm-85) REVERT: A 318 LYS cc_start: 0.7694 (mmpt) cc_final: 0.7174 (tppt) REVERT: A 400 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6977 (tp) REVERT: A 404 VAL cc_start: 0.8560 (p) cc_final: 0.8277 (t) REVERT: F 84 HIS cc_start: 0.5732 (p-80) cc_final: 0.5320 (p-80) REVERT: F 107 LYS cc_start: 0.8037 (tttt) cc_final: 0.7527 (ttpt) REVERT: F 148 MET cc_start: 0.6920 (mmm) cc_final: 0.6691 (mmm) REVERT: F 200 GLN cc_start: 0.6602 (mp10) cc_final: 0.5952 (mp10) REVERT: F 207 ARG cc_start: 0.7893 (ptm160) cc_final: 0.7660 (tmm-80) REVERT: B 83 TYR cc_start: 0.8220 (m-80) cc_final: 0.8019 (m-80) REVERT: B 187 PHE cc_start: 0.5765 (OUTLIER) cc_final: 0.4756 (t80) REVERT: B 406 VAL cc_start: 0.8392 (p) cc_final: 0.8155 (t) REVERT: B 429 ARG cc_start: 0.7856 (mmp-170) cc_final: 0.6851 (ttm170) REVERT: B 445 MET cc_start: 0.8292 (mmm) cc_final: 0.7702 (mmt) outliers start: 80 outliers final: 56 residues processed: 491 average time/residue: 0.3313 time to fit residues: 247.7719 Evaluate side-chains 478 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 414 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 181 LYS Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 172 TRP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 161 TYR Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 172 TRP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 161 TYR Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 42 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 149 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21878 Z= 0.193 Angle : 0.648 11.096 29606 Z= 0.329 Chirality : 0.042 0.338 3296 Planarity : 0.004 0.051 3766 Dihedral : 4.184 20.347 2922 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.29 % Favored : 93.63 % Rotamer: Outliers : 3.61 % Allowed : 22.74 % Favored : 73.65 % 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: 0.00 (0.17), residues: 2606 helix: 0.81 (0.13), residues: 1742 sheet: None (None), residues: 0 loop : -1.64 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 129 HIS 0.004 0.001 HIS F 84 PHE 0.018 0.001 PHE A 194 TYR 0.026 0.001 TYR C 444 ARG 0.011 0.000 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 430 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: C 146 GLU cc_start: 0.7887 (pp20) cc_final: 0.7355 (pt0) REVERT: C 193 PHE cc_start: 0.7913 (t80) cc_final: 0.7675 (t80) REVERT: C 224 ARG cc_start: 0.5066 (mmt-90) cc_final: 0.4748 (mtp85) REVERT: C 238 MET cc_start: 0.5517 (mtt) cc_final: 0.5296 (ttm) REVERT: C 240 PHE cc_start: 0.8369 (m-80) cc_final: 0.7845 (m-80) REVERT: C 299 ARG cc_start: 0.7568 (mmt-90) cc_final: 0.7130 (mtm-85) REVERT: C 318 LYS cc_start: 0.7704 (mmpt) cc_final: 0.7199 (tppt) REVERT: C 329 PHE cc_start: 0.8443 (t80) cc_final: 0.8178 (t80) REVERT: C 400 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6915 (tp) REVERT: C 404 VAL cc_start: 0.8562 (p) cc_final: 0.8290 (t) REVERT: H 107 LYS cc_start: 0.8084 (tttt) cc_final: 0.7610 (ttpt) REVERT: H 181 LYS cc_start: 0.6253 (OUTLIER) cc_final: 0.5727 (tptp) REVERT: D 187 PHE cc_start: 0.5776 (OUTLIER) cc_final: 0.4760 (t80) REVERT: D 406 VAL cc_start: 0.8388 (p) cc_final: 0.8157 (t) REVERT: D 429 ARG cc_start: 0.7766 (mmp-170) cc_final: 0.6840 (ttm170) REVERT: D 445 MET cc_start: 0.8278 (mmm) cc_final: 0.7714 (mmt) REVERT: A 19 TRP cc_start: 0.7247 (p90) cc_final: 0.6994 (p90) REVERT: A 60 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7926 (pm20) REVERT: A 146 GLU cc_start: 0.7884 (pp20) cc_final: 0.7356 (pt0) REVERT: A 193 PHE cc_start: 0.7909 (t80) cc_final: 0.7641 (t80) REVERT: A 224 ARG cc_start: 0.5081 (mmt-90) cc_final: 0.4763 (mtp85) REVERT: A 238 