Starting phenix.real_space_refine on Thu Apr 11 09:44:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs7_29416/04_2024/8fs7_29416_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs7_29416/04_2024/8fs7_29416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs7_29416/04_2024/8fs7_29416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs7_29416/04_2024/8fs7_29416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs7_29416/04_2024/8fs7_29416_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs7_29416/04_2024/8fs7_29416_updated.pdb" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 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 71 5.49 5 Mg 4 5.21 5 S 114 5.16 5 C 13864 2.51 5 N 3819 2.21 5 O 4323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "D PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 314": "OE1" <-> "OE2" Residue "G GLU 325": "OE1" <-> "OE2" Residue "G GLU 329": "OE1" <-> "OE2" Residue "H GLU 38": "OE1" <-> "OE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "H TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 251": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22195 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3580 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 421} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2586 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2668 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain breaks: 1 Chain: "F" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2276 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 6 Chain: "G" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2315 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 5, 'TRANS': 286} Chain breaks: 2 Chain: "H" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2330 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 4 Chain: "I" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "J" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 313 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.95, per 1000 atoms: 0.54 Number of scatterers: 22195 At special positions: 0 Unit cell: (113.436, 120.888, 139.932, 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 114 16.00 P 71 15.00 Mg 4 11.99 O 4323 8.00 N 3819 7.00 C 13864 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: 9.33 Conformation dependent library (CDL) restraints added in 3.8 seconds 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 16 sheets defined 44.8% alpha, 14.4% beta 22 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 9.58 Creating SS restraints... Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 82 through 95 removed outlier: 3.643A pdb=" N ALA A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.803A pdb=" N ILE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 162 through 173 removed outlier: 4.626A pdb=" N PHE A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 239 through 242 No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 246 through 249 No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 270 through 290 removed outlier: 6.032A pdb=" N LYS A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 374 through 386 removed outlier: 5.271A pdb=" N ASN A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.655A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 446 through 467 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 487 through 498 Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 56 through 71 removed outlier: 7.900A pdb=" N ARG B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N SER B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.927A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 245 through 256 Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 282 through 301 Processing helix chain 'B' and resid 306 through 321 Processing helix chain 'C' and resid 10 through 12 No H-bonds generated for 'chain 'C' and resid 10 through 12' Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 75 through 78 No H-bonds generated for 'chain 'C' and resid 75 through 78' Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.927A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 124 through 136 removed outlier: 4.111A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 256 through 270 removed outlier: 4.049A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.912A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 316 through 331 Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 43 through 54 removed outlier: 3.572A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 91 Proline residue: D 85 - end of helix removed outlier: 4.617A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.744A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 147 through 159 removed outlier: 4.371A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 194 through 207 removed outlier: 5.257A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 228 through 245 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 265 through 276 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 316 through 335 removed outlier: 3.514A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 21 through 31 Processing helix chain 'E' and resid 33 through 35 No H-bonds generated for 'chain 'E' and resid 33 through 35' Processing helix chain 'E' and resid 49 through 61 Processing helix chain 'E' and resid 103 through 117 removed