Starting phenix.real_space_refine on Thu Nov 14 16:41:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggb_40001/11_2024/8ggb_40001.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggb_40001/11_2024/8ggb_40001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggb_40001/11_2024/8ggb_40001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggb_40001/11_2024/8ggb_40001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggb_40001/11_2024/8ggb_40001.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggb_40001/11_2024/8ggb_40001.cif" } resolution = 3.5 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= 0.020 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 3 5.49 5 S 37 5.16 5 C 4281 2.51 5 N 1204 2.21 5 O 1250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6775 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2234 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 342 Unresolved non-hydrogen angles: 423 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 219 Chain: "B" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2462 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "G" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 352 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1680 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 7, 'TRANS': 257} Chain breaks: 3 Unresolved non-hydrogen bonds: 455 Unresolved non-hydrogen angles: 590 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 216 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.09, per 1000 atoms: 0.75 Number of scatterers: 6775 At special positions: 0 Unit cell: (84.1669, 135.361, 100.653, 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 37 16.00 P 3 15.00 O 1250 8.00 N 1204 7.00 C 4281 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 - 3.00 Amino acid : True - 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: 2.07 Conformation dependent library (CDL) restraints added in 1.2 seconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 49.6% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.686A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.547A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 removed outlier: 3.571A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 152 removed outlier: 3.514A pdb=" N ALA A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 166 through 169 removed outlier: 3.638A pdb=" N TYR A 169 " --> pdb=" O SER A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.548A pdb=" N PHE A 178 " --> pdb=" O CYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.093A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.703A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.961A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.511A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.680A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 removed outlier: 3.631A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 383 " --> pdb=" O CYS A 379 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.682A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.782A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.009A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.608A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.621A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 32 through 59 Processing helix chain 'R' and resid 68 through 86 removed outlier: 4.241A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 96 removed outlier: 3.781A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS R 93 " --> pdb=" O PHE R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 4.355A pdb=" N VAL R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 145 removed outlier: 4.472A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 172 removed outlier: 3.679A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE R 166 " --> pdb=" O GLY R 162 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 180 through 187 removed outlier: 4.459A pdb=" N CYS R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 208 Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.859A pdb=" N LEU R 212 " --> pdb=" O PHE R 208 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE R 217 " --> pdb=" O VAL R 213 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 removed outlier: 4.171A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.858A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'R' and resid 317 through 326 removed outlier: 3.782A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 6.247A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.781A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.936A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.501A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.275A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.694A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.768A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.619A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 981 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: 2.12 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1770 1.33 - 1.45: 1292 1.45 - 1.57: 3784 1.57 - 1.69: 6 1.69 - 1.81: 51 Bond restraints: 6903 Sorted by residual: bond pdb=" C PHE R 194 " pdb=" N THR R 195 " ideal model delta sigma weight residual 1.333 1.270 0.062 1.38e-02 5.25e+03 2.05e+01 bond pdb=" C PHE R 193 " pdb=" N PHE R 194 " ideal model delta sigma weight residual 1.331 1.277 0.054 1.28e-02 6.10e+03 1.79e+01 bond pdb=" C GLY R 50 " pdb=" O GLY R 50 " ideal model delta sigma weight residual 1.234 1.278 -0.045 1.21e-02 6.83e+03 1.36e+01 bond pdb=" N VAL R 34 " pdb=" CA VAL R 34 " ideal model delta sigma weight residual 1.461 1.503 -0.043 1.19e-02 7.06e+03 1.28e+01 bond pdb=" CA ARG A 389 " pdb=" C ARG A 389 