Starting phenix.real_space_refine on Sun Feb 18 10:30:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5q_25707/02_2024/7t5q_25707_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5q_25707/02_2024/7t5q_25707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5q_25707/02_2024/7t5q_25707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5q_25707/02_2024/7t5q_25707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5q_25707/02_2024/7t5q_25707_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t5q_25707/02_2024/7t5q_25707_updated.pdb" } resolution = 3.4 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 3 5.21 5 S 108 5.16 5 C 13760 2.51 5 N 3705 2.21 5 O 4087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 11": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ASP 246": "OD1" <-> "OD2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ASP 59": "OD1" <-> "OD2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "H ASP 56": "OD1" <-> "OD2" Residue "H ASP 222": "OD1" <-> "OD2" Residue "H PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 311": "OD1" <-> "OD2" Residue "I PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21671 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3080 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 24, 'TRANS': 359} Chain breaks: 1 Chain: "B" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2972 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2578 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2287 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 9, 'TRANS': 273} Chain: "E" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1414 Classifications: {'peptide': 174} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 162} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1364 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 161} Chain: "G" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 482 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain breaks: 1 Chain: "H" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2812 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2295 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 10, 'TRANS': 272} Chain breaks: 1 Chain: "J" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2295 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.40, per 1000 atoms: 0.53 Number of scatterers: 21671 At special positions: 0 Unit cell: (162.54, 141.04, 166.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 8 15.00 Mg 3 11.99 O 4087 8.00 N 3705 7.00 C 13760 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: 8.73 Conformation dependent library (CDL) restraints added in 4.2 seconds 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 26 sheets defined 36.2% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.14 Creating SS restraints... Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 86 through 98 removed outlier: 3.753A pdb=" N ARG A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 120 through 134 removed outlier: 3.608A pdb=" N THR A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.507A pdb=" N ALA A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N SER A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 197 through 210 removed outlier: 3.953A pdb=" N ASP A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 249 through 252 No H-bonds generated for 'chain 'A' and resid 249 through 252' Processing helix chain 'A' and resid 279 through 282 removed outlier: 3.738A pdb=" N PHE A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.545A pdb=" N VAL A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 removed outlier: 4.147A pdb=" N ARG A 312 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ARG A 313 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Proline residue: A 314 - end of helix No H-bonds generated for 'chain 'A' and resid 309 through 316' Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 331 through 354 removed outlier: 3.656A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.850A pdb=" N TYR A 391 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 63 removed outlier: 4.373A pdb=" N GLU B 63 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.596A pdb=" N VAL B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 147 removed outlier: 3.573A pdb=" N LEU B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 186 through 200 removed outlier: 3.573A pdb=" N ILE B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.955A pdb=" N MET B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 236 Processing helix chain 'B' and resid 256 through 264 removed outlier: 3.788A pdb=" N PHE B 259 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 260 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA B 261 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Proline residue: B 262 - end of helix No H-bonds generated for 'chain 'B' and resid 256 through 264' Processing helix chain 'B' and resid 268 through 271 removed outlier: 3.849A pdb=" N ILE B 271 " --> pdb=" O PRO B 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 268 through 271' Processing helix chain 'B' and resid 277 through 288 removed outlier: 3.983A pdb=" N ALA B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 4.208A pdb=" N SER B 295 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.665A pdb=" N LEU B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU B 318 " --> pdb=" O PRO B 314 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 364 removed outlier: 3.534A pdb=" N ALA B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 380 removed outlier: 3.511A pdb=" N GLN B 379 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 375 through 380' Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 64 through 70 Processing helix chain 'D' and resid 72 through 83 removed outlier: 3.603A pdb=" N GLY D 81 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N SER D 82 " --> pdb=" O ARG D 78 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 134 removed outlier: 3.660A pdb=" N VAL D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET D 115 " --> pdb=" O HIS D 111 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LYS D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ARG D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D 133 " --> pdb=" O PHE D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 191 removed outlier: 3.894A pdb=" N VAL D 176 " --> pdb=" O ASP D 172 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE D 185 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS D 186 " --> pdb=" O MET D 182 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU D 187 " --> pdb=" O GLN D 183 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ARG D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 210 No H-bonds generated for 'chain 'D' and resid 207 through 210' Processing helix chain 'D' and resid 237 through 244 Processing helix chain 'D' and resid 248 through 280 removed outlier: 3.683A pdb=" N LYS D 259 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG D 265 " --> pdb=" O TYR D 261 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 47 Processing helix chain 'E' and resid 49 through 52 No H-bonds generated for 'chain 'E' and resid 49 through 52' Processing helix chain 'E' and resid 64 through 81 removed outlier: 4.130A pdb=" N ILE E 69 " --> pdb=" O ARG E 66 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE E 71 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR E 72 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE E 75 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER E 76 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 99 Processing helix chain 'E' and resid 114 through 116 No H-bonds generated for 'chain 'E' and resid 114 through 116' Processing helix chain 'E' and resid 125 through 148 removed outlier: 4.243A pdb=" N GLY E 141 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU E 142 " --> pdb=" O GLN E 138 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 44 through 46 No H-bonds generated for 'chain 'F' and resid 