outlier: 4.186A pdb=" N ARG E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 107 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL E 108 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 109 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL E 116 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA E 117 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 150 through 160 removed outlier: 4.027A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 291 Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 315 through 333 Processing helix chain 'E' and resid 338 through 353 Processing helix chain 'F' and resid 13 through 29 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 89 No H-bonds generated for 'chain 'F' and resid 87 through 89' Processing helix chain 'F' and resid 97 through 112 removed outlier: 3.510A pdb=" N MET F 111 " --> pdb=" O TYR F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 218 Processing helix chain 'F' and resid 241 through 253 removed outlier: 4.642A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL F 253 " --> pdb=" O PHE F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 424 removed outlier: 3.617A pdb=" N ALA F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 28 removed outlier: 4.077A pdb=" N LEU G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 87 through 92 Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 239 through 245 removed outlier: 3.975A pdb=" N LYS G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 329 Processing helix chain 'H' and resid 10 through 26 Processing helix chain 'H' and resid 98 through 102 Processing helix chain 'H' and resid 234 through 243 Processing helix chain 'H' and resid 327 through 338 removed outlier: 4.075A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Proline residue: H 337 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 260 through 264 removed outlier: 6.591A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE A 263 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 106 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 219 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU A 107 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 221 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY A 109 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 223 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N THR A 224 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 159 through 163 removed outlier: 6.235A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 162 through 166 removed outlier: 3.607A pdb=" N GLY C 53 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 185 through 189 removed outlier: 3.592A pdb=" N GLY D 65 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 186 through 190 removed outlier: 6.371A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 69 through 75 Processing sheet with id= G, first strand: chain 'F' and resid 79 through 83 removed outlier: 3.911A pdb=" N LEU F 79 " --> pdb=" O ILE F 6 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 231 through 235 removed outlier: 4.741A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU F 68 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL F 207 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 409 through 411 Processing sheet with id= J, first strand: chain 'G' and resid 11 through 15 Processing sheet with id= K, first strand: chain 'G' and resid 80 through 85 removed outlier: 7.189A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE G 48 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE G 304 " --> pdb=" O SER G 271 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER G 271 " --> pdb=" O ILE G 304 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE G 306 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 190 through 197 Processing sheet with id= M, first strand: chain 'H' and resid 64 through 66 removed outlier: 3.561A pdb=" N PHE H 3 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU H 139 " --> pdb=" O LYS H 114 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE H 116 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL H 137 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE H 118 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE H 135 " --> pdb=" O ILE H 118 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 295 through 297 removed outlier: 3.587A pdb=" N PHE H 353 " --> pdb=" O ASN H 228 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN H 348 " --> pdb=" O GLN H 365 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN H 365 " --> pdb=" O ASN H 348 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 94 through 96 Processing sheet with id= P, first strand: chain 'H' and resid 261 through 265 955 hydrogen bonds defined for protein. 2769 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 8.25 Time building geometry restraints manager: 9.