Starting phenix.real_space_refine on Fri Mar 15 15:27:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpl_34932/03_2024/8hpl_34932_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpl_34932/03_2024/8hpl_34932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpl_34932/03_2024/8hpl_34932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpl_34932/03_2024/8hpl_34932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpl_34932/03_2024/8hpl_34932_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpl_34932/03_2024/8hpl_34932_updated.pdb" } resolution = 4.29 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= 0.009 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 16 5.16 5 C 7576 2.51 5 N 2025 2.21 5 O 2390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 236": "NH1" <-> "NH2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 311": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "D ARG 8": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E ARG 175": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 259": "NH1" <-> "NH2" Residue "E PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 343": "NH1" <-> "NH2" Residue "E ARG 389": "NH1" <-> "NH2" Residue "E PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 418": "NH1" <-> "NH2" Residue "E ARG 430": "NH1" <-> "NH2" Residue "E ASP 440": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12013 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 1941 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 14, 'TRANS': 267} Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1882 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 16, 'TRANS': 253} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2547 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 475 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 209 Chain: "D" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2554 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 220 Chain: "E" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3004 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 31, 'TRANS': 405} Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 219 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.81, per 1000 atoms: 0.57 Number of scatterers: 12013 At special positions: 0 Unit cell: (82.82, 95.94, 168.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 6 15.00 O 2390 8.00 N 2025 7.00 C 7576 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 Links applied ALPHA1-1 " GLC G 1 " - " GLC G 2 " Time building additional restraints: 5.20 Conformation dependent library (CDL) restraints added in 2.4 seconds 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3258 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 13 sheets defined 48.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 18 through 49 Proline residue: A 30 - end of helix removed outlier: 3.948A pdb=" N TYR A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 69 through 75 removed outlier: 3.940A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 110 removed outlier: 3.627A pdb=" N VAL A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 162 through 191 removed outlier: 3.670A pdb=" N VAL A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP A 175 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR A 178 " --> pdb=" O TRP A 175 " (cutoff:3.500A) Proline residue: A 179 - end of helix removed outlier: 3.545A pdb=" N ALA A 190 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 207 through 235 Proline residue: A 217 - end of helix Proline residue: A 221 - end of helix 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 254 through 263 removed outlier: 3.639A pdb=" N ASN A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 291 removed outlier: 3.697A pdb=" N ILE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 36 Proline residue: B 27 - end of helix removed outlier: 4.090A pdb=" N LEU B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 64 through 92 removed outlier: 3.699A pdb=" N MET B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 108 through 115 removed outlier: 3.590A pdb=" N MET B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 131 removed outlier: 3.590A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 138 through 163 Proline residue: B 144 - end of helix Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 179 through 207 removed outlier: 3.616A pdb=" N LYS B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ALA B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Proline residue: B 189 - end of helix Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 243 through 272 Proline residue: B 255 - end of helix removed outlier: 3.886A pdb=" N ILE B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ARG B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 54 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 97 through 107 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 112 through 125 Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 141 through 155 removed outlier: 5.238A pdb=" N ARG C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 168 removed outlier: 4.491A pdb=" N ASN C 168 " --> pdb=" O PRO C 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 165 through 168' Processing helix chain 'C' and resid 171 through 188 removed outlier: 3.789A pdb=" N GLN