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.30e-02 5.92e+03 1.14e+01 ... (remaining 6898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 9150 2.11 - 4.23: 240 4.23 - 6.34: 41 6.34 - 8.46: 13 8.46 - 10.57: 3 Bond angle restraints: 9447 Sorted by residual: angle pdb=" N ARG A 13 " pdb=" CA ARG A 13 " pdb=" C ARG A 13 " ideal model delta sigma weight residual 111.28 104.36 6.92 1.09e+00 8.42e-01 4.02e+01 angle pdb=" N ARG A 389 " pdb=" CA ARG A 389 " pdb=" C ARG A 389 " ideal model delta sigma weight residual 111.28 104.52 6.76 1.09e+00 8.42e-01 3.84e+01 angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 105.31 5.97 1.09e+00 8.42e-01 3.00e+01 angle pdb=" C GLY R 50 " pdb=" N ASN R 51 " pdb=" CA ASN R 51 " ideal model delta sigma weight residual 120.28 113.15 7.13 1.34e+00 5.57e-01 2.83e+01 angle pdb=" C PHE R 194 " pdb=" CA PHE R 194 " pdb=" CB PHE R 194 " ideal model delta sigma weight residual 110.24 102.76 7.48 1.46e+00 4.69e-01 2.62e+01 ... (remaining 9442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.37: 3914 30.37 - 60.74: 92 60.74 - 91.12: 8 91.12 - 121.49: 3 121.49 - 151.86: 2 Dihedral angle restraints: 4019 sinusoidal: 1200 harmonic: 2819 Sorted by residual: dihedral pdb=" O2G GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 177.30 -30.84 -151.86 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -161.19 -129.54 1 2.00e+01 2.50e-03 3.93e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual -56.21 -175.84 119.64 1 2.00e+01 2.50e-03 3.59e+01 ... (remaining 4016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 878 0.053 - 0.106: 191 0.106 - 0.159: 43 0.159 - 0.212: 9 0.212 - 0.265: 6 Chirality restraints: 1127 Sorted by residual: chirality pdb=" CA ILE R 38 " pdb=" N ILE R 38 " pdb=" C ILE R 38 " pdb=" CB ILE R 38 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ILE R 47 " pdb=" N ILE R 47 " pdb=" C ILE R 47 " pdb=" CB ILE R 47 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C3' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C4' GTP A 401 " pdb=" O3' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.71 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1124 not shown) Planarity restraints: 1214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 48 " -0.019 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C VAL R 48 " 0.068 2.00e-02 2.50e+03 pdb=" O VAL R 48 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE R 49 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 26 " 0.018 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ILE A 26 " -0.065 2.00e-02 2.50e+03 pdb=" O ILE A 26 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU A 27 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 35 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C GLY R 35 " 0.059 2.00e-02 2.50e+03 pdb=" O GLY R 35 " -0.022 2.00e-02 2.50e+03 pdb=" N MET R 36 " -0.020 2.00e-02 2.50e+03 ... (remaining 1211 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2191 2.82 - 3.34: 6171 3.34 - 3.86: 10113 3.86 - 4.38: 11073 4.38 - 4.90: 20089 Nonbonded interactions: 49637 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.306 3.040 nonbonded pdb=" O CYS A 162 " pdb=" OH TYR A 169 " model vdw 2.329 3.040 nonbonded pdb=" OD2 ASP B 212 " pdb=" NH2 ARG B 219 " model vdw 2.356 3.120 nonbonded pdb=" O SER B 160 " pdb=" OG SER B 160 " model vdw 2.358 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.359 3.040 ... (remaining 49632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 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: 2.270 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.920 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6903 Z= 0.347 Angle : 0.795 10.573 9447 Z= 0.524 Chirality : 0.051 0.265 1127 Planarity : 0.004 0.039 1214 Dihedral : 14.627 151.861 2181 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.18 % Allowed : 0.89 % Favored : 98.93 % 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: 0.27 (0.27), residues: 942 helix: 1.68 (0.26), residues: 405 sheet: -1.01 (0.44), residues: 157 loop : -0.90 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 99 HIS 0.003 0.001 HIS B 183 PHE 0.021 0.001 PHE B 234 TYR 0.017 0.001 TYR A 177 ARG 0.006 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8190 (m-80) cc_final: 0.7975 (m-80) REVERT: R 172 HIS cc_start: 0.6287 (m90) cc_final: 0.5972 (t-170) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.1724 time to fit residues: 23.3862 Evaluate side-chains 87 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 39 optimal weight: 0.1980 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 74 optimal weight: 0.0570 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6903 Z= 0.133 Angle : 0.477 6.789 9447 Z= 0.252 Chirality : 0.041 0.153 1127 Planarity : 0.003 0.030 1214 Dihedral : 8.881 128.672 1049 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.07 % Allowed : 8.93 % Favored : 90.00 % 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: 0.54 (0.28), residues: 942 helix: 1.89 (0.26), residues: 428 sheet: -0.87 (0.42), residues: 162 loop : -0.92 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 234 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE R 289 TYR 0.008 0.001 TYR A 391 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.822 Fit side-chains REVERT: R 332 PHE cc_start: 0.6798 (t80) cc_final: 0.6394 (t80) outliers start: 6 outliers final: 2 residues processed: 102 average time/residue: 0.1670 time to fit residues: 23.8232 Evaluate side-chains 89 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain R residue 201 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 71 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6903 Z= 0.164 Angle : 0.454 6.846 9447 Z= 0.238 Chirality : 0.041 0.163 1127 Planarity : 0.003 0.030 1214 Dihedral : 8.057 129.256 1049 