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7207 1.36 - 1.51: 6083 1.51 - 1.66: 9230 1.66 - 1.80: 79 1.80 - 1.95: 90 Bond restraints: 22689 Sorted by residual: bond pdb=" N SER E 90 " pdb=" CA SER E 90 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.04e-02 9.25e+03 8.84e+00 bond pdb=" N HIS E 93 " pdb=" CA HIS E 93 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.21e-02 6.83e+03 8.09e+00 bond pdb=" N VAL D 256 " pdb=" CA VAL D 256 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.01e+00 bond pdb=" N VAL D 262 " pdb=" CA VAL D 262 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.17e-02 7.31e+03 7.66e+00 bond pdb=" N ILE C 198 " pdb=" CA ILE C 198 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.58e+00 ... (remaining 22684 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.77: 891 106.77 - 114.18: 13519 114.18 - 121.60: 11381 121.60 - 129.01: 4969 129.01 - 136.43: 149 Bond angle restraints: 30909 Sorted by residual: angle pdb=" CB ILE H 161 " pdb=" CG1 ILE H 161 " pdb=" CD1 ILE H 161 " ideal model delta sigma weight residual 113.80 122.52 -8.72 2.10e+00 2.27e-01 1.72e+01 angle pdb=" C VAL D 216 " pdb=" N LEU D 217 " pdb=" CA LEU D 217 " ideal model delta sigma weight residual 121.54 129.07 -7.53 1.91e+00 2.74e-01 1.55e+01 angle pdb=" CA ILE H 161 " pdb=" CB ILE H 161 " pdb=" CG1 ILE H 161 " ideal model delta sigma weight residual 110.40 116.75 -6.35 1.70e+00 3.46e-01 1.40e+01 angle pdb=" CA SER E 90 " pdb=" C SER E 90 " pdb=" N PRO E 91 " ideal model delta sigma weight residual 117.96 120.97 -3.01 8.10e-01 1.52e+00 1.38e+01 angle pdb=" CA ILE E 107 " pdb=" CB ILE E 107 " pdb=" CG1 ILE E 107 " ideal model delta sigma weight residual 110.40 116.71 -6.31 1.70e+00 3.46e-01 1.38e+01 ... (remaining 30904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.71: 12717 31.71 - 63.43: 970 63.43 - 95.14: 32 95.14 - 126.85: 1 126.85 - 158.57: 2 Dihedral angle restraints: 13722 sinusoidal: 6046 harmonic: 7676 Sorted by residual: dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 98.57 -158.57 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 72.96 -132.96 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 64.39 -124.39 1 2.00e+01 2.50e-03 3.76e+01 ... (remaining 13719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2496 0.036 - 0.071: 766 0.071 - 0.107: 218 0.107 - 0.143: 82 0.143 - 0.178: 12 Chirality restraints: 3574 Sorted by residual: chirality pdb=" CA ILE F 468 " pdb=" N ILE F 468 " pdb=" C ILE F 468 " pdb=" CB ILE F 468 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CA VAL E 88 " pdb=" N VAL E 88 " pdb=" C VAL E 88 " pdb=" CB VAL E 88 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CB ILE E 211 " pdb=" CA ILE E 211 " pdb=" CG1 ILE E 211 " pdb=" CG2 ILE E 211 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 3571 not shown) Planarity restraints: 3695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 217 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C LEU D 217 " -0.055 2.00e-02 2.50e+03 pdb=" O LEU D 217 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU D 218 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO E 63 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 97 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO E 98 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " -0.035 5.00e-02 4.00e+02 ... (remaining 3692 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 257 2.63 - 3.20: 19123 3.20 - 3.77: 35967 3.77 - 4.33: 49747 4.33 - 4.90: 81386 Nonbonded interactions: 186480 Sorted by model distance: nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.068 2.170 nonbonded pdb="MG MG C 401 " pdb=" O2G AGS C 402 " model vdw 2.070 2.170 nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 401 " model vdw 2.075 2.170 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.078 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.098 2.170 ... (remaining 186475 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: 5.550 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: 0.010 Extract box with map and model: 16.900 Check model and map are aligned: 0.340 Set scattering table: 0.230 Process input model: 66.580 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.090 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.003 0.041 22689 Z= 0.172 Angle : 0.559 10.118 30909 Z= 0.316 Chirality : 0.041 0.178 3574 Planarity : 0.004 0.079 3695 Dihedral : 19.012 158.569 8718 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.37 % Allowed : 25.66 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2570 helix: 1.16 (0.15), residues: 1235 sheet: 0.25 (0.24), residues: 548 loop : -0.40 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 259 HIS 0.006 0.001 HIS E 93 PHE 0.012 0.001 PHE H 152 TYR 0.025 0.001 TYR B 186 ARG 0.011 0.000 ARG D 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 288 time to evaluate : 2.371 Fit side-chains revert: symmetry clash REVERT: A 284 ASN cc_start: 0.7204 (m-40) cc_final: 0.6977 (m110) REVERT: C 87 ASP cc_start: 0.7902 (t70) cc_final: 0.7647 (t0) REVERT: F 41 ARG cc_start: 0.5911 (OUTLIER) cc_final: 0.5591 (ptp-110) REVERT: F 470 ARG cc_start: 0.7572 (ptt90) cc_final: 0.7345 (ptt180) REVERT: G 151 ARG cc_start: 0.7635 (tpp80) cc_final: 0.7390 (mpp80) REVERT: G 202 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6839 (m-80) REVERT: H 45 ASN cc_start: 0.7840 (t0) cc_final: 0.7613 (t0) REVERT: H 63 GLU cc_start: 0.6966 (pm20) cc_final: 0.6576 (pm20) REVERT: H 250 ASP cc_start: 0.7759 (p0) cc_final: 0.7555 (p0) REVERT: H 284 MET cc_start: 0.7030 (ttt) cc_final: 0.6811 (ttm) outliers start: 56 outliers final: 43 residues processed: 338 average time/residue: 1.2514 time to fit residues: 489.7563 Evaluate side-chains 306 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 261 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 369 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 