C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 223 through 229 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.582A pdb=" N LYS C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 290 No H-bonds generated for 'chain 'C' and resid 288 through 290' Processing helix chain 'C' and resid 300 through 304 removed outlier: 4.185A pdb=" N ARG C 304 " --> pdb=" O ALA C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 344 Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'D' and resid 47 through 54 Processing helix chain 'D' and resid 97 through 107 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 112 through 125 Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 141 through 155 removed outlier: 5.285A pdb=" N ARG D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 188 Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 267 through 275 Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 336 through 344 removed outlier: 5.231A pdb=" N ASP D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 376 No H-bonds generated for 'chain 'D' and resid 374 through 376' Processing helix chain 'E' and resid 38 through 54 removed outlier: 5.887A pdb=" N ALA E 42 " --> pdb=" O ASN E 39 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL E 47 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU E 53 " --> pdb=" O ARG E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 82 removed outlier: 3.514A pdb=" N LEU E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA E 78 " --> pdb=" O ARG E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 103 removed outlier: 3.579A pdb=" N THR E 98 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA E 99 " --> pdb=" O VAL E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 123 Processing helix chain 'E' and resid 128 through 134 Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 166 through 178 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 224 through 242 removed outlier: 3.637A pdb=" N THR E 242 " --> pdb=" O LYS E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 252 No H-bonds generated for 'chain 'E' and resid 250 through 252' Processing helix chain 'E' and resid 255 through 263 Processing helix chain 'E' and resid 274 through 286 Proline residue: E 278 - end of helix removed outlier: 3.535A pdb=" N GLU E 282 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 314 through 325 Processing helix chain 'E' and resid 360 through 370 Processing helix chain 'E' and resid 373 through 380 Processing helix chain 'E' and resid 390 through 394 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 403 through 413 removed outlier: 4.493A pdb=" N GLU E 406 " --> pdb=" O PRO E 403 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 412 " --> pdb=" O ARG E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 436 removed outlier: 3.585A pdb=" N THR E 434 " --> pdb=" O ARG E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 458 Processing sheet with id= A, first strand: chain 'C' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'C' and resid 216 through 222 removed outlier: 6.912A pdb=" N VAL C 211 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE C 220 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 209 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE C 36 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL C 210 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 38 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N MET C 212 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL C 40 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR C 192 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU C 39 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR C 194 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE C 160 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N VAL C 195 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N MET C 162 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 245 through 250 removed outlier: 3.940A pdb=" N PHE C 247 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 284 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 308 through 311 Processing sheet with id= E, first strand: chain 'C' and resid 314 through 316 Processing sheet with id= F, first strand: chain 'D' and resid 29 through 31 Processing sheet with id= G, first strand: chain 'D' and resid 216 through 221 removed outlier: 6.827A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE D 220 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL D 209 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG D 208 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR D 192 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU D 39 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR D 194 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE D 160 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL D 195 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N MET D 162 " --> pdb=" O VAL D 195 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 255 through 257 removed outlier: 3.942A pdb=" N ILE D 282 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 308 through 311 Processing sheet with id= J, first strand: chain 'D' and resid 314 through 317 removed outlier: 3.665A pdb=" N ILE D 314 " --> pdb=" O HIS D 325 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 31 through 37 removed