Starting phenix.real_space_refine on Thu Jul 25 09:11:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/07_2024/7ste_25426_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/07_2024/7ste_25426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/07_2024/7ste_25426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/07_2024/7ste_25426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/07_2024/7ste_25426_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ste_25426/07_2024/7ste_25426_neut_trim.cif" } resolution = 2.73 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= 0.035 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: 7 Type Number sf(0) Gaussians P 11 5.49 5 Mg 1 5.21 5 S 67 5.16 5 C 8982 2.51 5 N 2487 2.21 5 O 2701 1.98 5 H 14379 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B ASP 255": "OD1" <-> "OD2" Residue "C ASP 225": "OD1" <-> "OD2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "E ASP 6": "OD1" <-> "OD2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 28628 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 5028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5028 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5146 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 12, 'TRANS': 311} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5218 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "E" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5470 Classifications: {'peptide': 340} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 7626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7626 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 17, 'TRANS': 450} Chain breaks: 6 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.05, per 1000 atoms: 0.46 Number of scatterers: 28628 At special positions: 0 Unit cell: (113.988, 122.248, 123.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 67 16.00 P 11 15.00 Mg 1 11.99 O 2701 8.00 N 2487 7.00 C 8982 6.00 H 14379 1.00 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: 21.64 Conformation dependent library (CDL) restraints added in 2.9 seconds 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 7 sheets defined 67.9% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.691A pdb=" N TYR B 15 " --> pdb=" O TRP B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 67 Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.804A pdb=" N VAL B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 99 " --> pdb=" O HIS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 166 through 183 removed outlier: 3.989A pdb=" N ASP B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.674A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 262 through 276 removed outlier: 3.713A pdb=" N ASN B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.861A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 44 removed outlier: 4.171A pdb=" N LYS C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 103 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.889A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 293 through 312 removed outlier: 3.591A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 removed outlier: 3.854A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 42 through 56 Processing helix chain 'D' and resid 70 through 81 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.626A pdb=" N ARG D 91 " --> pdb=" O LEU D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 91' Processing helix chain 'D' and resid 104 through 116 Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.521A pdb=" N ASN D 128 " --> pdb=" O HIS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 160 Processing helix chain 'D' and resid 172 through 176 removed outlier: 3.518A pdb=" N ARG D 175 " --> pdb=" O TYR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 193 through 209 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.703A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 removed outlier: 3.528A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.588A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.731A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 32 through 36 Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 105 through 119 Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.771A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 removed outlier: 3.703A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.393A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 114 through 131 removed outlier: 3.509A pdb=" N ILE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.881A 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 165 through 176 removed outlier: 3.803A pdb=" N TYR A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.512A pdb=" N ILE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 245 