133 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 19 ASN E 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22689 Z= 0.175 Angle : 0.486 9.589 30909 Z= 0.255 Chirality : 0.040 0.154 3574 Planarity : 0.004 0.055 3695 Dihedral : 16.321 166.418 3570 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.52 % Allowed : 22.99 % Favored : 72.49 % 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: 0.86 (0.17), residues: 2570 helix: 1.35 (0.15), residues: 1239 sheet: 0.25 (0.23), residues: 552 loop : -0.29 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 259 HIS 0.005 0.001 HIS H 259 PHE 0.024 0.001 PHE G 40 TYR 0.017 0.001 TYR B 186 ARG 0.006 0.000 ARG D 230 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 285 time to evaluate : 2.318 Fit side-chains revert: symmetry clash REVERT: A 302 ASP cc_start: 0.7747 (m-30) cc_final: 0.7509 (m-30) REVERT: B 291 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: C 94 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7873 (mtp180) REVERT: C 167 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8459 (pt0) REVERT: C 305 ASP cc_start: 0.8091 (m-30) cc_final: 0.7860 (m-30) REVERT: D 178 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7665 (t0) REVERT: F 224 MET cc_start: 0.6263 (OUTLIER) cc_final: 0.5678 (mmt) REVERT: F 232 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7874 (mpp) REVERT: G 159 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7923 (ptmm) REVERT: G 202 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6889 (m-80) REVERT: H 55 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8075 (mtm180) REVERT: H 284 MET cc_start: 0.7101 (ttt) cc_final: 0.6861 (ttm) outliers start: 107 outliers final: 43 residues processed: 359 average time/residue: 1.2709 time to fit residues: 525.5638 Evaluate side-chains 300 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 248 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 162 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 212 optimal weight: 0.7980 chunk 236 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 191 optimal weight: 10.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 203 GLN B 91 ASN C 74 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 141 ASN E 144 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22689 Z= 0.208 Angle : 0.495 8.994 30909 Z= 0.261 Chirality : 0.040 0.145 3574 Planarity : 0.004 0.046 3695 Dihedral : 16.201 162.901 3525 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.07 % Allowed : 22.82 % Favored : 72.10 % 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: 0.89 (0.17), residues: 2570 helix: 1.38 (0.15), residues: 1229 sheet: 0.31 (0.22), residues: 546 loop : -0.31 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 324 HIS 0.006 0.001 HIS E 18 PHE 0.026 0.001 PHE G 40 TYR 0.012 0.001 TYR A 235 ARG 0.007 0.000 ARG F 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 254 time to evaluate : 2.637 Fit side-chains REVERT: A 247 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8103 (mm-30) REVERT: A 288 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7510 (mp) REVERT: A 307 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6800 (mt-10) REVERT: A 375 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6946 (t0) REVERT: B 247 ASP cc_start: 0.7339 (m-30) cc_final: 0.7138 (m-30) REVERT: C 94 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7938 (mtp180) REVERT: C 167 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8572 (pt0) REVERT: C 256 TRP cc_start: 0.9067 (OUTLIER) cc_final: 0.8723 (m100) REVERT: C 317 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8138 (mm-40) REVERT: D 207 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7985 (mm-40) REVERT: D 211 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6950 (mttp) REVERT: E 34 ARG cc_start: 0.7348 (mmp-170) cc_final: 0.6613 (mmm-85) REVERT: E 115 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: E 221 ARG cc_start: 0.7426 (mtp85) cc_final: 0.6994 (mtp-110) REVERT: E 227 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.7125 (t0) REVERT: F 71 THR cc_start: 0.7920 (m) cc_final: 0.7601 (p) REVERT: F 224 MET cc_start: 0.6245 (OUTLIER) cc_final: 0.5631 (mmt) REVERT: G 10 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7945 (mttm) REVERT: G 61 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7552 (mp) REVERT: G 202 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6592 (m-80) REVERT: H 55 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7366 (mtm-85) REVERT: H 284 MET cc_start: 0.7185 (ttt) cc_final: 0.6934 (ttm) outliers start: 120 outliers final: 61 residues processed: 343 average time/residue: 1.2569 time to fit residues: 500.2222 Evaluate side-chains 317 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 241 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 113 optimal weight: 0.4980 chunk 160 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 81 HIS A 231 ASN C 12 ASN C 74 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 110 GLN E 227 ASN F 263 HIS F 291 HIS H 100 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22689 Z= 0.327 Angle : 0.557 8.974 30909 Z= 0.291 Chirality : 0.043 0.155 3574 Planarity : 0.004 0.051 3695 Dihedral : 16.295 137.362 3522 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.32 % Favored : 95.64 % Rotamer: Outliers : 6.00 % Allowed : 21.94 % Favored : 72.06 % 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: 0.56 (0.17), residues: 2570 helix: 1.04 (0.15), residues: 1239 sheet: 0.29 (0.22), residues: 539 loop : -0.46 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 324 HIS 0.008 0.002 HIS B 232 PHE 0.020 0.002 PHE G 40 TYR 0.017 0.002 TYR B 186 ARG 0.009 0.001 ARG D 230 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 257 time to evaluate : 2.640 Fit side-chains REVERT: A 225 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7645 (mt-10) REVERT: A 247 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8071 (mm-30) REVERT: A 288 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7501 (mp) REVERT: A 307 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6612 (mt-10) REVERT: B 100 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8410 (tmtt) REVERT: B 247 ASP cc_start: 0.7444 (m-30) cc_final: 0.7217 (m-30) REVERT: C 94 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8007 (mtp180) REVERT: C 167 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8630 (pt0) REVERT: C 256 TRP cc_start: 0.9114 (OUTLIER) cc_final: 0.8841 (m100) REVERT: D 211 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7001 (mttp) REVERT: D 279 ASP cc_start: 0.8006 (t70) cc_final: 0.7750 (t0) REVERT: E 9 ARG cc_start: 0.8087 (ttt-90) cc_final: 0.7723 (ttt-90) REVERT: E 34 ARG cc_start: 0.7323 (mmp-170) cc_final: 0.6611 (mmm-85) REVERT: F 202 MET cc_start: 0.7780 (mmm) cc_final: 0.7496 (tmm) REVERT: F 224 MET cc_start: 0.6271 (OUTLIER) cc_final: 0.5656 (mmm) REVERT: F 427 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: G 10 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8007 (mttm) REVERT: G 61 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7765 (mp) REVERT: G 159 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7681 (ptmm) REVERT: G 161 GLU cc_start: 0.7022 (mp0) cc_final: 0.6418 (mp0) REVERT: G 317 ASP cc_start: 0.4849 (OUTLIER) cc_final: 0.4411 (p0) outliers start: 142 outliers final: 71 residues processed: 366 average time/residue: 1.2965 time to fit residues: 546.6320 Evaluate side-chains 324 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 238 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 427 GLU Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 350 SER Chi-restraints excluded: chain H residue 361 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 188 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN C 317 GLN ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN H 286 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22689 Z= 0.180 Angle : 0.493 9.470 30909 Z= 0.260 Chirality : 0.040 0.138 3574 Planarity : 0.004 0.049 3695 Dihedral : 16.128 124.115 3518 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 4.86 % Allowed : 23.75 % Favored : 71.39 % 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: 0.74 (0.17), residues: 2570 helix: 1.22 (0.15), residues: 1237 sheet: 0.32 (0.22), residues: 540 loop : -0.41 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 324 HIS 0.006 0.001 HIS E 18 PHE 0.014 0.001 PHE G 40 TYR 0.012 0.001 TYR B 186 ARG 0.007 0.000 ARG D 230 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 250 time to evaluate : 2.667 Fit side-chains REVERT: A 247 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8075 (mm-30) REVERT: A 288 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7506 (mp) REVERT: A 307 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6625 (mt-10) REVERT: A 375 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6730 (t0) REVERT: B 100 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8425 (tmtt) REVERT: B 247 ASP cc_start: 0.7412 (m-30) cc_final: 0.7180 (m-30) REVERT: C 94 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8007 (mtp180) REVERT: C 167 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8512 (pt0) REVERT: C 256 TRP cc_start: 0.9049 (OUTLIER) cc_final: 0.8775 (m100) REVERT: D 211 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.6961 (mttp) REVERT: D 279 ASP cc_start: 0.7995 (t70) cc_final: 0.7733 (t0) REVERT: E 34 ARG cc_start: 0.7213 (mmp-170) cc_final: 0.6529 (mmm-85) REVERT: F 71 THR cc_start: 0.7935 (m) cc_final: 0.7647 (p) REVERT: F 224 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.5651 (mmt) REVERT: F 279 VAL cc_start: 0.7136 (OUTLIER) cc_final: 0.6904 (p) REVERT: F 427 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: G 10 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7967 (mttm) REVERT: G 61 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7655 (mp) REVERT: G 159 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7634 (ptmm) REVERT: G 161 GLU cc_start: 0.6980 (mp0) cc_final: 0.6386 (mp0) REVERT: G 169 ASP cc_start: 0.7755 (t0) cc_final: 0.7462 (t70) REVERT: H 55 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7318 (mtm-85) REVERT: H 284 MET cc_start: 0.7176 (ttt) cc_final: 0.6909 (ttm) outliers start: 115 outliers final: 63 residues processed: 334 average time/residue: 1.2861 time to fit residues: 500.0644 Evaluate side-chains 327 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 249 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 427 GLU Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 253 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22689 Z= 0.218 Angle : 0.504 9.038 30909 Z= 0.264 Chirality : 0.040 0.181 3574 Planarity : 0.004 0.048 3695 Dihedral : 16.042 118.309 3518 