44 through 46' Processing helix chain 'F' and resid 81 through 96 Processing helix chain 'F' and resid 120 through 124 Processing helix chain 'F' and resid 129 through 167 removed outlier: 3.712A pdb=" N GLU F 140 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 142 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 151 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA F 157 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG F 158 " --> pdb=" O ASN F 154 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL F 160 " --> pdb=" O ARG F 156 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 85 Processing helix chain 'G' and resid 102 through 115 removed outlier: 3.521A pdb=" N PHE G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 136 removed outlier: 3.659A pdb=" N GLU G 130 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 145 removed outlier: 4.027A pdb=" N VAL G 142 " --> pdb=" O VAL G 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'H' and resid 113 through 124 removed outlier: 4.242A pdb=" N GLU H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET H 119 " --> pdb=" O ASN H 115 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR H 120 " --> pdb=" O ARG H 116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE H 122 " --> pdb=" O LYS H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 145 removed outlier: 3.957A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 196 removed outlier: 3.735A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 215 removed outlier: 4.098A pdb=" N GLU H 207 " --> pdb=" O ALA H 204 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE H 208 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG H 210 " --> pdb=" O GLU H 207 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE H 212 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS H 215 " --> pdb=" O ILE H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 252 through 254 No H-bonds generated for 'chain 'H' and resid 252 through 254' Processing helix chain 'H' and resid 258 through 261 Processing helix chain 'H' and resid 277 through 283 removed outlier: 3.938A pdb=" N ILE H 282 " --> pdb=" O THR H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 293 No H-bonds generated for 'chain 'H' and resid 290 through 293' Processing helix chain 'H' and resid 309 through 318 removed outlier: 3.681A pdb=" N MET H 313 " --> pdb=" O ILE H 309 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR H 318 " --> pdb=" O GLN H 314 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 347 removed outlier: 3.522A pdb=" N SER H 338 " --> pdb=" O ARG H 335 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL H 339 " --> pdb=" O LYS H 336 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE H 341 " --> pdb=" O SER H 338 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY H 342 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE H 345 " --> pdb=" O GLY H 342 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA H 347 " --> pdb=" O SER H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 353 removed outlier: 3.930A pdb=" N GLN H 353 " --> pdb=" O SER H 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 350 through 353' Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 369 through 371 No H-bonds generated for 'chain 'H' and resid 369 through 371' Processing helix chain 'I' and resid 10 through 22 Processing helix chain 'I' and resid 30 through 39 Processing helix chain 'I' and resid 43 through 49 removed outlier: 4.096A pdb=" N GLU I 48 " --> pdb=" O ASN I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 61 Processing helix chain 'I' and resid 118 through 133 removed outlier: 3.553A pdb=" N ALA I 130 " --> pdb=" O SER I 126 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR I 131 " --> pdb=" O ALA I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 248 removed outlier: 4.476A pdb=" N ALA I 225 " --> pdb=" O GLU I 221 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS I 226 " --> pdb=" O ALA I 222 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU I 227 " --> pdb=" O GLN I 223 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE I 228 " --> pdb=" O THR I 224 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE I 229 " --> pdb=" O ALA I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 253 No H-bonds generated for 'chain 'I' and resid 250 through 253' Processing helix chain 'I' and resid 271 through 275 Processing helix chain 'I' and resid 312 through 323 removed outlier: 3.693A pdb=" N GLN I 317 " --> pdb=" O MET I 313 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS I 318 " --> pdb=" O GLU I 314 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG I 319 " --> pdb=" O VAL I 315 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 15 removed outlier: 3.505A pdb=" N ARG J 15 " --> pdb=" O ASP J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 31 removed outlier: 5.932A pdb=" N GLU J 22 " --> pdb=" O GLN J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 42 removed outlier: 3.906A pdb=" N LEU J 40 " --> pdb=" O CYS J 36 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER J 41 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER J 42 " --> pdb=" O ASP J 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 36 through 42' Processing helix chain 'J' and resid 91 through 111 removed outlier: 4.095A pdb=" N LYS J 95 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU J 96 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA J 100 " --> pdb=" O LEU J 96 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP J 105 " --> pdb=" O ASN J 101 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU J 110 " --> pdb=" O GLN J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 230 Processing helix chain 'J' and resid 234 through 243 removed outlier: 4.001A pdb=" N ASP J 238 " --> pdb=" O GLY J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 254 No H-bonds generated for 'chain 'J' and resid 251 through 254' Processing helix chain 'J' and resid 256 through 273 removed outlier: 3.694A pdb=" N ILE J 271 " --> pdb=" O THR J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 301 removed outlier: 4.512A pdb=" N MET J 300 " --> pdb=" O VAL J 296 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU J 301 " --> pdb=" O GLY J 297 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 12 Processing sheet with id= B, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= C, first strand: chain 'A' and resid 109 through 113 removed outlier: 6.674A pdb=" N GLY A 138 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU A 112 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR A 140 " --> pdb=" O LEU A 112 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.237A pdb=" N THR A 166 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N SER A 322 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE A 168 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 254 through 259 removed outlier: 3.669A pdb=" N LYS A 254 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.199A pdb=" N LYS B 106 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N CYS B 11 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B 108 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLY B 135 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 109 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR B 137 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLU B 111 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA B 139 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 36 through 38 Processing sheet with id= H, first strand: chain 'B' and resid 301 through 304 removed outlier: 6.472A pdb=" N VAL B 155 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER B 304 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL B 157 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 242 through 245 Processing sheet with id= J, first strand: chain 'C' and resid 3 through 5 removed outlier: 4.760A pdb=" N ALA C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY C 347 