MET cc_start: 0.5471 (mtt) cc_final: 0.5264 (ttm) REVERT: A 299 ARG cc_start: 0.7551 (mmt-90) cc_final: 0.7007 (mtm-85) REVERT: A 318 LYS cc_start: 0.7715 (mmpt) cc_final: 0.7214 (tppt) REVERT: A 400 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6896 (tp) REVERT: A 404 VAL cc_start: 0.8572 (p) cc_final: 0.8291 (t) REVERT: F 107 LYS cc_start: 0.8090 (tttt) cc_final: 0.7603 (ttpt) REVERT: F 148 MET cc_start: 0.6930 (mmm) cc_final: 0.6571 (mmm) REVERT: F 200 GLN cc_start: 0.6564 (mp10) cc_final: 0.5923 (mp10) REVERT: B 187 PHE cc_start: 0.5832 (OUTLIER) cc_final: 0.4804 (t80) REVERT: B 406 VAL cc_start: 0.8388 (p) cc_final: 0.8164 (t) REVERT: B 429 ARG cc_start: 0.7793 (mmp-170) cc_final: 0.6855 (ttm170) REVERT: B 445 MET cc_start: 0.8283 (mmm) cc_final: 0.7715 (mmt) outliers start: 83 outliers final: 61 residues processed: 486 average time/residue: 0.3350 time to fit residues: 249.5700 Evaluate side-chains 476 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 408 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 181 LYS Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 172 TRP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 415 GLN Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 161 TYR Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 172 TRP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 161 TYR Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 42 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 45 GLN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21878 Z= 0.223 Angle : 0.676 11.426 29606 Z= 0.343 Chirality : 0.043 0.366 3296 Planarity : 0.004 0.035 3766 Dihedral : 4.237 20.588 2922 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.22 % Favored : 93.71 % Rotamer: Outliers : 3.65 % Allowed : 23.17 % Favored : 73.17 % 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: -0.02 (0.17), residues: 2606 helix: 0.78 (0.13), residues: 1740 sheet: None (None), residues: 0 loop : -1.61 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP C 19 HIS 0.003 0.001 HIS H 84 PHE 0.021 0.002 PHE F 178 TYR 0.024 0.001 TYR C 444 ARG 0.006 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 418 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: C 146 GLU cc_start: 0.7917 (pp20) cc_final: 0.7392 (pt0) REVERT: C 224 ARG cc_start: 0.5047 (mmt-90) cc_final: 0.4776 (mtp85) REVERT: C 238 MET cc_start: 0.5446 (mtt) cc_final: 0.5219 (ttm) REVERT: C 299 ARG cc_start: 0.7572 (mmt-90) cc_final: 0.7131 (mtm-85) REVERT: C 318 LYS cc_start: 0.7757 (mmpt) cc_final: 0.7264 (tppt) REVERT: C 400 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6967 (tp) REVERT: C 404 VAL cc_start: 0.8579 (p) cc_final: 0.8308 (t) REVERT: H 84 HIS cc_start: 0.5036 (p-80) cc_final: 0.4690 (p-80) REVERT: H 107 LYS cc_start: 0.8104 (tttt) cc_final: 0.7627 (ttpt) REVERT: H 181 LYS cc_start: 0.6368 (OUTLIER) cc_final: 0.5888 (tptp) REVERT: H 182 MET cc_start: 0.3155 (mmm) cc_final: 0.2918 (mmm) REVERT: H 200 GLN cc_start: 0.6217 (OUTLIER) cc_final: 0.5934 (mp10) REVERT: D 83 TYR cc_start: 0.8138 (m-80) cc_final: 0.7932 (m-80) REVERT: D 187 PHE cc_start: 0.5592 (OUTLIER) cc_final: 0.4727 (t80) REVERT: D 406 VAL cc_start: 0.8390 (p) cc_final: 0.8182 (t) REVERT: D 429 ARG cc_start: 0.7813 (mmp-170) cc_final: 0.6871 (ttm170) REVERT: D 445 MET cc_start: 0.8311 (mmm) cc_final: 0.7791 (mmt) REVERT: E 206 MET cc_start: 0.6568 (mmp) cc_final: 0.6100 (mmp) REVERT: A 60 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: A 146 GLU cc_start: 0.7916 (pp20) cc_final: 0.7391 (pt0) REVERT: A 224 ARG cc_start: 0.5063 (mmt-90) cc_final: 0.4784 (mtp85) REVERT: A 238 MET cc_start: 0.5429 (mtt) cc_final: 