through 250' Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 292 removed outlier: 5.762A pdb=" N LYS A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N MET A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.740A pdb=" N VAL A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.539A pdb=" N LYS A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 removed outlier: 3.601A pdb=" N LEU A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 391 removed outlier: 5.297A pdb=" N ASN A 388 " --> pdb=" O ASN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 410 removed outlier: 3.723A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.823A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 472 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 486 through 503 Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'A' and resid 565 through 584 Processing sheet with id=AA1, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.205A pdb=" N LEU B 76 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 79 through 83 removed outlier: 5.927A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.069A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.274A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.747A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.150A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.372A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE A 263 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 106 " --> pdb=" O ILE A 263 " (cutoff:3.500A) 825 hydrogen bonds defined for protein. 2397 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: 10.06 Time building geometry restraints manager: 22.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14348 1.03 - 1.23: 33 1.23 - 1.42: 5817 1.42 - 1.62: 8566 1.62 - 1.81: 103 Bond restraints: 28867 Sorted by residual: bond pdb=" N ASP B 229 " pdb=" CA ASP B 229 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.83e-02 2.99e+03 1.96e+00 bond pdb=" C4 ADP D 801 " pdb=" C5 ADP D 801 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 ... (remaining 28862 not shown) Histogram of bond angle deviations from ideal: 98.82 - 107.03: 448 107.03 - 115.23: 37358 115.23 - 123.43: 12225 123.43 - 131.64: 2266 131.64 - 139.84: 27 Bond angle restraints: 52324 Sorted by residual: angle pdb=" C VAL B 228 " pdb=" N ASP B 229 " pdb=" CA ASP B 229 " ideal model delta sigma weight residual 126.32 134.35 -8.03 1.74e+00 3.30e-01 2.13e+01 angle pdb=" C ASP B 229 " pdb=" CA ASP B 229 " pdb=" CB ASP B 229 " ideal model delta sigma weight residual 110.04 105.42 4.62 1.51e+00 4.39e-01 9.36e+00 angle pdb=" C2' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" O3' ATP A 801 " ideal model delta sigma weight residual 111.83 105.64 6.19 2.67e+00 1.40e-01 5.37e+00 angle pdb=" C1' ATP A 801 " pdb=" C2' ATP A 801 " pdb=" O2' ATP A 801 " ideal model delta sigma weight residual 110.58 104.34 6.24 2.79e+00 1.28e-01 4.99e+00 angle pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" O3' ATP A 801 " ideal model delta sigma weight residual 111.06 105.50 5.56 2.50e+00 1.60e-01 4.95e+00 ... (remaining 52319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.52: 13156 34.52 - 69.05: 259 69.05 - 103.57: 10 103.57 - 138.09: 5 138.09 - 172.62: 4 Dihedral angle restraints: 13434 sinusoidal: 7530 harmonic: 5904 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 127.39 172.62 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.08 -149.08 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 82.53 -142.53 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 13431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1994 0.059 - 0.117: 235 0.117 - 0.176: 20 0.176 - 0.235: 1 0.235 - 0.293: 2 Chirality restraints: 2252 Sorted by residual: chirality pdb=" C3' ATP A 801 " pdb=" C2' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" O3' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C2' ATP A 801 " pdb=" C1' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" O2' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O4' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2249 not shown) Planarity restraints: 4172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " -0.037 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO E 63 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 287 " 0.011 2.00e-02 2.50e+03 9.19e-03 2.53e+00 pdb=" CG TYR E 287 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR E 287 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR E 287 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 287 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 287 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 287 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 287 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR E 287 