outlier: 5.802A pdb=" N GLN E 60 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR E 34 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA E 62 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR E 36 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ARG E 64 " --> pdb=" O THR E 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 90 through 94 removed outlier: 5.633A pdb=" N LEU E 351 " --> pdb=" O PRO E 144 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 151 through 154 removed outlier: 3.688A pdb=" N ASN E 272 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N TRP E 184 " --> pdb=" O ALA E 268 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU E 270 " --> pdb=" O TRP E 184 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA E 186 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN E 272 " --> pdb=" O ALA E 186 " (cutoff:3.500A) 566 hydrogen bonds defined for protein. 1455 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 5.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2216 1.31 - 1.44: 2864 1.44 - 1.57: 7124 1.57 - 1.69: 10 1.69 - 1.82: 28 Bond restraints: 12242 Sorted by residual: bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.82e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.77e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C5 GLC G 1 " pdb=" O5 GLC G 1 " ideal model delta sigma weight residual 1.415 1.548 -0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 12237 not shown) Histogram of bond angle deviations from ideal: 98.46 - 106.00: 424 106.00 - 113.54: 6390 113.54 - 121.08: 6098 121.08 - 128.62: 3895 128.62 - 136.17: 60 Bond angle restraints: 16867 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.37 19.50 1.00e+00 1.00e+00 3.80e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 120.56 16.27 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.74 16.09 1.00e+00 1.00e+00 2.59e+02 angle pdb=" C5 ATP D 501 " pdb=" C4 ATP D 501 " pdb=" N3 ATP D 501 " ideal model delta sigma weight residual 126.80 118.66 8.14 1.00e+00 1.00e+00 6.62e+01 ... (remaining 16862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 6731 16.77 - 33.55: 426 33.55 - 50.32: 96 50.32 - 67.09: 13 67.09 - 83.87: 12 Dihedral angle restraints: 7278 sinusoidal: 2238 harmonic: 5040 Sorted by residual: dihedral pdb=" CA ARG E 64 " pdb=" C ARG E 64 " pdb=" N ASN E 65 " pdb=" CA ASN E 65 " ideal model delta harmonic sigma weight residual 180.00 -150.94 -29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ALA B 94 " pdb=" C ALA B 94 " pdb=" N VAL B 95 " pdb=" CA VAL B 95 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA TYR B 93 " pdb=" C TYR B 93 " pdb=" N ALA B 94 " pdb=" CA ALA B 94 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 7275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1433 0.087 - 0.173: 521 0.173 - 0.260: 103 0.260 - 0.346: 17 0.346 - 0.433: 2 Chirality restraints: 2076 Sorted by residual: chirality pdb=" C1 GLC G 1 " pdb=" C2 GLC G 1 " pdb=" O5 GLC G 1 " pdb=" O1 GLC G 2 " both_signs ideal model delta sigma weight residual False 2.40 2.32 0.08 2.00e-02 2.50e+03 1.80e+01 chirality pdb=" CA THR A 178 " pdb=" N THR A 178 " pdb=" C THR A 178 " pdb=" CB THR A 178 " both_signs ideal model delta sigma weight residual False 2.53 2.09 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA SER C 309 " pdb=" N SER C 309 " pdb=" C SER C 309 " pdb=" CB SER C 309 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 2073 not shown) Planarity restraints: 2225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 79 " 0.188 2.00e-02 2.50e+03 9.58e-02 2.30e+02 pdb=" CG TRP A 79 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 79 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 79 " -0.093 2.00e-02 2.50e+03 pdb=" NE1 TRP A 79 " -0.058 2.00e-02 2.50e+03 pdb=" CE2 TRP A 79 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP A 79 " -0.134 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 79 " 0.104 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 79 " -0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP A 79 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 207 " -0.116 2.00e-02 2.50e+03 5.55e-02 7.71e+01 pdb=" CG TRP B 207 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B 207 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 207 " 0.059 2.00e-02 2.50e+03 pdb=" NE1 TRP B 207 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP B 207 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP B 207 " 0.067 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 207 " -0.055 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 207 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP B 207 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 424 " -0.113 2.00e-02 2.50e+03 6.11e-02 7.47e+01 pdb=" CG TYR E 424 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 424 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR E 424 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR E 424 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR E 424 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR E 424 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR E 424 " -0.093 2.00e-02 2.50e+03 ... (remaining 2222 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1773 2.80 - 3.32: 14376 3.32 - 3.85: 20105 3.85 - 4.37: 22795 4.37 - 4.90: 36473 Nonbonded interactions: 95522 Sorted