0.5207 (ttm) REVERT: A 299 ARG cc_start: 0.7541 (mmt-90) cc_final: 0.7031 (mtm-85) REVERT: A 318 LYS cc_start: 0.7812 (mmpt) cc_final: 0.7343 (tppt) REVERT: A 400 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6962 (tp) REVERT: A 404 VAL cc_start: 0.8585 (p) cc_final: 0.8313 (t) REVERT: F 84 HIS cc_start: 0.5163 (p-80) cc_final: 0.4794 (p-80) REVERT: F 107 LYS cc_start: 0.8110 (tttt) cc_final: 0.7625 (ttpt) REVERT: F 148 MET cc_start: 0.6922 (mmm) cc_final: 0.6689 (mmm) REVERT: F 200 GLN cc_start: 0.6593 (mp10) cc_final: 0.5912 (mp10) REVERT: B 176 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7329 (tm-30) REVERT: B 187 PHE cc_start: 0.5755 (OUTLIER) cc_final: 0.4768 (t80) REVERT: B 406 VAL cc_start: 0.8398 (p) cc_final: 0.8175 (t) REVERT: B 429 ARG cc_start: 0.7783 (mmp-170) cc_final: 0.6834 (ttm170) REVERT: B 445 MET cc_start: 0.8317 (mmm) cc_final: 0.7779 (mmt) outliers start: 84 outliers final: 69 residues processed: 475 average time/residue: 0.3151 time to fit residues: 232.0515 Evaluate side-chains 474 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 397 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 181 LYS Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 172 TRP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 415 GLN Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 161 TYR Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 200 GLN Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 172 TRP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 161 TYR Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 3.9990 chunk 246 optimal weight: 7.9990 chunk 150 optimal weight: 0.0030 chunk 117 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 259 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 GLN ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 45 GLN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21878 Z= 0.203 Angle : 0.683 11.860 29606 Z= 0.346 Chirality : 0.043 0.350 3296 Planarity : 0.004 0.036 3766 Dihedral : 4.220 19.941 2922 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 3.30 % Allowed : 24.09 % Favored : 72.61 % 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 (0.17), residues: 2606 helix: 0.79 (0.13), residues: 1742 sheet: None (None), residues: 0 loop : -1.60 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP A 19 HIS 0.004 0.001 HIS F 84 PHE 0.019 0.001 PHE C 194 TYR 0.036 0.001 TYR H 90 ARG 0.006 0.000 ARG C 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 426 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 132 ASN cc_start: 0.7638 (m110) cc_final: 0.7105 (t0) REVERT: C 60 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7870 (pm20) REVERT: C 146 GLU cc_start: 0.7909 (pp20) cc_final: 0.7383 (pt0) REVERT: C 193 PHE cc_start: 0.7912 (t80) cc_final: 0.7652 (t80) REVERT: C 224 ARG cc_start: 0.5091 (mmt-90) cc_final: 0.4788 (mtp85) REVERT: C 238 MET cc_start: 0.5421 (mtt) cc_final: 0.5203 (ttm) REVERT: C 240 PHE cc_start: 0.8403 (m-80) cc_final: 0.7799 (m-80) REVERT: C 299 ARG cc_start: 0.7574 (mmt-90) cc_final: 0.7083 (mtm-85) REVERT: C 318 LYS cc_start: 0.7719 (mmpt) cc_final: 0.7214 (tppt) REVERT: C 400 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.6984 (tp) REVERT: C 404 VAL cc_start: 0.8606 (p) cc_final: 0.8347 (t) REVERT: H 84 HIS cc_start: 0.5044 (p-80) cc_final: 0.4738 (p-80) REVERT: H 107 LYS cc_start: 0.8049 (tttt) cc_final: 0.7639 (tttt) REVERT: H 172 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6906 (pmt-80) REVERT: H 181 LYS cc_start: 0.6430 (OUTLIER) cc_final: 0.5943 (tptp) REVERT: H 182 MET cc_start: 0.3058 (mmm) cc_final: 0.2817 (mmm) REVERT: H 200 GLN cc_start: 0.6347 (OUTLIER) cc_final: 0.5941 (mp10) REVERT: D 83 TYR cc_start: 0.8293 (m-80) cc_final: 0.7956 (m-80) REVERT: D 176 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7274 (tm-30) REVERT: D 187 PHE cc_start: 0.5713 (t80) cc_final: 0.4798 (t80) REVERT: D 406 VAL cc_start: 0.8391 (p) cc_final: 0.8177 (t) REVERT: D 429 ARG cc_start: 0.7789 (mmp-170) cc_final: 0.6947 (ttm170) REVERT: D 445 MET cc_start: 0.8301 (mmm) cc_final: 0.7826 (mmt) REVERT: E 132 ASN cc_start: 0.7593 (m110) cc_final: 0.7169 (t0) REVERT: E 206 MET cc_start: 0.6405 (mmp) cc_final: 0.5976 (mmp) REVERT: A 60 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: A 146 GLU cc_start: 0.7909 (pp20) cc_final: 0.7384 (pt0) REVERT: A 193 PHE cc_start: 0.7941 (t80) cc_final: 0.7640 (t80) REVERT: A 224 ARG cc_start: 0.5096 (mmt-90) cc_final: 0.4791 (mtp85) REVERT: A 238 MET cc_start: 0.5392 (mtt) cc_final: 0.5182 (ttm) REVERT: A 240 PHE cc_start: 0.8365 (m-80) cc_final: 0.7803 (m-80) REVERT: A 299 ARG cc_start: 0.7557 (mmt-90) cc_final: 0.7019 (mtm-85) REVERT: A 318 LYS cc_start: 0.7778 (mmpt) cc_final: 0.7287 (tppt) REVERT: A 400 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.6940 (tp) REVERT: A 404 VAL cc_start: 0.8617 (p) cc_final: 0.8349 (t) REVERT: F 84 HIS cc_start: 0.5062 (p-80) cc_final: 0.4748 (p-80) REVERT: F 107 LYS cc_start: 0.8021 (tttt) cc_final: 0.7578 (tttt) REVERT: F 148 MET cc_start: 0.6835 (mmm) cc_final: 0.6626 (mmm) REVERT: F 214 ASN cc_start: 0.7551 (p0) cc_final: 0.7228 (p0) REVERT: B 187 PHE cc_start: 0.5827 (OUTLIER) cc_final: 0.4813 (t80) REVERT: B 406 VAL cc_start: 0.8385 (p) cc_final: 0.8177 (t) REVERT: B 429 ARG cc_start: 0.7777 (mmp-170) cc_final: 0.6856 (ttm170) REVERT: B 445 MET cc_start: 0.8284 (mmm) cc_final: 0.7762 (mmt) outliers start: 76 outliers final: 63 residues processed: 479 average time/residue: 0.3125 time to fit residues: 231.5447 Evaluate side-chains 478 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 407 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 181 LYS Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 172 TRP Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 415 GLN Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 161 TYR Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 200 GLN Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 172 TRP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 161 TYR Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 63 optimal weight: 0.0370 chunk 190 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 45 GLN E 80 GLN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.134535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.107719 restraints weight = 51911.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.106838 restraints weight = 43602.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.107352 restraints weight = 41204.314| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 21878 Z= 0.255 Angle : 0.891 59.200 29606 Z= 0.497 Chirality : 0.044 0.355 3296 Planarity : 0.005 0.138 3766 Dihedral : 4.214 19.917 2922 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.94 % Rotamer: Outliers : 3.70 % Allowed : 24.30 % Favored : 72.00 % Cbeta Deviations : 0.04 % 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: 0.00 (0.17), residues: 2606 helix: 0.79 (0.13), residues: 1742 sheet: None (None), residues: 0 loop : -1.59 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 19 HIS 0.003 0.001 HIS F 84 PHE 0.027 0.001 PHE C 329 TYR 0.025 0.001 TYR H 90 ARG 0.027 0.001 ARG C 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4879.61 seconds wall clock time: 88 minutes 23.76 seconds (5303.76 seconds total)