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 4.90 % Allowed : 23.96 % Favored : 71.13 % 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: 0.77 (0.17), residues: 2570 helix: 1.21 (0.15), residues: 1238 sheet: 0.35 (0.22), residues: 545 loop : -0.34 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 324 HIS 0.006 0.001 HIS E 18 PHE 0.014 0.001 PHE A 201 TYR 0.011 0.001 TYR B 186 ARG 0.010 0.000 ARG D 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 251 time to evaluate : 2.711 Fit side-chains REVERT: A 247 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8079 (mm-30) REVERT: A 250 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.7323 (mmm) REVERT: A 288 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7488 (mp) REVERT: A 307 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6617 (mt-10) REVERT: A 375 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6758 (t0) REVERT: B 100 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8442 (tmtt) REVERT: B 247 ASP cc_start: 0.7458 (m-30) cc_final: 0.7189 (m-30) REVERT: B 291 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: B 301 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: C 94 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8001 (mtp180) REVERT: C 167 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8531 (pt0) REVERT: C 256 TRP cc_start: 0.9054 (OUTLIER) cc_final: 0.8775 (m100) REVERT: D 279 ASP cc_start: 0.8001 (t70) cc_final: 0.7731 (t0) REVERT: E 34 ARG cc_start: 0.7229 (mmp-170) cc_final: 0.6526 (mmm-85) REVERT: F 71 THR cc_start: 0.7950 (m) cc_final: 0.7648 (p) REVERT: F 100 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6923 (mp) REVERT: F 224 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.5651 (mmt) REVERT: F 427 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: G 10 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7982 (mttm) REVERT: G 61 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7648 (mp) REVERT: G 159 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7635 (ptmm) REVERT: G 161 GLU cc_start: 0.6937 (mp0) cc_final: 0.6346 (mp0) REVERT: G 169 ASP cc_start: 0.7774 (t0) cc_final: 0.7476 (t70) REVERT: G 317 ASP cc_start: 0.4805 (OUTLIER) cc_final: 0.4401 (p0) REVERT: H 55 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7248 (mtm-85) REVERT: H 284 MET cc_start: 0.7316 (ttt) cc_final: 0.7025 (ttm) outliers start: 116 outliers final: 66 residues processed: 336 average time/residue: 1.3284 time to fit residues: 516.2161 Evaluate side-chains 329 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 244 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 427 GLU Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 350 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 252 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 153 optimal weight: 8.9990 chunk 116 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: B 146 GLN C 74 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN ** E 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22689 Z= 0.182 Angle : 0.492 9.279 30909 Z= 0.258 Chirality : 0.040 0.164 3574 Planarity : 0.004 0.046 3695 Dihedral : 15.948 118.498 3517 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 4.86 % Allowed : 23.96 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2570 helix: 1.27 (0.15), residues: 1243 sheet: 0.37 (0.22), residues: 547 loop : -0.32 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 324 HIS 0.009 0.001 HIS E 292 PHE 0.014 0.001 PHE G 40 TYR 0.011 0.001 TYR G 181 ARG 0.009 0.000 ARG D 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 253 time to evaluate : 2.826 Fit side-chains REVERT: A 247 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8071 (mm-30) REVERT: A 250 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.7381 (mmm) REVERT: A 288 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7527 (mp) REVERT: A 307 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6661 (mt-10) REVERT: A 375 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6741 (t0) REVERT: B 100 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8411 (tmtt) REVERT: B 247 ASP cc_start: 0.7460 (m-30) cc_final: 0.7189 (m-30) REVERT: B 291 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: B 301 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: C 87 ASP cc_start: 0.8102 (t70) cc_final: 0.7811 (t0) REVERT: C 94 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7988 (mtp180) REVERT: C 167 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8496 (pt0) REVERT: C 256 TRP cc_start: 0.9025 (OUTLIER) cc_final: 0.8758 (m100) REVERT: D 211 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6961 (mttp) REVERT: D 279 ASP cc_start: 0.7976 (t70) cc_final: 0.7695 (t0) REVERT: E 34 ARG cc_start: 0.7248 (mmp-170) cc_final: 0.6519 (mmm-85) REVERT: F 71 THR cc_start: 0.7932 (m) cc_final: 0.7656 (p) REVERT: F 224 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.5663 (mmt) REVERT: G 10 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7850 (mtpp) REVERT: G 61 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7607 (mp) REVERT: G 159 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7614 (ptmm) REVERT: G 161 GLU cc_start: 0.6959 (mp0) cc_final: 0.6343 (mp0) REVERT: G 169 ASP cc_start: 0.7763 (t0) cc_final: 0.7452 (t70) REVERT: H 55 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7181 (mtm-85) REVERT: H 284 MET