by model distance: nonbonded pdb=" OG SER C 309 " pdb=" CG GLN C 367 " model vdw 2.269 3.440 nonbonded pdb=" O LEU A 51 " pdb=" N GLY A 66 " model vdw 2.320 2.520 nonbonded pdb=" CB LEU A 51 " pdb=" O GLY A 66 " model vdw 2.342 3.440 nonbonded pdb=" O ILE A 237 " pdb=" OG SER A 255 " model vdw 2.352 2.440 nonbonded pdb=" OD2 ASP C 313 " pdb=" NE2 HIS C 325 " model vdw 2.371 2.520 ... (remaining 95517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 36 or (resid 37 through 39 and (name N or name C \ A or name C or name O or name CB )) or resid 40 through 73 or (resid 74 through \ 76 and (name N or name CA or name C or name O or name CB )) or resid 77 through \ 84 or (resid 85 and (name N or name CA or name C or name O or name CB )) or resi \ d 86 through 88 or (resid 89 through 90 and (name N or name CA or name C or name \ O or name CB )) or resid 91 through 93 or (resid 94 and (name N or name CA or n \ ame C or name O or name CB )) or resid 95 through 132 or (resid 133 through 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 14 \ 4 or (resid 145 through 149 and (name N or name CA or name C or name O or name C \ B )) or resid 150 through 159 or (resid 160 and (name N or name CA or name C or \ name O or name CB )) or resid 161 through 193 or (resid 194 and (name N or name \ CA or name C or name O or name CB )) or resid 195 through 219 or (resid 220 and \ (name N or name CA or name C or name O or name CB )) or resid 221 through 274 or \ (resid 275 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 6 through 328 or (resid 329 and (name N or name CA or name C or name O or name C \ B )) or resid 330 through 362 or (resid 363 and (name N or name CA or name C or \ name O or name CB )) or resid 364 through 376 or (resid 377 and (name N or name \ CA or name C or name O or name CB )) or resid 378 through 386 or (resid 387 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ resid 501)) selection = (chain 'D' and (resid 2 through 4 or (resid 5 through 6 and (name N or name CA o \ r name C or name O or name CB )) or resid 7 through 34 or (resid 35 through 39 a \ nd (name N or name CA or name C or name O or name CB )) or resid 40 through 63 o \ r (resid 64 through 67 and (name N or name CA or name C or name O or name CB )) \ or resid 68 through 69 or (resid 70 through 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 78 or (resid 79 through 81 and (name \ N or name CA or name C or name O or name CB )) or resid 82 through 106 or (resi \ d 107 through 109 and (name N or name CA or name C or name O or name CB )) or re \ sid 110 through 125 or (resid 126 and (name N or name CA or name C or name O or \ name CB )) or resid 127 through 130 or (resid 131 through 135 and (name N or nam \ e CA or name C or name O or name CB )) or resid 136 through 148 or (resid 149 an \ d (name N or name CA or name C or name O or name CB )) or (resid 150 through 153 \ and (name N or name CA or name C or name O or name CB )) or resid 154 through 1 \ 75 or (resid 176 through 179 and (name N or name CA or name C or name O or name \ CB )) or resid 180 through 195 or (resid 196 and (name N or name CA or name C or \ name O or name CB )) or resid 197 through 209 or (resid 210 and (name N or name \ CA or name C or name O or name CB )) or resid 211 through 226 or (resid 227 and \ (name N or name CA or name C or name O or name CB )) or resid 228 through 299 o \ r (resid 300 through 301 and (name N or name CA or name C or name O or name CB ) \ ) or resid 302 through 379 or (resid 380 and (name N or name CA or name C or nam \ e O or name CB )) or resid 381 through 383 or (resid 384 and (name N or name CA \ or name C or name O or name CB )) or resid 385 through 391 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 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: 12.260 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 34.200 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.133 12242 Z= 0.790 Angle : 1.777 19.500 16867 Z= 1.209 Chirality : 0.091 0.433 2076 Planarity : 0.012 0.096 2225 Dihedral : 12.898 83.868 4020 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Cbeta Deviations : 0.06 % 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: -2.47 (0.18), residues: 1743 helix: -1.29 (0.15), residues: 847 sheet: -1.83 (0.43), residues: 127 loop : -1.90 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.188 0.020 TRP A 79 HIS 0.018 0.004 HIS D 325 PHE 0.064 0.013 PHE E 398 TYR 0.113 0.018 TYR E 424 ARG 0.003 0.001 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8278 (tpt) cc_final: 0.8023 (tpt) REVERT: A 267 ASN cc_start: 0.9095 (t0) cc_final: 0.8879 (t0) REVERT: A 287 PHE cc_start: 0.9358 (t80) cc_final: 0.9114 (t80) REVERT: B 185 LYS cc_start: 0.9232 (mttt) cc_final: 0.8727 (tppt) REVERT: C 170 ASP cc_start: 0.9022 (p0) cc_final: 0.8494 (p0) REVERT: C 172 LYS cc_start: 0.9453 (mttp) cc_final: 0.9101 (mppt) REVERT: C 194 TYR cc_start: 0.8182 (t80) cc_final: 0.7975 (t80) REVERT: C 218 GLN cc_start: 0.8770 (mm110) cc_final: 0.8272 (mm-40) REVERT: C 284 VAL cc_start: 0.9108 (m) cc_final: 0.8543 (t) REVERT: C 326 PHE cc_start: 0.9539 (p90) cc_final: 0.9143 (p90) REVERT: D 139 LEU cc_start: 0.7995 (mt) cc_final: 0.7096 (tp) REVERT: D 164 GLN cc_start: 0.8974 (mt0) cc_final: 0.8625 (mm-40) REVERT: D 177 MET cc_start: 0.9446 (mtp) cc_final: 0.9178 (ttm) REVERT: D 195 VAL cc_start: 0.7767 (p) cc_final: 0.7383 (t) REVERT: D 218 GLN cc_start: 0.9176 (mm110) cc_final: 0.8643 (mp10) REVERT: D 276 GLN cc_start: 0.8262 (mm110) cc_final: 0.7869 (mm-40) REVERT: D 316 GLU cc_start: 0.9497 (pm20) cc_final: 0.9276 (pm20) REVERT: D 353 ILE cc_start: 0.8707 (mt) cc_final: 0.8497 (mt) REVERT: E 86 LYS cc_start: 0.9269 (mmmt) cc_final: 0.8893 (mmmt) REVERT: E 198 TRP cc_start: 0.8989 (t60) cc_final: 0.8782 (t60) REVERT: E 259 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7609 (ptp-110) REVERT: E 276 VAL cc_start: 0.8331 (p) cc_final: 0.7901 (p) REVERT: E 388 VAL cc_start: 0.8774 (m) cc_final: 0.8555 (p) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2280 time to fit residues: 98.2533 Evaluate side-chains 200 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 136 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 261 ASN C 197 HIS D 290 HIS D 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 12242 Z= 0.433 Angle : 0.808 10.107 16867 Z= 0.436 Chirality : 0.046 0.206 2076 Planarity : 0.005 0.042 2225 Dihedral : 8.862 85.972 1927 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.19 % Allowed : 5.53 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.68 (0.19), residues: 1743 helix: -0.52 (0.16), residues: 859 sheet: -2.05 (0.36), residues: 166 loop : -1.47 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 207 HIS 0.011 0.002 HIS B 118 PHE 0.021 0.003 PHE E 317 TYR 0.023 0.003 TYR B 155 ARG 0.006 0.001 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 251 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8773 (t70) cc_final: 0.8342 (t0) REVERT: A 267 ASN cc_start: 0.9132 (t0) cc_final: 0.8848 (t0) REVERT: A 270 LEU cc_start: 0.9577 (mt) cc_final: 0.9345 (mt) REVERT: B 157 LEU cc_start: 0.9762 (mt) cc_final: 0.9552 (mt) REVERT: B 185 LYS cc_start: 0.9266 (mttt) cc_final: 0.8902 (tppt) REVERT: C 170 ASP cc_start: 0.9043 (p0) cc_final: 0.8598 (p0) REVERT: C 172 LYS cc_start: 0.9589 (mttp) cc_final: 0.9259 (mppt) REVERT: C 234 PHE cc_start: 0.9344 (t80) cc_final: 0.8697 (t80) REVERT: C 318 LEU cc_start: 0.9570 (mp) cc_final: 0.9247 (mp) REVERT: C 326 PHE cc_start: 0.9556 (p90) cc_final: 0.9340 (p90) REVERT: D 8 ARG cc_start: 0.9630 (mmt90) cc_final: 0.9221 (mmm-85) REVERT: D 164 GLN cc_start: 0.9121 (mt0) cc_final: 0.8666 (mm110) REVERT: D 276 GLN cc_start: 0.8228 (mm110) cc_final: 0.7580 (mp10) REVERT: D 380 PHE cc_start: 0.9450 (m-80) cc_final: 0.9027 (m-80) REVERT: E 35 TYR cc_start: 0.8683 (m-80) cc_final: 0.8242 (m-80) REVERT: E 159 MET cc_start: 0.5869 (ttp) cc_final: 0.5074 (tmm) REVERT: E 259 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7551 (ptp-110) outliers start: 2 outliers final: 2 residues processed: 253 average time/residue: 0.2092 time to fit residues: 79.0909 Evaluate side-chains 170 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 171 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 0.0270 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 HIS D 218 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12242 Z= 0.209 Angle : 0.635 8.415 16867 Z= 0.333 Chirality : 0.043 0.187 2076 Planarity : 0.005 0.041 2225 Dihedral : 8.169 86.504 1927 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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 (0.20), residues: 1743 helix: 0.23 (0.18), residues: 846 sheet: -1.61 (0.38), residues: 165 loop : -1.01 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 79 HIS 0.005 0.001 HIS D 268 PHE 0.018 0.002 PHE E 317 TYR 0.026 0.002 TYR A 78 ARG 0.003 0.000 ARG E 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8796 (t70) cc_final: 0.8516 (p0) REVERT: A 267 ASN cc_start: 0.9178 (t0) cc_final: 0.8811 (t0) REVERT: A 270 LEU cc_start: 0.9524 (mt) cc_final: 0.9284 (mt) REVERT: B 136 ASP cc_start: 0.8744 (p0) cc_final: 0.8357 (m-30) REVERT: B 185 LYS cc_start: 0.9249 (mttt) cc_final: 0.8885 (tppt) REVERT: C 168 ASN cc_start: 0.9287 (t0) cc_final: 0.8888 (t0) REVERT: C 170 ASP cc_start: 0.9066 (p0) cc_final: 0.8662 (p0) REVERT: C 172 LYS cc_start: 0.9560 (mttp) cc_final: 0.9219 (mppt) REVERT: C 234 PHE cc_start: 0.9260 (t80) cc_final: 0.8576 (t80) REVERT: C 326 PHE cc_start: 0.9513 (p90) cc_final: 0.9279 (p90) REVERT: C 351 GLN cc_start: 0.9193 (mp10) cc_final: 0.8983 (mp10) REVERT: D 8 ARG cc_start: 0.9614 (mmt90) cc_final: 0.9173 (mmm-85) REVERT: D 276 GLN cc_start: 0.8203 (mm110) cc_final: 0.7625 (mp10) REVERT: D 370 LEU cc_start: 0.9289 (mt) cc_final: 0.9054 (pp) REVERT: D 376 LYS cc_start: 0.6814 (ptpp) cc_final: 0.6527 (ptpp) REVERT: D 380 PHE cc_start: 0.9302 (m-80) cc_final: 0.8992 (m-80) REVERT: E 35 TYR cc_start: 0.8410 (m-80) cc_final: 0.7795 (m-80) REVERT: E 193 GLU cc_start: 0.9156 (mp0) cc_final: 0.8816 (mm-30) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1948 time to fit residues: 71.8787 Evaluate side-chains 184 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 30.0000 chunk 106 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 HIS E 84 ASN ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12242 Z= 0.259 Angle : 0.634 8.039 16867 Z= 0.334 Chirality : 0.042 0.184 2076 Planarity : 0.005 0.042 2225 Dihedral : 7.981 89.145 1927 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.64 % 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: -0.64 (0.20), residues: 1743 helix: 0.28 (0.18), residues: 848 sheet: -1.39 (0.39), residues: 165 