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR E 287 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR E 287 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR E 287 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 228 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C VAL B 228 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL B 228 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP B 229 " 0.009 2.00e-02 2.50e+03 ... (remaining 4169 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1524 2.20 - 2.80: 59738 2.80 - 3.40: 79489 3.40 - 4.00: 102140 4.00 - 4.60: 160883 Nonbonded interactions: 403774 Sorted by model distance: nonbonded pdb=" OE1 GLU B 301 " pdb=" HH TYR C 308 " model vdw 1.600 1.850 nonbonded pdb="HH22 ARG D 91 " pdb=" O SER D 119 " model vdw 1.626 1.850 nonbonded pdb=" O ASN A 383 " pdb=" HG1 THR A 386 " model vdw 1.627 1.850 nonbonded pdb=" H LYS D 71 " pdb=" O3B ADP D 801 " model vdw 1.651 1.850 nonbonded pdb=" OD1 ASP D 37 " pdb=" HZ1 LYS D 50 " model vdw 1.663 1.850 ... (remaining 403769 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: 3.530 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: 0.400 Extract box with map and model: 1.020 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 85.360 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.002 0.026 14488 Z= 0.115 Angle : 0.483 8.034 19588 Z= 0.238 Chirality : 0.037 0.293 2252 Planarity : 0.003 0.057 2476 Dihedral : 14.056 172.618 5543 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 3.20 (0.21), residues: 1748 helix: 3.26 (0.16), residues: 1048 sheet: -0.05 (0.41), residues: 166 loop : 0.53 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 66 HIS 0.005 0.001 HIS B 60 PHE 0.009 0.001 PHE A 96 TYR 0.027 0.001 TYR E 287 ARG 0.005 0.000 ARG E 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.7945 (mpp) cc_final: 0.7586 (mpp) REVERT: B 119 MET cc_start: 0.4585 (tmm) cc_final: 0.3584 (mtt) REVERT: E 72 VAL cc_start: 0.8831 (t) cc_final: 0.8487 (t) REVERT: E 74 GLN cc_start: 0.7855 (mp10) cc_final: 0.7567 (mp-120) REVERT: E 161 TYR cc_start: 0.6916 (m-80) cc_final: 0.6709 (m-80) REVERT: A 287 MET cc_start: 0.5507 (ptm) cc_final: 0.5291 (ptm) REVERT: A 497 TYR cc_start: 0.7584 (t80) cc_final: 0.7331 (t80) REVERT: A 500 LYS cc_start: 0.8339 (mmtm) cc_final: 0.8100 (tmmt) outliers start: 0 outliers final: 1 residues processed: 300 average time/residue: 2.8692 time to fit residues: 942.0025 Evaluate side-chains 160 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 99 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 53 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN D 196 ASN E 336 ASN A 341 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14488 Z= 0.298 Angle : 0.568 7.040 19588 Z= 0.281 Chirality : 0.038 0.137 2252 Planarity : 0.004 0.075 2476 Dihedral : 10.631 164.681 1993 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.01 % Allowed : 9.10 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.21), residues: 1748 helix: 3.01 (0.16), residues: 1065 sheet: -0.02 (0.40), residues: 166 loop : 0.48 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 4 HIS 0.007 0.001 HIS C 260 PHE 0.015 0.001 PHE E 305 TYR 0.015 0.001 TYR B 186 ARG 0.007 0.001 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.7642 (mpp) cc_final: 0.7240 (mpp) REVERT: B 77 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8128 (mp0) REVERT: B 119 MET cc_start: 0.5039 (tmm) cc_final: 0.4059 (mtt) REVERT: B 301 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: C 94 ARG cc_start: 0.8513 (ttp80) cc_final: 0.8295 (tmm-80) REVERT: D 207 GLN cc_start: 0.8350 (mp10) cc_final: 0.8135 (mp10) REVERT: E 72 VAL cc_start: 0.8938 (t) cc_final: 0.8663 (t) REVERT: E 74 GLN cc_start: 0.7942 (mp10) cc_final: 0.7666 (mp-120) REVERT: A 497 TYR cc_start: 0.7616 (t80) cc_final: 0.7381 (t80) REVERT: A 500 LYS cc_start: 0.8360 (mmtm) cc_final: 0.8139 (tmmt) outliers start: 16 outliers final: 6 residues processed: 174 average time/residue: 2.7279 time to fit residues: 524.4638 Evaluate side-chains 140 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14488 Z= 0.282 Angle : 0.553 8.589 19588 Z= 0.272 Chirality : 0.038 0.132 2252 Planarity : 0.004 0.053 2476 Dihedral : 10.540 174.226 1991 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.01 % Allowed : 10.24 % Favored : 88.75 % 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: 2.74 (0.21), residues: 1748 helix: 2.84 (0.16), residues: 1067 sheet: -0.07 (0.40), residues: 169 loop : 0.30 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 256 HIS 0.008 0.001 HIS C 260 PHE 0.016 0.001 PHE E 305 TYR 0.011 0.001 TYR D 286 ARG 0.006 0.000 ARG E 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.5505 (tmm) cc_final: 0.4509 (mtt) REVERT: B 301 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: E 32 