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 14 through 16 removed outlier: 5.822A pdb=" N LYS C 36 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LYS C 44 " --> pdb=" O LYS C 36 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 86 through 90 Processing sheet with id= M, first strand: chain 'C' and resid 131 through 137 removed outlier: 4.376A pdb=" N LEU C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 115 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.759A pdb=" N GLY C 160 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU C 148 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA C 158 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TRP C 150 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU C 156 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 161 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER C 170 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU C 194 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 238 through 243 removed outlier: 4.071A pdb=" N THR C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY C 209 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 249 through 254 removed outlier: 6.999A pdb=" N ALA C 263 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL C 252 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL C 261 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N PHE C 254 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N SER C 259 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C 284 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASN C 273 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE C 282 " --> pdb=" O ASN C 273 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 43 through 46 removed outlier: 3.682A pdb=" N VAL D 93 " --> pdb=" O ILE D 59 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 142 through 144 removed outlier: 3.512A pdb=" N VAL D 154 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR D 222 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER D 201 " --> pdb=" O TYR D 222 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 114 through 119 removed outlier: 3.995A pdb=" N GLU F 59 " --> pdb=" O ASN F 56 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN F 56 " --> pdb=" O GLU F 59 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL F 61 " --> pdb=" O SER F 54 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER F 54 " --> pdb=" O VAL F 61 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE F 63 " --> pdb=" O THR F 52 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR F 52 " --> pdb=" O ILE F 63 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 103 through 105 removed outlier: 6.513A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 150 through 153 Processing sheet with id= V, first strand: chain 'H' and resid 238 through 241 Processing sheet with id= W, first strand: chain 'I' and resid 64 through 66 Processing sheet with id= X, first strand: chain 'I' and resid 140 through 148 removed outlier: 3.501A pdb=" N VAL I 189 " --> pdb=" O LYS I 178 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 49 through 51 Processing sheet with id= Z, first strand: chain 'J' and resid 116 through 121 751 hydrogen bonds defined for protein. 2040 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: 6.19 Time building geometry restraints manager: 9.40 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: 6808 1.34 - 1.46: 3738 1.46 - 1.58: 11409 1.58 - 1.70: 13 1.70 - 1.82: 173 Bond restraints: 22141 Sorted by residual: bond pdb=" C ILE A 193 " pdb=" N PRO A 194 " ideal model delta sigma weight residual 1.334 1.370 -0.037 8.40e-03 1.42e+04 1.93e+01 bond pdb=" CA GLU I 68 " pdb=" C GLU I 68 " ideal model delta sigma weight residual 1.523 1.569 -0.045 1.34e-02 5.57e+03 1.14e+01 bond pdb=" C GLY E 30 " pdb=" N PRO E 31 " ideal model delta sigma weight residual 1.335 1.362 -0.027 8.70e-03 1.32e+04 9.60e+00 bond pdb=" CE1 HIC H 73 " pdb=" NE2 HIC H 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.49e+00 bond pdb=" CG HIC H 73 " pdb=" CD2 HIC H 73 " ideal model delta sigma weight residual 1.369 1.409 -0.040 2.00e-02 2.50e+03 4.07e+00 ... (remaining 22136 not shown) Histogram of bond angle deviations from ideal: 98.85 - 107.05: 733 107.05 - 115.25: 13113 115.25 - 123.45: 14819 123.45 - 131.64: 1248 131.64 - 139.84: 52 Bond angle restraints: 29965 Sorted by residual: angle pdb=" C ASP B 346 " pdb=" N PRO B 347 " pdb=" CA PRO B 347 " ideal model delta sigma weight residual 119.66 122.79 -3.13 7.20e-01 1.93e+00 1.89e+01 angle pdb=" CA GLN E 124 " pdb=" CB GLN E 124 " pdb=" CG GLN E 124 " ideal model delta sigma weight residual 114.10 121.77 -7.67 2.00e+00 2.50e-01 1.47e+01 angle pdb=" O PRO B 347 " pdb=" C PRO B 347 " pdb=" N PRO B 348 " ideal model delta sigma weight residual 121.15 122.91 -1.76 4.70e-01 4.53e+00 1.40e+01 angle pdb=" CA MET D 182 " pdb=" CB MET D 182 " pdb=" CG MET D 182 " ideal model delta sigma weight residual 114.10 121.17 -7.07 2.00e+00 2.50e-01 1.25e+01 angle pdb=" CA GLU I 68 " pdb=" C GLU I 68 " pdb=" O GLU I 68 " ideal model delta sigma weight residual 120.51 115.70 4.81 1.43e+00 4.89e-01 1.13e+01 ... (remaining 29960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 12065 17.79 - 35.57: 1060 35.57 - 53.36: 207 53.36 - 71.15: 26 71.15 - 88.94: 14 Dihedral angle restraints: 13372 sinusoidal: 5512 harmonic: 7860 Sorted by residual: dihedral pdb=" O1B ADP H 401 " pdb=" O3A ADP H 401 " pdb=" PB ADP H 401 " pdb=" PA ADP H 401 " ideal model delta sinusoidal sigma weight residual -60.00 -143.42 83.42 1 2.00e+01 2.50e-03 2.12e+01 dihedral pdb=" CA ILE J 249 " pdb=" C ILE J 249 " pdb=" N PRO J 250 " pdb=" CA PRO J 250 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA PRO I 26 " pdb=" C PRO I 26 " pdb=" N GLY I 27 " pdb=" CA GLY I 27 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 13369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2739 0.061 - 0.123: 479 0.123 - 0.184: 71 0.184 - 0.246: 2 0.246 - 0.307: 4 Chirality restraints: 3295 Sorted by residual: chirality pdb=" C2' ATP B 502 " pdb=" C1' ATP B 502 " pdb=" C3' ATP B 502 " pdb=" O2' ATP B 502 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C2' ATP A 502 " pdb=" C1' ATP A 502 " pdb=" C3' ATP A 502 " pdb=" O2' ATP A 502 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C3' ATP A 502 " pdb=" C2' ATP A 502 " pdb=" C4' ATP A 502 " pdb=" O3' ATP A 502 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 3292 not shown) Planarity restraints: 3845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 183 " -0.052 5.00e-02 4.00e+02 7.87e-02 9.92e+00 pdb=" N PRO C 184 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO C 184 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 184 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO I 183 " 0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO I 184 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO I 184 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 184 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 249 " -0.048 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO J 250 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO J 250 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 250 " -0.041 5.00e-02 4.00e+02 ... (remaining 3842 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 100 2.57 - 3.15: 16331 3.15 - 3.73: 30906 3.73 - 4.32: 42011 4.32 - 4.90: 72325 Nonbonded interactions: 161673 Sorted by model distance: nonbonded pdb="MG MG B 501 " pdb=" O1B ATP B 502 " model vdw 1.984 2.170 nonbonded pdb=" O2B ADP H 401 " pdb="MG MG H 402 " model vdw 1.998 2.170 nonbonded pdb=" O1B ADP H 401 " pdb="MG MG H 402 " model vdw 2.018 2.170 nonbonded pdb=" O ILE A 129 " pdb=" OG SER A 133 " model vdw 2.079 2.440 nonbonded pdb=" O GLU I 200 " pdb=" OH TYR J 232 " model vdw 2.114 2.440 ... (remaining 161668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 10.100 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 56.580 Find NCS groups from input model: 0.830 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 : 0.005 0.060 22141 Z= 0.340 Angle : 0.862 10.444 29965 Z= 0.467 Chirality : 0.049 0.307 3295 Planarity : 0.006 0.079 3845 Dihedral : 13.793 88.937 8298 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.08 % Allowed : 0.17 % Favored : 99.75 % 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: -1.49 (0.15), residues: 2664 helix: -0.51 (0.16), residues: 915 sheet: -0.20 (0.21), residues: 585 loop : -1.74 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 131 HIS 0.014 0.001 HIS C 30 PHE 0.031 0.002 PHE B 371 TYR 0.021 0.002 TYR D 146 ARG 0.010 0.001 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 603 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7484 (m-30) cc_final: 0.7225 (m-30) REVERT: A 302 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7503 (tm-30) REVERT: B 361 LEU cc_start: 0.8564 (tp) cc_final: 0.8333 (tt) REVERT: B 368 LYS cc_start: 0.8085 (pptt) cc_final: 0.7768 (pptt) REVERT: B 372 TRP cc_start: 0.8508 (m100) cc_final: 0.8132 (m100) REVERT: C 242 LEU cc_start: 0.7487 (tp) cc_final: 0.7238 (tp) REVERT: C 245 GLU cc_start: 0.7903 (pm20) cc_final: 0.7698 (pm20) REVERT: C 257 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7450 (mm-30) REVERT: E 87 SER cc_start: 0.7440 (t) cc_final: 0.7164 (p) REVERT: E 92 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7384 (tm-30) REVERT: E 95 MET cc_start: 0.7818 (mtm) cc_final: 0.7495 (mtm) REVERT: F 83 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6708 (mm-30) REVERT: F 154 ASN cc_start: 0.8177 (t0) cc_final: 0.7944 (t0) REVERT: G 111 TYR cc_start: 0.7388 (m-80) cc_final: 0.7175 (m-80) REVERT: H 61 LYS cc_start: 0.7814 (mttm) cc_final: 0.7597 (mttm) REVERT: H 195 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7191 (tm-30) REVERT: H 215 LYS cc_start: 0.8434 (ptpp) cc_final: 0.8025 (ptpp) REVERT: H 282 ILE cc_start: 0.7727 (tt) cc_final: 0.7459 (tt) REVERT: I 12 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6379 (mm-30) REVERT: I 15 ARG cc_start: 0.7202 (ptt-90) cc_final: 0.6716 (ptt-90) REVERT: I 21 ILE cc_start: 0.8397 (tp) cc_final: 0.8197 (tp) REVERT: I 56 GLN cc_start: 0.7370 (tp-100) cc_final: 0.6780 (tp-100) REVERT: I 234 ASN cc_start: 0.7130 (t0) cc_final: 0.6181 (t0) REVERT: I 238 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7280 (mm-30) REVERT: I 316 MET cc_start: 0.7886 (tpp) cc_final: 0.7542 (tpp) REVERT: I 321 LYS cc_start: 0.8387 (tttm) cc_final: 0.7834 (tttm) REVERT: J 10 LEU cc_start: 0.8537 (mt) cc_final: 0.8011 (mt) REVERT: J 11 ASP cc_start: 0.8005 (m-30) cc_final: 0.7390 (m-30) REVERT: J 63 ASP cc_start: 0.8269 (t70) cc_final: 0.8016 (t70) REVERT: J 151 ILE cc_start: 0.8601 (mt) cc_final: 0.8389 (mm) REVERT: J 220 MET cc_start: 0.7503 (tpp) cc_final: 0.7275 (mpp) outliers start: 2 outliers final: 0 residues processed: 604 average time/residue: 0.3923 time to fit residues: 342.8218 Evaluate side-chains 562 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 562 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 1.9990 chunk 201 optimal weight: 0.0770 chunk 111 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 241 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN C 28 ASN C 30 HIS I 167 ASN I 197 HIS I 205 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22141 Z= 0.190 Angle : 0.559 7.640 29965 Z= 0.287 Chirality : 0.044 0.184 3295 Planarity : 0.004 0.061 3845 Dihedral : 6.616 87.586 3008 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.16 % Rotamer: Outliers : 1.31 % Allowed : 8.83 % Favored : 89.86 % 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: -1.00 (0.16), residues: 2664 helix: 0.09 (0.17), residues: 922 sheet: 0.11 (0.21), residues: 578 loop : -1.67 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 131 HIS 0.003 0.001 HIS H 275 PHE 0.018 0.001 PHE C 169 TYR 0.018 0.001 TYR D 250 ARG 0.006 0.000 ARG J 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 575 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7509 (m-30) cc_final: 0.7261 (m-30) REVERT: A 266 GLU cc_start: 0.7391 (pm20) cc_final: 0.7054 (pm20) REVERT: A 274 GLU cc_start: 0.7373 (pm20) cc_final: 0.7063 (pm20) REVERT: A 302 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7521 (tm-30) REVERT: A 397 LYS cc_start: 0.7273 (tppt) cc_final: 0.7018 (tppt) REVERT: B 96 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6990 (tm-30) REVERT: B 211 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7393 (mm-30) REVERT: B 363 ASP cc_start: 0.8160 (t0) cc_final: 0.7930 (t0) REVERT: B 372 TRP cc_start: 0.8503 (m100) cc_final: 0.8178 (m100) REVERT: C 165 LYS cc_start: 0.8430 (mmtp) cc_final: 0.8208 (mmtp) REVERT: C 215 SER cc_start: 0.8513 (t) cc_final: 0.8245 (t) REVERT: C 257 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7452 (mm-30) REVERT: D 171 ASP cc_start: 0.7177 (t0) cc_final: 0.6774 (t0) REVERT: D 237 ARG cc_start: 0.7525 (ttp-110) cc_final: 0.7302 (ttp-110) REVERT: E 9 MET cc_start: 0.6300 (mmm) cc_final: 0.6030 (mmm) REVERT: E 92 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7396 (tm-30) REVERT: E 94 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8054 (mt-10) REVERT: E 95 MET cc_start: 0.7888 (mtm) cc_final: 0.7585 (mtm) REVERT: E 155 LYS cc_start: 0.7666 (mtmm) cc_final: 0.7423 (mtmm) REVERT: F 83 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6649 (mm-30) REVERT: F 146 ILE cc_start: 0.7450 (mt) cc_final: 0.7161 (pt) REVERT: F 163 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7069 (mm-30) REVERT: H 167 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7136 (mm-30) REVERT: H 195 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7258 (tm-30) REVERT: H 215 LYS cc_start: 0.8512 (ptpp) cc_final: 0.8108 (ptpp) REVERT: H 288 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7422 (t0) REVERT: H 325 MET cc_start: 0.7921 (ptp) cc_final: 0.7464 (ptt) REVERT: I 21 ILE cc_start: 0.8374 (tp) cc_final: 0.8153 (tp) REVERT: I 56 GLN cc_start: 0.7270 (tp-100) cc_final: 0.6599 (tp-100) REVERT: I 59 MET cc_start: 0.7139 (mmt) cc_final: 0.6883 (mpp) REVERT: I 138 ASN cc_start: 0.7087 (t0) cc_final: 0.6732 (t0) REVERT: I 238 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7323 (mm-30) REVERT: I 318 LYS cc_start: 0.8196 (mmpt) cc_final: 0.7757 (mmtt) REVERT: I 321 LYS cc_start: 0.8366 (tttm) cc_final: 0.8057 (tttm) REVERT: J 151 ILE cc_start: 0.8702 (mt) cc_final: 0.8451 (mm) REVERT: J 220 MET cc_start: 0.7501 (tpp) cc_final: 0.7215 (mpp) outliers start: 31 outliers final: 16 residues processed: 581 average time/residue: 0.3990 time to fit residues: 336.8061 Evaluate side-chains 569 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 552 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 240 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 239 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN C 30 HIS D 119 ASN H 161 HIS ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN J 212 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22141 Z= 0.336 Angle : 0.602 8.461 29965 Z= 0.315 Chirality : 0.046 0.159 3295 Planarity : 0.005 0.058 3845 Dihedral : 6.282 88.029 3008 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.01 % Favored : 93.96 % Rotamer: Outliers : 2.07 % Allowed : 12.55 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 2664 helix: 0.14 (0.17), residues: 916 sheet: 0.11 (0.21), residues: 589 loop : -1.65 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 122 HIS 0.006 0.001 HIS C 265 PHE 0.024 0.002 PHE C 169 TYR 0.024 0.002 TYR D 250 ARG 0.008 0.001 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 592 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7079 (ttt180) REVERT: A 161 ARG cc_start: 0.7748 (mmt90) cc_final: 0.7249 (mmt180) REVERT: A 266 GLU cc_start: 0.7428 (pm20) cc_final: 0.7089 (pm20) REVERT: A 302 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7540 (tm-30) REVERT: A 372 MET cc_start: 0.7692 (mtm) cc_final: 0.7379 (mtm) REVERT: B 149 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8519 (mm-40) REVERT: B 211 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7473 (mm-30) REVERT: B 242 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6822 (mm-30) REVERT: B 298 TYR cc_start: 0.8319 (m-10) cc_final: 0.8038 (m-80) REVERT: B 325 TYR cc_start: 0.7822 (t80) cc_final: 0.7546 (t80) REVERT: B 372 TRP cc_start: 0.8550 (m100) cc_final: 0.8193 (m100) REVERT: C 28 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7398 (t0) REVERT: C 257 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7511 (mm-30) REVERT: C 352 MET cc_start: 0.7608 (tmm) cc_final: 0.6985 (tmm) REVERT: D 171 ASP cc_start: 0.7209 (t0) cc_final: 0.6838 (t0) REVERT: E 70 TYR cc_start: 0.7484 (t80) cc_final: 0.6852 (t80) REVERT: E 92 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7433 (tm-30) REVERT: E 94 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8084 (mt-10) REVERT: E 95 MET cc_start: 0.7934 (mtm) cc_final: 0.7581 (mtm) REVERT: E 155 LYS cc_start: 0.7607 (mtmm) cc_final: 0.7349 (mtmm) REVERT: F 163 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7106 (mm-30) REVERT: G 111 TYR cc_start: 0.7678 (m-80) cc_final: 0.7472 (m-80) REVERT: H 167 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7328 (mm-30) REVERT: H 195 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7274 (tm-30) REVERT: H 214 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7043 (mt-10) REVERT: H 215 LYS cc_start: 0.8490 (ptpp) cc_final: 0.8055 (ptpp) REVERT: H 238 LYS cc_start: 0.8223 (mmtm) cc_final: 0.7964 (tppt) REVERT: H 285 CYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8516 (m) REVERT: H 288 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7519 (t0) REVERT: H 291 LYS cc_start: 0.8418 (tppt) cc_final: 0.8197 (tppt) REVERT: H 334 GLU cc_start: 0.7121 (pp20) cc_final: 0.6702 (pp20) REVERT: I 21 ILE cc_start: 0.8512 (tp) cc_final: 0.8235 (tp) REVERT: I 56 GLN cc_start: 0.7336 (tp-100) cc_final: 0.6662 (tp-100) REVERT: I 138 ASN cc_start: 0.7185 (t0) cc_final: 0.6889 (t0) REVERT: I 167 ASN cc_start: 0.7734 (t160) cc_final: 0.7315 (t0) REVERT: I 238 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7398 (mm-30) REVERT: I 318 LYS cc_start: 0.8241 (mmpt) cc_final: 0.7903 (mmtt) REVERT: I 321 LYS cc_start: 0.8433 (tttm) cc_final: 0.8089 (tttm) REVERT: J 63 ASP cc_start: 0.8438 (t70) cc_final: 0.8222 (t0) REVERT: J 151 ILE cc_start: 0.8750 (mt) cc_final: 0.8476 (mm) REVERT: J 219 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7836 (t70) outliers start: 49 outliers final: 36 residues processed: 607 average time/residue: 0.3870 time to fit residues: 342.0701 Evaluate side-chains 616 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 575 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 219 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 242 optimal weight: 8.9990 chunk 257 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 230 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN C 30 HIS C 75 ASN D 21 ASN D 119 ASN D 278 ASN H 12 ASN H 371 HIS ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22141 Z= 0.218 Angle : 0.551 8.458 29965 Z= 0.285 Chirality : 0.044 0.143 3295 Planarity : 0.004 0.057 3845 Dihedral : 6.022 85.118 3008 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.03 % Favored : 94.93 % Rotamer: Outliers : 2.62 % Allowed : 15.00 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 2664 helix: 0.30 (0.18), residues: 924 sheet: 0.14 (0.21), residues: 587 loop : -1.61 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 16 HIS 0.003 0.001 HIS C 265 PHE 0.021 0.002 PHE C 111 TYR 0.018 0.001 TYR D 250 ARG 0.006 0.000 ARG J 244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 568 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7071 (ttt180) REVERT: A 99 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8162 (mttt) REVERT: A 161 ARG cc_start: 0.7715 (mmt90) cc_final: 0.7152 (mmt180) REVERT: A 274 GLU cc_start: 0.7285 (pm20) cc_final: 0.7021 (pm20) REVERT: B 149 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8514 (mm-40) REVERT: B 211 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7468 (mm-30) REVERT: B 325 TYR cc_start: 0.7841 (t80) cc_final: 0.7555 (t80) REVERT: B 372 TRP cc_start: 0.8555 (m100) cc_final: 0.8089 (m100) REVERT: C 257 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7482 (mm-30) REVERT: C 352 MET cc_start: 0.7624 (tmm) cc_final: 0.6936 (tmm) REVERT: D 171 ASP cc_start: 0.7165 (t0) cc_final: 0.6815 (t0) REVERT: D 278 ASN cc_start: 0.8210 (t160) cc_final: 0.7974 (t0) REVERT: E 70 TYR cc_start: 0.7495 (t80) cc_final: 0.6892 (t80) REVERT: E 92 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7535 (tm-30) REVERT: E 94 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8066 (mt-10) REVERT: E 95 MET cc_start: 0.7925 (mtm) cc_final: 0.7719 (mtm) REVERT: E 155 LYS cc_start: 0.7608 (mtmm) cc_final: 0.7383 (mtmm) REVERT: F 78 GLN cc_start: 0.8056 (mp10) cc_final: 0.7810 (mp10) REVERT: F 113 ASP cc_start: 0.8425 (m-30) cc_final: 0.8218 (m-30) REVERT: F 163 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7118 (mm-30) REVERT: H 61 LYS cc_start: 0.7922 (mttm) cc_final: 0.7551 (tttm) REVERT: H 122 ILE cc_start: 0.8202 (tt) cc_final: 0.7987 (tt) REVERT: H 195 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7292 (tm-30) REVERT: H 214 GLU cc_start: 0.7299 (mt-10) cc_final: 0.7029 (mt-10) REVERT: H 215 LYS cc_start: 0.8499 (ptpp) cc_final: 0.8032 (ptpp) REVERT: H 285 CYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8478 (m) REVERT: H 288 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7467 (t0) REVERT: I 21 ILE cc_start: 0.8487 (tp) cc_final: 0.8211 (tp) REVERT: I 56 GLN cc_start: 0.7322 (tp-100) cc_final: 0.6640 (tp-100) REVERT: I 138 ASN cc_start: 0.7195 (t0) cc_final: 0.6868 (t0) REVERT: I 167 ASN cc_start: 0.7638 (t160) cc_final: 0.7134 (t0) REVERT: I 238 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7375 (mm-30) REVERT: I 318 LYS cc_start: 0.8240 (mmpt) cc_final: 0.7897 (mmtt) REVERT: I 321 LYS cc_start: 0.8407 (tttm) cc_final: 0.8070 (tttm) REVERT: J 63 ASP cc_start: 0.8421 (t70) cc_final: 0.8177 (t0) REVERT: J 151 ILE cc_start: 0.8717 (mt) cc_final: 0.8442 (mm) REVERT: J 219 ASP cc_start: 0.8382 (t70) cc_final: 0.7576 (t0) outliers start: 62 outliers final: 41 residues processed: 589 average time/residue: 0.3885 time to fit residues: 333.3328 Evaluate side-chains 603 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 559 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 164 GLN Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 244 SER Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 210 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 3 optimal weight: 0.3980 chunk 191 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 219 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 HIS C 30 HIS D 119 ASN I 42 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 22141 Z= 0.345 Angle : 0.608 13.961 29965 Z= 0.316 Chirality : 0.046 0.175 3295 Planarity : 0.005 0.056 3845 Dihedral : 6.158 90.766 3008 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.38 % Favored : 93.58 % Rotamer: Outliers : 3.38 % Allowed : 16.06 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.16), residues: 2664 helix: 0.21 (0.17), residues: 926 sheet: 0.06 (0.21), residues: 602 loop : -1.59 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 16 HIS 0.006 0.001 HIS C 265 PHE 0.024 0.002 PHE C 169 TYR 0.023 0.002 TYR E 74 ARG 0.005 0.000 ARG J 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 584 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7138 (ttt90) REVERT: A 99 LYS cc_start: 0.8386 (ttpt) cc_final: 0.8149 (mttt) REVERT: A 161 ARG cc_start: 0.7690 (mmt90) cc_final: 0.7105 (mmt180) REVERT: B 149 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8540 (mm-40) REVERT: B 211 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7560 (mm-30) REVERT: B 242 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6873 (mm-30) REVERT: B 325 TYR cc_start: 0.7864 (t80) cc_final: 0.7543 (t80) REVERT: C 257 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7503 (mm-30) REVERT: C 352 MET cc_start: 0.7698 (tmm) cc_final: 0.6948 (tmm) REVERT: D 222 TYR cc_start: 0.8118 (m-80) cc_final: 0.7852 (m-80) REVERT: E 70 TYR cc_start: 0.7535 (t80) cc_final: 0.6941 (t80) REVERT: E 92 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7514 (tm-30) REVERT: E 94 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8097 (mt-10) REVERT: E 155 LYS cc_start: 0.7689 (mtmm) cc_final: 0.7440 (mtmm) REVERT: F 78 GLN cc_start: 0.8073 (mp10) cc_final: 0.7845 (mp10) REVERT: F 83 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6705 (mm-30) REVERT: F 163 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7114 (mm-30) REVERT: G 111 TYR cc_start: 0.7691 (m-80) cc_final: 0.7409 (m-80) REVERT: H 61 LYS cc_start: 0.7949 (mttm) cc_final: 0.7568 (tttm) REVERT: H 122 ILE cc_start: 0.8304 (tt) cc_final: 0.8098 (tt) REVERT: H 195 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7304 (tm-30) REVERT: H 214 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7021 (mt-10) REVERT: H 215 LYS cc_start: 0.8495 (ptpp) cc_final: 0.7998 (ptpp) REVERT: H 285 CYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8537 (m) REVERT: H 286 ASP cc_start: 0.7787 (m-30) cc_final: 0.7338 (m-30) REVERT: H 288 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7527 (t0) REVERT: H 334 GLU cc_start: 0.7282 (pp20) cc_final: 0.6815 (pp20) REVERT: I 21 ILE cc_start: 0.8581 (tp) cc_final: 0.8245 (tp) REVERT: I 56 GLN cc_start: 0.7346 (tp-100) cc_final: 0.6656 (tp-100) REVERT: I 111 GLU cc_start: 0.7786 (pp20) cc_final: 0.7113 (pp20) REVERT: I 138 ASN cc_start: 0.7295 (t0) cc_final: 0.7014 (t0) REVERT: I 167 ASN cc_start: 0.7760 (t160) cc_final: 0.6959 (t0) REVERT: I 238 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7420 (mm-30) REVERT: I 247 TYR cc_start: 0.7274 (t80) cc_final: 0.6931 (t80) REVERT: I 272 ASN cc_start: 0.7760 (t0) cc_final: 0.7515 (t0) REVERT: I 318 LYS cc_start: 0.8233 (mmpt) cc_final: 0.7882 (mmtt) REVERT: I 321 LYS cc_start: 0.8390 (tttm) cc_final: 0.8055 (tttm) REVERT: J 63 ASP cc_start: 0.8497 (t70) cc_final: 0.8198 (t0) REVERT: J 151 ILE cc_start: 0.8717 (mt) cc_final: 0.8450 (mm) REVERT: J 219 ASP cc_start: 0.8472 (t70) cc_final: 0.7646 (t70) outliers start: 80 outliers final: 57 residues processed: 615 average time/residue: 0.3933 time to fit residues: 352.7499 Evaluate side-chains 635 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 575 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 164 GLN Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 210 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 0.0020 chunk 63 optimal weight: 0.7980 chunk 257 optimal weight: 0.0980 chunk 213 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 HIS D 119 ASN F 129 HIS ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22141 Z= 0.172 Angle : 0.547 10.517 29965 Z= 0.281 Chirality : 0.043 0.186 3295 Planarity : 0.004 0.063 3845 Dihedral : 5.835 82.841 3008 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.27 % Rotamer: Outliers : 2.70 % Allowed : 18.47 % Favored : 78.83 % 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: -0.71 (0.16), residues: 2664 helix: 0.46 (0.18), residues: 924 sheet: 0.05 (0.21), residues: 608 loop : -1.53 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 16 HIS 0.002 0.001 HIS I 197 PHE 0.021 0.001 PHE C 111 TYR 0.019 0.001 TYR E 74 ARG 0.005 0.000 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 570 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8335 (mt) cc_final: 0.8077 (mt) REVERT: A 79 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.7208 (ttt180) REVERT: A 161 ARG cc_start: 0.7689 (mmt90) cc_final: 0.7166 (mmt180) REVERT: B 149 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8559 (mm-40) REVERT: B 211 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7478 (mm-30) REVERT: B 242 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6871 (mm-30) REVERT: B 325 TYR cc_start: 0.7855 (t80) cc_final: 0.7563 (t80) REVERT: B 372 TRP cc_start: 0.8552 (m100) cc_final: 0.8078 (m100) REVERT: C 257 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7458 (mm-30) REVERT: C 352 MET cc_start: 0.7696 (tmm) cc_final: 0.6954 (tmm) REVERT: D 152 MET cc_start: 0.7779 (ttm) cc_final: 0.7542 (ttt) REVERT: E 14 LYS cc_start: 0.7067 (tmmt) cc_final: 0.6814 (ptmm) REVERT: E 70 TYR cc_start: 0.7527 (t80) cc_final: 0.6961 (t80) REVERT: E 92 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7497 (tm-30) REVERT: E 94 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8067 (mt-10) REVERT: F 83 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6606 (mm-30) REVERT: F 163 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7139 (mm-30) REVERT: G 111 TYR cc_start: 0.7673 (m-80) cc_final: 0.7367 (m-80) REVERT: H 61 LYS cc_start: 0.7929 (mttm) cc_final: 0.7552 (tttm) REVERT: H 82 MET cc_start: 0.5804 (tpt) cc_final: 0.5058 (tpt) REVERT: H 195 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7295 (tm-30) REVERT: H 214 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7015 (mt-10) REVERT: H 215 LYS cc_start: 0.8484 (ptpp) cc_final: 0.8003 (ptpp) REVERT: H 285 CYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8450 (m) REVERT: H 286 ASP cc_start: 0.7750 (m-30) cc_final: 0.7290 (m-30) REVERT: H 288 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7461 (t0) REVERT: I 21 ILE cc_start: 0.8522 (tp) cc_final: 0.8211 (tp) REVERT: I 56 GLN cc_start: 0.7295 (tp-100) cc_final: 0.6556 (tp-100) REVERT: I 58 ASN cc_start: 0.7872 (m110) cc_final: 0.7543 (m110) REVERT: I 59 MET cc_start: 0.7496 (mpp) cc_final: 0.7130 (mpp) REVERT: I 111 GLU cc_start: 0.7767 (pp20) cc_final: 0.7231 (pp20) REVERT: I 138 ASN cc_start: 0.7225 (t0) cc_final: 0.6913 (t0) REVERT: I 167 ASN cc_start: 0.7542 (t160) cc_final: 0.6779 (t0) REVERT: I 238 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7385 (mm-30) REVERT: I 247 TYR cc_start: 0.7218 (t80) cc_final: 0.6883 (t80) REVERT: I 272 ASN cc_start: 0.7696 (t0) cc_final: 0.7443 (t0) REVERT: I 318 LYS cc_start: 0.8204 (mmpt) cc_final: 0.7881 (mmtt) REVERT: I 321 LYS cc_start: 0.8397 (tttm) cc_final: 0.8076 (tttm) REVERT: J 5 GLN cc_start: 0.7928 (pm20) cc_final: 0.7717 (pm20) REVERT: J 108 ARG cc_start: 0.6811 (mtm110) cc_final: 0.6542 (mtm-85) REVERT: J 197 MET cc_start: 0.7126 (ppp) cc_final: 0.6800 (tmm) outliers start: 64 outliers final: 45 residues processed: 596 average time/residue: 0.3882 time to fit residues: 337.9939 Evaluate side-chains 611 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 563 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 294 TYR Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 164 GLN Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 244 SER Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 210 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 187 optimal weight: 0.0770 chunk 145 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 HIS ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22141 Z= 0.268 Angle : 0.575 10.945 29965 Z= 0.298 Chirality : 0.045 0.198 3295 Planarity : 0.004 0.063 3845 Dihedral : 5.962 87.158 3008 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.92 % Rotamer: Outliers : 3.21 % Allowed : 19.06 % Favored : 77.73 % 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: -0.75 (0.16), residues: 2664 helix: 0.41 (0.18), residues: 928 sheet: 0.04 (0.21), residues: 594 loop : -1.53 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 16 HIS 0.009 0.001 HIS I 197 PHE 0.023 0.002 PHE C 111 TYR 0.018 0.002 TYR D 250 ARG 0.005 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 572 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8373 (mt) cc_final: 0.8130 (mt) REVERT: A 79 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7226 (ttt180) REVERT: A 161 ARG cc_start: 0.7670 (mmt90) cc_final: 0.7140 (mmt180) REVERT: B 149 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8556 (mm-40) REVERT: B 325 TYR cc_start: 0.7871 (t80) cc_final: 0.7576 (t80) REVERT: C 257 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7491 (mm-30) REVERT: C 352 MET cc_start: 0.7721 (tmm) cc_final: 0.6953 (tmm) REVERT: D 152 MET cc_start: 0.7784 (ttm) cc_final: 0.7557 (ttt) REVERT: E 70 TYR cc_start: 0.7553 (t80) cc_final: 0.6985 (t80) REVERT: E 92 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7528 (tm-30) REVERT: E 94 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8102 (mt-10) REVERT: E 155 LYS cc_start: 0.7819 (mtmm) cc_final: 0.7508 (mtmm) REVERT: F 83 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6559 (mm-30) REVERT: F 163 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7142 (mm-30) REVERT: G 111 TYR cc_start: 0.7793 (m-80) cc_final: 0.7453 (m-80) REVERT: H 61 LYS cc_start: 0.7948 (mttm) cc_final: 0.7557 (tttm) REVERT: H 82 MET cc_start: 0.5898 (tpt) cc_final: 0.5146 (tpt) REVERT: H 195 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7300 (tm-30) REVERT: H 214 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7064 (mt-10) REVERT: H 215 LYS cc_start: 0.8471 (ptpp) cc_final: 0.7952 (ptpp) REVERT: H 285 CYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8520 (m) REVERT: H 286 ASP cc_start: 0.7806 (m-30) cc_final: 0.7359 (m-30) REVERT: H 288 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7499 (t0) REVERT: I 21 ILE cc_start: 0.8609 (tp) cc_final: 0.8262 (tp) REVERT: I 56 GLN cc_start: 0.7326 (tp-100) cc_final: 0.6658 (tp-100) REVERT: I 58 ASN cc_start: 0.7917 (m110) cc_final: 0.7583 (m110) REVERT: I 59 MET cc_start: 0.7623 (mpp) cc_final: 0.7347 (mpp) REVERT: I 111 GLU cc_start: 0.7928 (pp20) cc_final: 0.7238 (pp20) REVERT: I 138 ASN cc_start: 0.7307 (t0) cc_final: 0.7008 (t0) REVERT: I 167 ASN cc_start: 0.7675 (t160) cc_final: 0.6934 (t0) REVERT: I 238 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7406 (mm-30) REVERT: I 247 TYR cc_start: 0.7190 (t80) cc_final: 0.6714 (t80) REVERT: I 272 ASN cc_start: 0.7734 (t0) cc_final: 0.7470 (t0) REVERT: I 318 LYS cc_start: 0.8241 (mmpt) cc_final: 0.7907 (mmtt) REVERT: I 321 LYS cc_start: 0.8395 (tttm) cc_final: 0.8071 (tttm) REVERT: J 108 ARG cc_start: 0.6924 (mtm110) cc_final: 0.6699 (mtm-85) REVERT: J 197 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6905 (tmm) outliers start: 76 outliers final: 62 residues processed: 605 average time/residue: 0.3947 time to fit residues: 350.4495 Evaluate side-chains 633 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 567 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 294 TYR Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 164 GLN Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 178 GLN Chi-restraints excluded: chain J residue 197 MET Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 219 ASP Chi-restraints excluded: chain J residue 222 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 126 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 HIS D 278 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22141 Z= 0.185 Angle : 0.556 11.551 29965 Z= 0.285 Chirality : 0.043 0.224 3295 Planarity : 0.004 0.068 3845 Dihedral : 5.801 83.117 3008 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.88 % Favored : 95.08 % Rotamer: Outliers : 2.75 % Allowed : 19.99 % Favored : 77.26 % 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: -0.66 (0.16), residues: 2664 helix: 0.52 (0.18), residues: 928 sheet: 0.07 (0.21), residues: 589 loop : -1.49 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 173 HIS 0.002 0.001 HIS I 135 PHE 0.022 0.001 PHE C 246 TYR 0.015 0.001 TYR E 132 ARG 0.005 0.000 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 561 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8329 (mt) cc_final: 0.8066 (mt) REVERT: A 79 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7209 (ttt180) REVERT: A 161 ARG cc_start: 0.7646 (mmt90) cc_final: 0.7098 (mmt180) REVERT: B 90 ASP cc_start: 0.7505 (m-30) cc_final: 0.7072 (m-30) REVERT: B 120 ARG cc_start: 0.7984 (ttt90) cc_final: 0.7776 (ttt180) REVERT: B 121 GLU cc_start: 0.7654 (mp0) cc_final: 0.7083 (mp0) REVERT: B 149 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8571 (mm-40) REVERT: B 242 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6875 (mm-30) REVERT: B 325 TYR cc_start: 0.7877 (t80) cc_final: 0.7616 (t80) REVERT: B 372 TRP cc_start: 0.8550 (m100) cc_final: 0.8087 (m100) REVERT: C 257 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7452 (mm-30) REVERT: C 352 MET cc_start: 0.7686 (tmm) cc_final: 0.6932 (tmm) REVERT: D 152 MET cc_start: 0.7786 (ttm) cc_final: 0.7575 (ttt) REVERT: E 14 LYS cc_start: 0.7122 (ptmm) cc_final: 0.6733 (ptmm) REVERT: E 70 TYR cc_start: 0.7590 (t80) cc_final: 0.7032 (t80) REVERT: E 92 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7510 (tm-30) REVERT: E 94 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8097 (mt-10) REVERT: E 155 LYS cc_start: 0.7783 (mtmm) cc_final: 0.7476 (mtmm) REVERT: F 83 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6633 (mm-30) REVERT: F 163 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7154 (mm-30) REVERT: G 111 TYR cc_start: 0.7707 (m-80) cc_final: 0.7486 (m-80) REVERT: H 61 LYS cc_start: 0.7933 (mttm) cc_final: 0.7556 (tttm) REVERT: H 82 MET cc_start: 0.5756 (tpt) cc_final: 0.5025 (tpt) REVERT: H 195 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7302 (tm-30) REVERT: H 214 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7062 (mt-10) REVERT: H 215 LYS cc_start: 0.8478 (ptpp) cc_final: 0.7960 (ptpp) REVERT: H 285 CYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8461 (m) REVERT: H 286 ASP cc_start: 0.7782 (m-30) cc_final: 0.7312 (m-30) REVERT: H 288 ASP cc_start: 0.7858 (m-30) cc_final: 0.7541 (t0) REVERT: I 21 ILE cc_start: 0.8562 (tp) cc_final: 0.8227 (tp) REVERT: I 56 GLN cc_start: 0.7287 (tp-100) cc_final: 0.6518 (tp-100) REVERT: I 58 ASN cc_start: 0.7927 (m110) cc_final: 0.7588 (m110) REVERT: I 59 MET cc_start: 0.7596 (mpp) cc_final: 0.7165 (mpp) REVERT: I 138 ASN cc_start: 0.7200 (t0) cc_final: 0.6895 (t0) REVERT: I 167 ASN cc_start: 0.7551 (t160) cc_final: 0.6776 (t0) REVERT: I 238 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7369 (mm-30) REVERT: I 247 TYR cc_start: 0.7295 (t80) cc_final: 0.6915 (t80) REVERT: I 272 ASN cc_start: 0.7706 (t0) cc_final: 0.7446 (t0) REVERT: I 318 LYS cc_start: 0.8234 (mmpt) cc_final: 0.7930 (mmtt) REVERT: I 321 LYS cc_start: 0.8381 (tttm) cc_final: 0.8083 (tttm) outliers start: 65 outliers final: 54 residues processed: 588 average time/residue: 0.3840 time to fit residues: 328.2546 Evaluate side-chains 611 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 555 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 294 TYR Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 164 GLN Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 178 GLN Chi-restraints excluded: chain J residue 197 MET Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 219 ASP Chi-restraints excluded: chain J residue 264 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 chunk 238 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 225 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 30 HIS D 119 ASN D 278 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22141 Z= 0.224 Angle : 0.571 12.341 29965 Z= 0.293 Chirality : 0.044 0.234 3295 Planarity : 0.004 0.076 3845 Dihedral : 5.823 83.857 3008 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.56 % Favored : 94.41 % Rotamer: Outliers : 3.21 % Allowed : 19.91 % Favored : 76.88 % 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: 2664 helix: 0.51 (0.18), residues: 930 sheet: 0.08 (0.21), residues: 591 loop : -1.49 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 75 HIS 0.004 0.001 HIS I 197 PHE 0.024 0.001 PHE C 246 TYR 0.016 0.001 TYR D 250 ARG 0.006 0.000 ARG I 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 565 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8339 (mt) cc_final: 0.8071 (mt) REVERT: A 79 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7203 (ttt180) REVERT: A 89 MET cc_start: 0.7891 (tpp) cc_final: 0.7273 (tpp) REVERT: B 90 ASP cc_start: 0.7511 (m-30) cc_final: 0.7080 (m-30) REVERT: B 96 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6935 (tm-30) REVERT: B 149 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8567 (mm-40) REVERT: B 227 ILE cc_start: 0.7901 (mm) cc_final: 0.7602 (mm) REVERT: B 242 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6882 (mm-30) REVERT: B 325 TYR cc_start: 0.7886 (t80) cc_final: 0.7585 (t80) REVERT: C 94 ARG cc_start: 0.8767 (mtm-85) cc_final: 0.8213 (mtm-85) REVERT: C 342 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7742 (ptpt) REVERT: C 352 MET cc_start: 0.7695 (tmm) cc_final: 0.6942 (tmm) REVERT: E 14 LYS cc_start: 0.7014 (ptmm) cc_final: 0.6500 (ptmm) REVERT: E 70 TYR cc_start: 0.7601 (t80) cc_final: 0.7045 (t80) REVERT: E 92 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7516 (tm-30) REVERT: E 94 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8116 (mt-10) REVERT: E 123 LYS cc_start: 0.8767 (pttm) cc_final: 0.8559 (pttm) REVERT: E 155 LYS cc_start: 0.7789 (mtmm) cc_final: 0.7474 (mtmm) REVERT: F 83 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6700 (mm-30) REVERT: F 163 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7158 (mm-30) REVERT: G 111 TYR cc_start: 0.7741 (m-80) cc_final: 0.7528 (m-80) REVERT: H 61 LYS cc_start: 0.7939 (mttm) cc_final: 0.7551 (tttm) REVERT: H 82 MET cc_start: 0.5846 (tpt) cc_final: 0.5131 (tpt) REVERT: H 155 SER cc_start: 0.8419 (m) cc_final: 0.8175 (t) REVERT: H 195 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7310 (tm-30) REVERT: H 214 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7086 (mt-10) REVERT: H 215 LYS cc_start: 0.8463 (ptpp) cc_final: 0.7943 (ptpp) REVERT: H 285 CYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8510 (m) REVERT: H 286 ASP cc_start: 0.7792 (m-30) cc_final: 0.7348 (m-30) REVERT: H 288 ASP cc_start: 0.7855 (m-30) cc_final: 0.7538 (t0) REVERT: I 21 ILE cc_start: 0.8596 (tp) cc_final: 0.8226 (tp) REVERT: I 58 ASN cc_start: 0.7957 (m110) cc_final: 0.7603 (m110) REVERT: I 59 MET cc_start: 0.7601 (mpp) cc_final: 0.7371 (mpp) REVERT: I 111 GLU cc_start: 0.7614 (pp20) cc_final: 0.7135 (pp20) REVERT: I 138 ASN cc_start: 0.7267 (t0) cc_final: 0.6978 (t0) REVERT: I 167 ASN cc_start: 0.7597 (t160) cc_final: 0.6838 (t0) REVERT: I 238 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7371 (mm-30) REVERT: I 272 ASN cc_start: 0.7729 (t0) cc_final: 0.7461 (t0) REVERT: I 316 MET cc_start: 0.7862 (tpp) cc_final: 0.7495 (mpp) REVERT: I 318 LYS cc_start: 0.8239 (mmpt) cc_final: 0.7939 (mmtt) REVERT: I 321 LYS cc_start: 0.8394 (tttm) cc_final: 0.8083 (tttm) outliers start: 76 outliers final: 66 residues processed: 602 average time/residue: 0.3971 time to fit residues: 348.1950 Evaluate side-chains 632 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 564 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 294 TYR Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 164 GLN Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 178 GLN Chi-restraints excluded: chain J residue 197 MET Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 264 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 243 optimal weight: 7.9990 chunk 211 optimal weight: 3.9990 chunk 21 optimal weight: 0.0870 chunk 163 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 30 HIS D 47 ASN D 119 ASN D 278 ASN ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 222 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22141 Z= 0.356 Angle : 0.639 12.821 29965 Z= 0.330 Chirality : 0.047 0.219 3295 Planarity : 0.005 0.074 3845 Dihedral : 6.159 93.001 3008 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.46 % Favored : 93.51 % Rotamer: Outliers : 3.17 % Allowed : 20.12 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2664 helix: 0.35 (0.18), residues: 930 sheet: 0.03 (0.21), residues: 601 loop : -1.57 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 16 HIS 0.007 0.001 HIS I 135 PHE 0.027 0.002 PHE C 246 TYR 0.023 0.002 TYR D 250 ARG 0.007 0.001 ARG I 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 569 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7222 (ttt180) REVERT: A 161 ARG cc_start: 0.7591 (mmt90) cc_final: 0.7157 (mmt180) REVERT: B 96 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6796 (tm-30) REVERT: B 149 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8571 (mm-40) REVERT: B 227 ILE cc_start: 0.7974 (mm) cc_final: 0.7682 (mm) REVERT: B 242 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6882 (mm-30) REVERT: B 325 TYR cc_start: 0.7914 (t80) cc_final: 0.7539 (t80) REVERT: C 63 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7572 (mttt) REVERT: C 352 MET cc_start: 0.7701 (tmm) cc_final: 0.6898 (tmm) REVERT: E 14 LYS cc_start: 0.7080 (ptmm) cc_final: 0.6704 (ptmm) REVERT: E 70 TYR cc_start: 0.7617 (t80) cc_final: 0.7041 (t80) REVERT: E 92 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7513 (tm-30) REVERT: E 94 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8139 (mt-10) REVERT: E 155 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7521 (mtmm) REVERT: F 83 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6743 (mm-30) REVERT: F 163 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7185 (mm-30) REVERT: G 111 TYR cc_start: 0.7801 (m-80) cc_final: 0.7547 (m-80) REVERT: H 61 LYS cc_start: 0.7978 (mttm) cc_final: 0.7577 (tttm) REVERT: H 82 MET cc_start: 0.5934 (tpt) cc_final: 0.5222 (tpt) REVERT: H 155 SER cc_start: 0.8408 (m) cc_final: 0.8135 (t) REVERT: H 195 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7334 (tm-30) REVERT: H 214 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7073 (mt-10) REVERT: H 215 LYS cc_start: 0.8421 (ptpp) cc_final: 0.7878 (ptpp) REVERT: H 285 CYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8506 (m) REVERT: H 286 ASP cc_start: 0.7821 (m-30) cc_final: 0.7335 (m-30) REVERT: H 288 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7535 (t0) REVERT: H 290 ARG cc_start: 0.6997 (mtt90) cc_final: 0.6358 (ttt90) REVERT: H 334 GLU cc_start: 0.7462 (pp20) cc_final: 0.6935 (pp20) REVERT: I 21 ILE cc_start: 0.8679 (tp) cc_final: 0.8291 (tp) REVERT: I 58 ASN cc_start: 0.7982 (m110) cc_final: 0.7646 (m110) REVERT: I 59 MET cc_start: 0.7563 (mpp) cc_final: 0.7282 (mpp) REVERT: I 129 ARG cc_start: 0.7836 (tpp80) cc_final: 0.7203 (tpt-90) REVERT: I 167 ASN cc_start: 0.7814 (t160) cc_final: 0.7040 (t0) REVERT: I 238 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7406 (mm-30) REVERT: I 272 ASN cc_start: 0.7784 (t0) cc_final: 0.7510 (t0) REVERT: I 318 LYS cc_start: 0.8252 (mmpt) cc_final: 0.7929 (mmtt) REVERT: I 321 LYS cc_start: 0.8392 (tttm) cc_final: 0.8072 (tttm) outliers start: 75 outliers final: 62 residues processed: 606 average time/residue: 0.3793 time to fit residues: 335.6542 Evaluate side-chains 628 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 562 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 294 TYR Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 178 GLN Chi-restraints excluded: chain J residue 197 MET Chi-restraints excluded: chain J residue 210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.9980 chunk 64 optimal weight: 0.0000 chunk 194 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 HIS D 119 ASN D 242 ASN E 5 HIS ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.152254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.121829 restraints weight = 34544.386| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.81 r_work: 0.3413 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22141 Z= 0.199 Angle : 0.586 12.570 29965 Z= 0.296 Chirality : 0.044 0.224 3295 Planarity : 0.004 0.075 3845 Dihedral : 5.913 83.322 3008 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.07 % Favored : 94.89 % Rotamer: Outliers : 2.96 % Allowed : 20.67 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.67 (0.16), residues: 2664 helix: 0.46 (0.18), residues: 931 sheet: 0.08 (0.21), residues: 593 loop : -1.48 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 173 HIS 0.003 0.001 HIS I 135 PHE 0.027 0.001 PHE C 246 TYR 0.015 0.001 TYR E 132 ARG 0.007 0.000 ARG I 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6451.78 seconds wall clock time: 116 minutes 10.33 seconds (6970.33 seconds total)