loop : -0.91 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 141 HIS 0.002 0.001 HIS C 94 PHE 0.017 0.002 PHE A 287 TYR 0.022 0.002 TYR C 323 ARG 0.004 0.000 ARG C 311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 ASN cc_start: 0.9200 (t0) cc_final: 0.8882 (t0) REVERT: A 270 LEU cc_start: 0.9585 (mt) cc_final: 0.9285 (mt) REVERT: B 116 PHE cc_start: 0.9087 (t80) cc_final: 0.8573 (t80) REVERT: B 185 LYS cc_start: 0.9213 (mttt) cc_final: 0.8866 (tppt) REVERT: B 259 PHE cc_start: 0.9260 (m-10) cc_final: 0.8945 (m-80) REVERT: C 95 MET cc_start: 0.7400 (ptt) cc_final: 0.7197 (ptt) REVERT: C 168 ASN cc_start: 0.9304 (t0) cc_final: 0.8954 (t0) REVERT: C 170 ASP cc_start: 0.9038 (p0) cc_final: 0.8677 (p0) REVERT: C 172 LYS cc_start: 0.9567 (mttp) cc_final: 0.9194 (mppt) REVERT: C 234 PHE cc_start: 0.9264 (t80) cc_final: 0.8598 (t80) REVERT: C 326 PHE cc_start: 0.9550 (p90) cc_final: 0.9310 (p90) REVERT: D 276 GLN cc_start: 0.8267 (mm110) cc_final: 0.7909 (mp10) REVERT: D 370 LEU cc_start: 0.9291 (mt) cc_final: 0.9045 (pp) REVERT: D 376 LYS cc_start: 0.6709 (ptpp) cc_final: 0.6435 (ptpp) REVERT: D 380 PHE cc_start: 0.9267 (m-80) cc_final: 0.8958 (m-80) REVERT: E 35 TYR cc_start: 0.8552 (m-80) cc_final: 0.7980 (m-80) REVERT: E 297 ASP cc_start: 0.7564 (m-30) cc_final: 0.7135 (t0) outliers start: 1 outliers final: 1 residues processed: 240 average time/residue: 0.1964 time to fit residues: 71.1554 Evaluate side-chains 171 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 69 optimal weight: 0.2980 chunk 143 optimal weight: 2.9990 chunk 116 optimal weight: 0.0870 chunk 0 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 164 GLN C 197 HIS C 367 GLN D 176 GLN ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12242 Z= 0.161 Angle : 0.574 7.648 16867 Z= 0.296 Chirality : 0.042 0.173 2076 Planarity : 0.004 0.041 2225 Dihedral : 7.447 86.276 1927 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.21), residues: 1743 helix: 0.60 (0.18), residues: 844 sheet: -1.18 (0.40), residues: 167 loop : -0.82 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 79 HIS 0.010 0.001 HIS B 118 PHE 0.016 0.001 PHE E 321 TYR 0.018 0.001 TYR B 155 ARG 0.003 0.000 ARG E 430 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 252 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.9141 (pp20) cc_final: 0.8895 (pp20) REVERT: A 198 ASN cc_start: 0.9588 (m110) cc_final: 0.8762 (m110) REVERT: A 267 ASN cc_start: 0.9154 (t0) cc_final: 0.8805 (t0) REVERT: A 270 LEU cc_start: 0.9542 (mt) cc_final: 0.9274 (mt) REVERT: B 116 PHE cc_start: 0.8946 (t80) cc_final: 0.8362 (t80) REVERT: B 185 LYS cc_start: 0.9224 (mttt) cc_final: 0.8864 (tppt) REVERT: B 259 PHE cc_start: 0.9185 (m-10) cc_final: 0.8902 (m-80) REVERT: C 164 GLN cc_start: 0.9040 (tp40) cc_final: 0.8801 (tp-100) REVERT: C 168 ASN cc_start: 0.9262 (t0) cc_final: 0.8891 (t0) REVERT: C 170 ASP cc_start: 0.9010 (p0) cc_final: 0.8656 (p0) REVERT: C 172 LYS cc_start: 0.9543 (mttp) cc_final: 0.9177 (mppt) REVERT: C 234 PHE cc_start: 0.9310 (t80) cc_final: 0.8674 (t80) REVERT: C 318 LEU cc_start: 0.9590 (mp) cc_final: 0.9209 (mp) REVERT: C 351 GLN cc_start: 0.9163 (mp10) cc_final: 0.8956 (mp10) REVERT: C 353 ILE cc_start: 0.9421 (pt) cc_final: 0.8958 (mm) REVERT: D 276 GLN cc_start: 0.8251 (mm110) cc_final: 0.7899 (mp10) REVERT: D 370 LEU cc_start: 0.9355 (mt) cc_final: 0.9143 (pp) REVERT: D 376 LYS cc_start: 0.6691 (ptpp) cc_final: 0.6410 (ptpp) REVERT: D 380 PHE cc_start: 0.9276 (m-80) cc_final: 0.8955 (m-80) REVERT: E 193 GLU cc_start: 0.9054 (mp0) cc_final: 0.8756 (mm-30) REVERT: E 297 ASP cc_start: 0.7627 (m-30) cc_final: 0.7254 (t0) REVERT: E 319 ILE cc_start: 0.9560 (mt) cc_final: 0.9310 (tp) outliers start: 1 outliers final: 1 residues processed: 252 average time/residue: 0.2257 time to fit residues: 84.4585 Evaluate side-chains 196 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 0.0970 chunk 41 optimal weight: 0.0770 chunk 168 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 162 optimal weight: 30.0000 overall best weight: 2.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 164 GLN C 197 HIS D 176 GLN ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12242 Z= 0.202 Angle : 0.589 6.768 16867 Z= 0.304 Chirality : 0.042 0.170 2076 Planarity : 0.004 0.040 2225 Dihedral : 7.288 80.726 1927 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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: -0.21 (0.21), residues: 1743 helix: 0.67 (0.18), residues: 846 sheet: -1.07 (0.40), residues: 167 loop : -0.78 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 79 HIS 0.005 0.001 HIS B 118 PHE 0.015 0.002 PHE B 148 TYR 0.022 0.001 TYR B 145 ARG 0.003 0.000 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASN cc_start: 0.9575 (m110) cc_final: 0.8758 (m110) REVERT: A 267 ASN cc_start: 0.9202 (t0) cc_final: 0.8843 (t0) REVERT: A 270 LEU cc_start: 0.9539 (mt) cc_final: 0.9253 (mt) REVERT: B 90 MET cc_start: 0.8825 (ppp) cc_final: 0.8091 (mmt) REVERT: B 116 PHE cc_start: 0.9026 (t80) cc_final: 0.8465 (t80) REVERT: B 185 LYS cc_start: 0.9224 (mttt) cc_final: 0.8875 (tppt) REVERT: B 259 PHE cc_start: 0.9202 (m-10) cc_final: 0.8917 (m-80) REVERT: C 168 ASN cc_start: 0.9262 (t0) cc_final: 0.8575 (t0) REVERT: C 170 ASP cc_start: 0.9009 (p0) cc_final: 0.8687 (p0) REVERT: C 172 LYS cc_start: 0.9539 (mttp) cc_final: 0.9183 (mppt) REVERT: C 234 PHE cc_start: 0.9309 (t80) cc_final: 0.8688 (t80) REVERT: C 318 LEU cc_start: 0.9584 (mp) cc_final: 0.9143 (mp) REVERT: C 353 ILE cc_start: 0.9358 (pt) cc_final: 0.8929 (mm) REVERT: D 276 GLN cc_start: 0.8155 (mm110) cc_final: 0.7897 (mp10) REVERT: D 370 LEU cc_start: 0.9357 (mt) cc_final: 0.9141 (pp) REVERT: D 376 LYS cc_start: 0.6731 (ptpp) cc_final: 0.6444 (ptpp) REVERT: D 380 PHE cc_start: 0.9231 (m-80) cc_final: 0.8908 (m-80) REVERT: E 159 MET cc_start: 0.6493 (ttp) cc_final: 0.6190 (tmm) REVERT: E 297 ASP cc_start: 0.7549 (m-30) cc_final: 0.7103 (t0) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2124 time to fit residues: 76.9675 Evaluate side-chains 178 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 141 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 167 optimal weight: 0.0980 chunk 104 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 GLN C 197 HIS C 367 GLN D 176 GLN ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12242 Z= 0.176 Angle : 0.578 8.326 16867 Z= 0.296 Chirality : 0.041 0.172 2076 Planarity : 0.004 0.040 2225 Dihedral : 7.006 81.549 1927 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: -0.15 (0.21), residues: 1743 helix: 0.69 (0.18), residues: 842 sheet: -0.89 (0.41), residues: 165 loop : -0.74 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 79 HIS 0.004 0.001 HIS B 118 PHE 0.030 0.001 PHE E 321 TYR 0.023 0.001 TYR E 275 ARG 0.005 0.000 ARG E 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.9140 (pp20) cc_final: 0.8875 (pp20) REVERT: A 198 ASN cc_start: 0.9569 (m110) cc_final: 0.8717 (m110) REVERT: A 267 ASN cc_start: 0.9189 (t0) cc_final: 0.8866 (t0) REVERT: A 270 LEU cc_start: 0.9509 (mt) cc_final: 0.9247 (mt) REVERT: B 116 PHE cc_start: 0.9013 (t80) cc_final: 0.8389 (t80) REVERT: B 145 TYR cc_start: 0.8753 (m-80) cc_final: 0.8537 (m-80) REVERT: B 185 LYS cc_start: 0.9213 (mttt) cc_final: 0.8877 (tppt) REVERT: B 259 PHE cc_start: 0.9197 (m-10) cc_final: 0.8900 (m-80) REVERT: C 168 ASN cc_start: 0.9182 (t0) cc_final: 0.8799 (t0) REVERT: C 170 ASP cc_start: 0.9012 (p0) cc_final: 0.8669 (p0) REVERT: C 172 LYS cc_start: 0.9528 (mttp) cc_final: 0.9157 (mppt) REVERT: C 234 PHE cc_start: 0.9332 (t80) cc_final: 0.8996 (t80) REVERT: C 318 LEU cc_start: 0.9576 (mp) cc_final: 0.9129 (mp) REVERT: C 353 ILE cc_start: 0.9369 (pt) cc_final: 0.8955 (mm) REVERT: D 276 GLN cc_start: 0.8241 (mm110) cc_final: 0.7889 (mp10) REVERT: D 316 GLU cc_start: 0.9436 (pm20) cc_final: 0.9187 (pp20) REVERT: D 380 PHE cc_start: 0.9239 (m-80) cc_final: 0.8938 (m-80) REVERT: E 159 MET cc_start: 0.6360 (ttp) cc_final: 0.5596 (tmm) REVERT: E 297 ASP cc_start: 0.7395 (m-30) cc_final: 0.7002 (t0) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1982 time to fit residues: 74.3371 Evaluate side-chains 179 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 4.9990 chunk 50 optimal weight: 0.0870 chunk 32 optimal weight: 0.0040 chunk 106 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 82 optimal weight: 0.0870 chunk 15 optimal weight: 0.7980 chunk 131 optimal weight: 0.0870 chunk 152 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 overall best weight: 0.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN C 197 HIS ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12242 Z= 0.149 Angle : 0.567 6.702 16867 Z= 0.285 Chirality : 0.041 0.203 2076 Planarity : 0.004 0.040 2225 Dihedral : 6.366 82.284 1927 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1743 helix: 0.74 (0.19), residues: 830 sheet: -0.86 (0.41), residues: 165 loop : -0.73 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 79 HIS 0.004 0.001 HIS C 94 PHE 0.013 0.001 PHE B 160 TYR 0.019 0.001 TYR C 194 ARG 0.004 0.000 ARG D 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.9046 (pp20) cc_final: 0.8723 (pp20) REVERT: A 198 ASN cc_start: 0.9558 (m110) cc_final: 0.8709 (m110) REVERT: A 267 ASN cc_start: 0.9170 (t0) cc_final: 0.8756 (t0) REVERT: A 270 LEU cc_start: 0.9464 (mt) cc_final: 0.9160 (mm) REVERT: B 90 MET cc_start: 0.8559 (ppp) cc_final: 0.7786 (mmt) REVERT: B 93 TYR cc_start: 0.8987 (t80) cc_final: 0.8765 (t80) REVERT: B 145 TYR cc_start: 0.8722 (m-80) cc_final: 0.8492 (m-80) REVERT: B 185 LYS cc_start: 0.9228 (mttt) cc_final: 0.8925 (tppt) REVERT: B 203 PHE cc_start: 0.9267 (t80) cc_final: 0.9029 (t80) REVERT: B 259 PHE cc_start: 0.9144 (m-10) cc_final: 0.8895 (m-80) REVERT: C 168 ASN cc_start: 0.9145 (t0) cc_final: 0.8765 (t0) REVERT: C 170 ASP cc_start: 0.9000 (p0) cc_final: 0.8657 (p0) REVERT: C 172 LYS cc_start: 0.9520 (mttp) cc_final: 0.9149 (mppt) REVERT: C 234 PHE cc_start: 0.9552 (t80) cc_final: 0.9109 (t80) REVERT: C 318 LEU cc_start: 0.9568 (mp) cc_final: 0.9102 (mp) REVERT: C 323 TYR cc_start: 0.9555 (m-10) cc_final: 0.9344 (m-10) REVERT: C 351 GLN cc_start: 0.9233 (mp10) cc_final: 0.9006 (mp10) REVERT: D 276 GLN cc_start: 0.8253 (mm110) cc_final: 0.7912 (mp10) REVERT: D 316 GLU cc_start: 0.9425 (pm20) cc_final: 0.9195 (pp20) REVERT: D 380 PHE cc_start: 0.9325 (m-80) cc_final: 0.9010 (m-80) REVERT: E 159 MET cc_start: 0.6229 (ttp) cc_final: 0.5537 (tmm) REVERT: E 193 GLU cc_start: 0.9003 (mp0) cc_final: 0.8733 (mm-30) REVERT: E 297 ASP cc_start: 0.7373 (m-30) cc_final: 0.7003 (t0) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2028 time to fit residues: 77.3883 Evaluate side-chains 197 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.0040 