cc_start: 0.7296 (ttt) cc_final: 0.7007 (ttm) outliers start: 115 outliers final: 73 residues processed: 340 average time/residue: 1.2451 time to fit residues: 488.4365 Evaluate side-chains 332 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 242 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain H residue 350 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 150 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN B 145 ASN B 216 HIS C 74 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 227 ASN H 122 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22689 Z= 0.169 Angle : 0.488 9.360 30909 Z= 0.255 Chirality : 0.039 0.149 3574 Planarity : 0.003 0.046 3695 Dihedral : 15.819 119.179 3517 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 4.48 % Allowed : 24.43 % Favored : 71.09 % 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: 0.92 (0.17), residues: 2570 helix: 1.32 (0.15), residues: 1244 sheet: 0.44 (0.22), residues: 546 loop : -0.27 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 324 HIS 0.006 0.001 HIS E 292 PHE 0.013 0.001 PHE A 201 TYR 0.010 0.001 TYR H 229 ARG 0.008 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 256 time to evaluate : 2.518 Fit side-chains REVERT: A 247 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: A 250 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.7399 (mmm) REVERT: A 307 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6655 (mt-10) REVERT: A 375 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6732 (t0) REVERT: B 100 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8419 (tmtt) REVERT: B 201 ASP cc_start: 0.8323 (t0) cc_final: 0.7674 (t70) REVERT: B 247 ASP cc_start: 0.7457 (m-30) cc_final: 0.7179 (m-30) REVERT: B 291 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: B 301 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: C 87 ASP cc_start: 0.8089 (t70) cc_final: 0.7812 (t0) REVERT: C 94 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7956 (mtp180) REVERT: C 167 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8481 (pt0) REVERT: D 211 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6924 (mttp) REVERT: D 279 ASP cc_start: 0.7993 (t70) cc_final: 0.7722 (t0) REVERT: E 115 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6893 (tt0) REVERT: F 71 THR cc_start: 0.7931 (m) cc_final: 0.7683 (p) REVERT: F 224 MET cc_start: 0.6308 (OUTLIER) cc_final: 0.5680 (mmt) REVERT: G 10 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7868 (mtpp) REVERT: G 61 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7559 (mp) REVERT: G 159 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7616 (ptmm) REVERT: G 161 GLU cc_start: 0.6995 (mp0) cc_final: 0.6365 (mp0) REVERT: G 169 ASP cc_start: 0.7758 (t0) cc_final: 0.7450 (t70) REVERT: H 55 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7192 (mtm-85) REVERT: H 284 MET cc_start: 0.7312 (ttt) cc_final: 0.7028 (ttm) outliers start: 106 outliers final: 61 residues processed: 334 average time/residue: 1.2765 time to fit residues: 493.8248 Evaluate side-chains 317 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 240 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 322 ILE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain H residue 350 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 5.9990 chunk 241 optimal weight: 0.9990 chunk 220 optimal weight: 0.6980 chunk 235 optimal weight: 0.9990 chunk 141 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 72 optimal weight: 0.0270 chunk 212 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 234 optimal weight: 0.5980 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 216 HIS C 74 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN H 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22689 Z= 0.151 Angle : 0.484 10.529 30909 Z= 0.253 Chirality : 0.039 0.164 3574 Planarity : 0.003 0.046 3695 Dihedral : 15.733 120.393 3517 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.65 % Rotamer: Outliers : 3.93 % Allowed : 25.27 % Favored : 70.79 % 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: 1.01 (0.17), residues: 2570 helix: 1.40 (0.15), residues: 1244 sheet: 0.46 (0.22), residues: 545 loop : -0.21 (0.24), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 324 HIS 0.005 0.001 HIS E 292 PHE 0.014 0.001 PHE G 40 TYR 0.011 0.001 TYR H 229 ARG 0.010 0.000 ARG D 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 257 time to evaluate : 2.878 Fit side-chains REVERT: A 247 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8049 (mm-30) REVERT: A 307 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6667 (mt-10) REVERT: A 375 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6729 (t0) REVERT: B 100 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8409 (tmtt) REVERT: B 247 ASP cc_start: 0.7440 (m-30) cc_final: 0.7157 (m-30) REVERT: B 291 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: B 301 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: C 87 ASP cc_start: 0.8073 (t70) cc_final: 0.7806 (t0) REVERT: C 94 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7974 (mtp180) REVERT: C 167 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8424 (pt0) REVERT: D 211 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7029 (mttp) REVERT: D 279 ASP cc_start: 0.7979 (t70) cc_final: 0.7708 (t0) REVERT: F 71 THR cc_start: 0.7952 (m) cc_final: 0.7739 (p) REVERT: F 224 