GLN cc_start: 0.7684 (mp10) cc_final: 0.7310 (pm20) REVERT: E 72 VAL cc_start: 0.8988 (t) cc_final: 0.8717 (t) REVERT: E 74 GLN cc_start: 0.7892 (mp10) cc_final: 0.7656 (mp-120) REVERT: E 112 LEU cc_start: 0.9153 (mm) cc_final: 0.8857 (mm) outliers start: 16 outliers final: 4 residues processed: 158 average time/residue: 2.4786 time to fit residues: 435.1409 Evaluate side-chains 141 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 3.9990 chunk 119 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 151 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14488 Z= 0.257 Angle : 0.539 7.182 19588 Z= 0.263 Chirality : 0.037 0.134 2252 Planarity : 0.003 0.047 2476 Dihedral : 10.438 176.494 1991 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.88 % Allowed : 11.19 % Favored : 87.93 % 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: 2.69 (0.21), residues: 1748 helix: 2.79 (0.16), residues: 1068 sheet: 0.03 (0.39), residues: 168 loop : 0.26 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 256 HIS 0.007 0.001 HIS C 260 PHE 0.014 0.001 PHE E 305 TYR 0.020 0.001 TYR B 186 ARG 0.005 0.000 ARG E 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.5793 (tmm) cc_final: 0.4888 (mtt) REVERT: B 301 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: A 285 MET cc_start: 0.0982 (mmm) cc_final: 0.0774 (mmm) outliers start: 14 outliers final: 4 residues processed: 149 average time/residue: 2.6439 time to fit residues: 437.0771 Evaluate side-chains 130 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 116 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 151 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN C 128 ASN D 352 GLN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14488 Z= 0.183 Angle : 0.516 6.752 19588 Z= 0.250 Chirality : 0.036 0.133 2252 Planarity : 0.003 0.041 2476 Dihedral : 10.248 179.713 1991 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.07 % Allowed : 11.57 % Favored : 87.36 % 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: 2.78 (0.21), residues: 1748 helix: 2.87 (0.16), residues: 1068 sheet: 0.10 (0.42), residues: 149 loop : 0.25 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 256 HIS 0.006 0.001 HIS A 436 PHE 0.012 0.001 PHE E 305 TYR 0.012 0.001 TYR E 161 ARG 0.009 0.000 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.5857 (tmm) cc_final: 0.4716 (mmt) REVERT: B 301 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7118 (mt-10) REVERT: A 285 MET cc_start: 0.1057 (mmm) cc_final: 0.0823 (mmm) outliers start: 17 outliers final: 6 residues processed: 146 average time/residue: 2.5021 time to fit residues: 407.8065 Evaluate side-chains 137 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.9990 chunk 152 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14488 Z= 0.202 Angle : 0.520 6.984 19588 Z= 0.251 Chirality : 0.036 0.132 2252 Planarity : 0.003 0.038 2476 Dihedral : 10.018 179.873 1991 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.88 % Allowed : 12.20 % Favored : 86.92 % 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: 2.79 (0.21), residues: 1748 helix: 2.85 (0.16), residues: 1075 sheet: 0.14 (0.42), residues: 149 loop : 0.24 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 256 HIS 0.006 0.001 HIS A 436 PHE 0.012 0.001 PHE E 305 TYR 0.020 0.001 TYR B 186 ARG 0.007 0.000 ARG E 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.5920 (tmm) cc_final: 0.5012 (mtt) REVERT: B 301 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7113 (mt-10) REVERT: E 32 GLN cc_start: 0.7559 (mp10) cc_final: 0.7294 (pm20) REVERT: A 285 MET cc_start: 0.1082 (mmm) cc_final: 0.0837 (mmm) REVERT: A 351 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.7534 (m90) outliers start: 14 outliers final: 8 residues processed: 142 average time/residue: 2.5622 time to fit residues: 406.1160 Evaluate side-chains 138 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 142 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14488 Z= 0.191 Angle : 0.521 6.907 19588 Z= 0.251 Chirality : 0.036 0.132 2252 Planarity : 0.003 0.045 2476 Dihedral : 9.745 176.484 1991 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.88 % Allowed : 12.39 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.21), residues: 1748 helix: 2.88 (0.16), residues: 1073 sheet: 0.17 (0.42), residues: 149 loop : 0.24 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 256 HIS 0.005 0.001 HIS C 260 PHE 0.011 0.001 PHE D 203 TYR 0.012 0.001 TYR E 161 ARG 0.007 0.000 ARG E 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 301 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7118 (mt-10) REVERT: C 94 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8403 (tmm-80) REVERT: E 32 GLN cc_start: 0.7583 (mp10) cc_final: 0.7299 (pm20) REVERT: A 285 MET cc_start: 0.1424 (mmm) cc_final: 0.1157 (mmm) REVERT: A 351 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7534 (m90) REVERT: A 574 ASP cc_start: 0.8156 (p0) cc_final: 0.7927 (p0) outliers start: 14 outliers final: 10 residues processed: 139 average time/residue: 2.5608 time to fit residues: 396.7192 Evaluate side-chains 135 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14488 Z= 0.173 Angle : 0.526 8.062 19588 Z= 0.251 Chirality : 0.036 0.138 2252 Planarity : 0.003 0.053 2476 Dihedral : 9.407 171.318 1991 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.88 % Allowed : 12.58 % Favored : 86.54 % 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: 2.90 (0.21), residues: 1748 helix: 2.94 (0.16), residues: 1073 sheet: 0.22 (0.42), residues: 149 loop : 0.28 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 259 HIS 0.004 0.001 HIS C 260 PHE 0.015 0.001 PHE C 111 TYR 0.023 0.001 TYR B 186 ARG 0.007 0.000 ARG E 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.6316 (ppp) cc_final: 0.4527 (mmt) REVERT: B 186 TYR cc_start: 0.8171 (p90) cc_final: 0.7897 (p90) REVERT: B 301 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7128 (mt-10) REVERT: E 32 GLN cc_start: 0.7613 (mp10) cc_final: 0.7312 (pm20) REVERT: A 285 MET cc_start: 0.1482 (mmm) cc_final: 0.1220 (mmm) outliers start: 14 outliers final: 11 residues processed: 139 average time/residue: 2.4942 time to fit residues: 388.9622 Evaluate side-chains 136 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 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 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14488 Z= 0.229 Angle : 0.540 9.041 19588 Z= 0.260 Chirality : 0.036 0.136 2252 Planarity : 0.003 0.038 2476 Dihedral : 9.231 167.562 1991 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.63 % Allowed : 13.15 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.21), residues: 1748 helix: 2.87 (0.16), residues: 1075 sheet: 0.19 (0.42), residues: 149 loop : 0.23 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 259 HIS 0.005 0.001 HIS E 18 PHE 0.013 0.001 PHE E 305 TYR 0.018 0.001 TYR B 186 ARG 0.008 0.000 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 TYR cc_start: 0.8211 (p90) cc_final: 0.7947 (p90) REVERT: B 301 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7102 (mt-10) REVERT: E 32 GLN cc_start: 0.7672 (mp10) cc_final: 0.7383 (pm20) REVERT: A 285 MET cc_start: 0.1561 (mmm) cc_final: 0.1317 (mmm) outliers start: 10 outliers final: 8 residues processed: 137 average time/residue: 2.3291 time to fit residues: 358.2870 Evaluate side-chains 135 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 138 optimal weight: 30.0000 chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14488 Z= 0.207 Angle : 0.540 7.463 19588 Z= 0.259 Chirality : 0.036 0.140 2252 Planarity : 0.003 0.038 2476 Dihedral : 9.052 163.902 1991 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.57 % Allowed : 13.21 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.21), residues: 1748 helix: 2.85 (0.16), residues: 1075 sheet: 0.18 (0.42), residues: 149 loop : 0.24 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 259 HIS 0.005 0.001 HIS C 260 PHE 0.015 0.001 PHE D 203 TYR 0.018 0.001 TYR B 186 ARG 0.007 0.000 ARG C 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.5776 (ppp) cc_final: 0.3023 (mtt) REVERT: B 186 TYR cc_start: 0.8206 (p90) cc_final: 0.7967 (p90) REVERT: B 301 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7078 (mt-10) REVERT: E 32 GLN cc_start: 0.7681 (mp10) cc_final: 0.7395 (pm20) REVERT: A 285 MET cc_start: 0.1500 (mmm) cc_final: 0.1266 (mmm) outliers start: 9 outliers final: 8 residues processed: 136 average time/residue: 2.3016 time to fit residues: 351.9762 Evaluate side-chains 136 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 139 optimal weight: 30.0000 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 20.0000 chunk 17 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.139414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077524 restraints weight = 70041.345| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.92 r_work: 0.2881 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14488 Z= 0.274 Angle : 0.552 7.048 19588 Z= 0.269 Chirality : 0.037 0.143 2252 Planarity : 0.003 0.038 2476 Dihedral : 9.011 161.288 1991 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.70 % Allowed : 13.27 % Favored : 86.03 % 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: 2.71 (0.21), residues: 1748 helix: 2.76 (0.16), residues: 1076 sheet: 0.15 (0.39), residues: 169 loop : 0.27 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 259 HIS 0.006 0.001 HIS E 18 PHE 0.015 0.001 PHE E 305 TYR 0.018 0.001 TYR B 186 ARG 0.008 0.000 ARG C 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9740.96 seconds wall clock time: 168 minutes 46.37 seconds (10126.37 seconds total)