chunk 160 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 147 optimal weight: 0.0870 chunk 155 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 165 optimal weight: 0.0870 overall best weight: 0.3548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 164 GLN C 197 HIS D 176 GLN ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12242 Z= 0.150 Angle : 0.565 6.422 16867 Z= 0.285 Chirality : 0.041 0.204 2076 Planarity : 0.004 0.056 2225 Dihedral : 5.910 82.271 1927 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1743 helix: 0.75 (0.18), residues: 835 sheet: -0.84 (0.41), residues: 167 loop : -0.67 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 79 HIS 0.002 0.001 HIS D 268 PHE 0.029 0.002 PHE D 246 TYR 0.019 0.001 TYR B 155 ARG 0.006 0.000 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASN cc_start: 0.9552 (m110) cc_final: 0.8760 (m110) REVERT: B 90 MET cc_start: 0.8597 (ppp) cc_final: 0.7636 (mmp) REVERT: B 145 TYR cc_start: 0.8727 (m-80) cc_final: 0.8496 (m-80) REVERT: B 185 LYS cc_start: 0.9221 (mttt) cc_final: 0.8881 (tppt) REVERT: B 203 PHE cc_start: 0.9266 (t80) cc_final: 0.8979 (t80) REVERT: B 259 PHE cc_start: 0.9110 (m-10) cc_final: 0.8832 (m-80) REVERT: C 168 ASN cc_start: 0.9094 (t0) cc_final: 0.8713 (t0) REVERT: C 170 ASP cc_start: 0.9027 (p0) cc_final: 0.8680 (p0) REVERT: C 172 LYS cc_start: 0.9514 (mttp) cc_final: 0.9166 (mppt) REVERT: C 234 PHE cc_start: 0.9393 (t80) cc_final: 0.9120 (t80) REVERT: C 318 LEU cc_start: 0.9557 (mp) cc_final: 0.9060 (mp) REVERT: C 323 TYR cc_start: 0.9573 (m-10) cc_final: 0.9334 (m-10) REVERT: C 351 GLN cc_start: 0.9223 (mp10) cc_final: 0.9005 (mp10) REVERT: D 276 GLN cc_start: 0.8285 (mm110) cc_final: 0.7940 (mp10) REVERT: D 380 PHE cc_start: 0.9336 (m-80) cc_final: 0.9006 (m-80) REVERT: E 159 MET cc_start: 0.6058 (ttp) cc_final: 0.5386 (tmm) REVERT: E 193 GLU cc_start: 0.8992 (mp0) cc_final: 0.8759 (mm-30) REVERT: E 297 ASP cc_start: 0.7323 (m-30) cc_final: 0.6964 (t0) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2090 time to fit residues: 80.3109 Evaluate side-chains 200 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 114 optimal weight: 0.0970 chunk 173 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 14 optimal weight: 0.0000 chunk 106 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS D 176 GLN ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12242 Z= 0.142 Angle : 0.571 7.721 16867 Z= 0.288 Chirality : 0.041 0.200 2076 Planarity : 0.004 0.039 2225 Dihedral : 5.770 82.562 1927 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1743 helix: 0.77 (0.18), residues: 839 sheet: -0.88 (0.41), residues: 167 loop : -0.63 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 79 HIS 0.005 0.001 HIS B 118 PHE 0.012 0.001 PHE B 160 TYR 0.036 0.001 TYR B 93 ARG 0.003 0.000 ARG E 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASN cc_start: 0.9553 (m110) cc_final: 0.8756 (m110) REVERT: B 145 TYR cc_start: 0.8702 (m-80) cc_final: 0.8479 (m-80) REVERT: B 185 LYS cc_start: 0.9234 (mttt) cc_final: 0.8916 (tppt) REVERT: B 203 PHE cc_start: 0.9265 (t80) cc_final: 0.9018 (t80) REVERT: B 259 PHE cc_start: 0.9107 (m-10) cc_final: 0.8843 (m-80) REVERT: C 168 ASN cc_start: 0.9097 (t0) cc_final: 0.8738 (t0) REVERT: C 170 ASP cc_start: 0.9031 (p0) cc_final: 0.8687 (p0) REVERT: C 172 LYS cc_start: 0.9525 (mttp) cc_final: 0.9148 (mppt) REVERT: C 234 PHE cc_start: 0.9553 (t80) cc_final: 0.9053 (t80) REVERT: C 318 LEU cc_start: 0.9552 (mp) cc_final: 0.9045 (mp) REVERT: C 323 TYR cc_start: 0.9581 (m-10) cc_final: 0.9362 (m-10) REVERT: C 351 GLN cc_start: 0.9246 (mp10) cc_final: 0.9031 (mp10) REVERT: D 276 GLN cc_start: 0.8233 (mm110) cc_final: 0.7902 (mp10) REVERT: D 380 PHE cc_start: 0.9329 (m-80) cc_final: 0.9003 (m-80) REVERT: E 159 MET cc_start: 0.6025 (ttp) cc_final: 0.5368 (tmm) REVERT: E 193 GLU cc_start: 0.9005 (mp0) cc_final: 0.8770 (mm-30) REVERT: E 297 ASP cc_start: 0.7257 (m-30) cc_final: 0.6921 (t0) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2078 time to fit residues: 79.2382 Evaluate side-chains 198 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.1980 chunk 127 optimal weight: 6.9990 chunk 20 optimal weight: 0.0270 chunk 38 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 141 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 121 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 HIS D 176 GLN D 337 GLN ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.085825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.061468 restraints weight = 61860.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.063155 restraints weight = 41514.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.064332 restraints weight = 30960.039| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12242 Z= 0.141 Angle : 0.557 7.720 16867 Z= 0.282 Chirality : 0.041 0.202 2076 Planarity : 0.004 0.039 2225 Dihedral : 5.651 82.962 1927 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1743 helix: 0.80 (0.18), residues: 846 sheet: -0.92 (0.41), residues: 168 loop : -0.61 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 79 HIS 0.002 0.001 HIS C 197 PHE 0.026 0.001 PHE D 246 TYR 0.015 0.001 TYR E 275 ARG 0.002 0.000 ARG E 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2685.12 seconds wall clock time: 48 minutes 48.90 seconds (2928.90 seconds total)