MET cc_start: 0.6322 (OUTLIER) cc_final: 0.5694 (mmt) REVERT: G 10 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7867 (mtpp) REVERT: G 61 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7521 (mp) REVERT: G 159 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7571 (ptmm) REVERT: G 161 GLU cc_start: 0.7012 (mp0) cc_final: 0.6380 (mp0) REVERT: G 169 ASP cc_start: 0.7738 (t0) cc_final: 0.7432 (t70) REVERT: G 317 ASP cc_start: 0.4776 (OUTLIER) cc_final: 0.4377 (p0) REVERT: H 55 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7204 (mtm-85) REVERT: H 284 MET cc_start: 0.7305 (ttt) cc_final: 0.7030 (ttm) outliers start: 93 outliers final: 65 residues processed: 323 average time/residue: 1.2866 time to fit residues: 479.0934 Evaluate side-chains 331 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 251 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 122 ASN Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain H residue 350 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 151 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 240 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 160 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 HIS C 74 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN D 352 GLN H 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22689 Z= 0.224 Angle : 0.515 10.454 30909 Z= 0.268 Chirality : 0.041 0.159 3574 Planarity : 0.004 0.076 3695 Dihedral : 15.755 125.022 3517 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 3.89 % Allowed : 25.36 % Favored : 70.75 % 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: 0.93 (0.17), residues: 2570 helix: 1.30 (0.15), residues: 1244 sheet: 0.48 (0.22), residues: 544 loop : -0.23 (0.24), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 324 HIS 0.006 0.001 HIS E 292 PHE 0.015 0.001 PHE G 154 TYR 0.012 0.001 TYR H 229 ARG 0.014 0.000 ARG F 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 247 time to evaluate : 2.474 Fit side-chains REVERT: A 247 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8052 (mm-30) REVERT: A 307 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: A 375 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6749 (t0) REVERT: B 65 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: B 100 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8425 (tmtt) REVERT: B 201 ASP cc_start: 0.8325 (t70) cc_final: 0.7753 (t70) REVERT: B 247 ASP cc_start: 0.7495 (m-30) cc_final: 0.7198 (m-30) REVERT: B 291 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: B 301 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: C 87 ASP cc_start: 0.8095 (t70) cc_final: 0.7822 (t0) REVERT: C 94 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7974 (mtp180) REVERT: C 167 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8513 (pt0) REVERT: D 211 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6938 (mttp) REVERT: D 279 ASP cc_start: 0.7997 (t70) cc_final: 0.7724 (t0) REVERT: E 115 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6928 (tt0) REVERT: F 71 THR cc_start: 0.7942 (m) cc_final: 0.7666 (p) REVERT: F 224 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5683 (mmt) REVERT: G 10 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7880 (mtpp) REVERT: G 61 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7593 (mp) REVERT: G 159 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7580 (ptmm) REVERT: G 161 GLU cc_start: 0.7018 (mp0) cc_final: 0.6393 (mp0) REVERT: G 169 ASP cc_start: 0.7771 (t0) cc_final: 0.7463 (t70) REVERT: G 317 ASP cc_start: 0.4827 (OUTLIER) cc_final: 0.4391 (p0) REVERT: H 55 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7243 (mtm-85) REVERT: H 284 MET cc_start: 0.7325 (ttt) cc_final: 0.7053 (ttm) outliers start: 92 outliers final: 68 residues processed: 317 average time/residue: 1.2715 time to fit residues: 468.2634 Evaluate side-chains 330 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 245 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain H residue 350 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 0.6980 chunk 221 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 208 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 213 optimal weight: 0.7980 chunk 26 optimal weight: 0.0030 chunk 38 optimal weight: 5.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 216 HIS C 74 ASN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN H 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.171641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.136746 restraints weight = 24348.045| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.72 r_work: 0.3474 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22689 Z= 0.151 Angle : 0.490 11.865 30909 Z= 0.254 Chirality : 0.040 0.197 3574 Planarity : 0.004 0.069 3695 Dihedral : 15.643 128.749 3517 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Rotamer: Outliers : 3.63 % Allowed : 25.74 % Favored : 70.63 % 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: 1.05 (0.17), residues: 2570 helix: 1.43 (0.15), residues: 1243 sheet: 0.51 (0.22), residues: 546 loop : -0.21 (0.24), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 324 HIS 0.005 0.001 HIS E 18 PHE 0.013 0.001 PHE G 40 TYR 0.010 0.001 TYR G 181 ARG 0.014 0.000 ARG F 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8257.14 seconds wall clock time: 149 minutes 1.76 seconds (8941.76 seconds total)