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.43 % Allowed : 11.61 % Favored : 86.96 % 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: 0.72 (0.28), residues: 942 helix: 2.13 (0.26), residues: 429 sheet: -0.82 (0.41), residues: 171 loop : -0.95 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE B 234 TYR 0.013 0.001 TYR A 177 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.722 Fit side-chains REVERT: R 332 PHE cc_start: 0.6834 (t80) cc_final: 0.6448 (t80) outliers start: 8 outliers final: 6 residues processed: 95 average time/residue: 0.1654 time to fit residues: 21.9399 Evaluate side-chains 92 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 217 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 86 optimal weight: 0.0670 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6903 Z= 0.128 Angle : 0.431 6.602 9447 Z= 0.226 Chirality : 0.041 0.169 1127 Planarity : 0.003 0.028 1214 Dihedral : 7.536 129.998 1049 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.61 % Allowed : 12.68 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.28), residues: 942 helix: 2.29 (0.26), residues: 429 sheet: -0.70 (0.42), residues: 166 loop : -0.97 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE R 289 TYR 0.005 0.001 TYR R 308 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.792 Fit side-chains REVERT: R 332 PHE cc_start: 0.6874 (t80) cc_final: 0.6469 (t80) outliers start: 9 outliers final: 7 residues processed: 96 average time/residue: 0.1632 time to fit residues: 22.1136 Evaluate side-chains 95 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 217 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6903 Z= 0.163 Angle : 0.442 6.589 9447 Z= 0.232 Chirality : 0.041 0.174 1127 Planarity : 0.003 0.029 1214 Dihedral : 7.377 132.218 1049 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.96 % Allowed : 14.64 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.28), residues: 942 helix: 2.32 (0.26), residues: 429 sheet: -0.70 (0.41), residues: 171 loop : -1.02 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.012 0.001 PHE B 292 TYR 0.008 0.001 TYR A 339 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.781 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 96 average time/residue: 0.1838 time to fit residues: 24.4557 Evaluate side-chains 97 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 5.9990 chunk 82 optimal weight: 0.0070 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6903 Z= 0.129 Angle : 0.427 6.522 9447 Z= 0.224 Chirality : 0.041 0.178 1127 Planarity : 0.003 0.029 1214 Dihedral : 7.260 134.781 1049 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.61 % Allowed : 16.43 % Favored : 81.96 % 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: 0.94 (0.28), residues: 942 helix: 2.38 (0.26), residues: 429 sheet: -0.60 (0.42), residues: 166 loop : -1.01 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.014 0.001 PHE B 292 TYR 0.006 0.001 TYR A 339 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.892 Fit side-chains REVERT: A 59 GLN cc_start: 0.8177 (mm110) cc_final: 0.7914 (tp40) outliers start: 9 outliers final: 8 residues processed: 92 average time/residue: 0.1636 time to fit residues: 21.3683 Evaluate side-chains 92 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 201 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6903 Z= 0.185 Angle : 0.451 6.810 9447 Z= 0.238 Chirality : 0.042 0.175 1127 Planarity : 0.003 0.030 1214 Dihedral : 7.305 135.581 1049 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.14 % Allowed : 16.25 % Favored : 81.61 % 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: 0.92 (0.28), residues: 942 helix: 2.38 (0.26), residues: 429 sheet: -0.63 (0.41), residues: 169 loop : -1.04 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.001 PHE B 292 TYR 0.007 0.001 TYR B 59 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.820 Fit side-chains REVERT: A 59 GLN cc_start: 0.8236 (mm110) cc_final: 0.7998 (tp40) outliers start: 12 outliers final: 11 residues processed: 91 average time/residue: 0.1658 time to fit residues: 21.2033 Evaluate side-chains 93 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6903 Z= 0.202 Angle : 0.465 7.361 9447 Z= 0.246 Chirality : 0.042 0.177 1127 Planarity : 0.003 0.030 1214 Dihedral : 7.368 136.216 1049 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.14 % Allowed : 16.25 % Favored : 81.61 % 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: 0.86 (0.28), residues: 942 helix: 2.31 (0.26), residues: 429 sheet: -0.67 (0.40), residues: 174 loop : -1.04 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE B 292 TYR 0.008 0.001 TYR B 105 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.719 Fit side-chains REVERT: A 59 GLN cc_start: 0.8314 (mm110) cc_final: 0.8066 (tp40) REVERT: A 393 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7116 (mp) outliers start: 12 outliers final: 10 residues processed: 94 average time/residue: 0.1552 time to fit residues: 20.4625 Evaluate side-chains 94 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 67 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6903 Z= 0.151 Angle : 0.447 7.698 9447 Z= 0.235 Chirality : 0.041 0.167 1127 Planarity : 0.003 0.030 1214 Dihedral : 7.286 137.271 1049 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.14 % Allowed : 15.89 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.28), residues: 942 helix: 2.32 (0.26), residues: 429 sheet: -0.61 (0.41), residues: 169 loop : -1.02 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 99 HIS 0.003 0.001 HIS B 142 PHE 0.011 0.001 PHE B 241 TYR 0.007 0.001 TYR B 59 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.857 Fit side-chains REVERT: A 23 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7428 (t0) REVERT: A 59 GLN cc_start: 0.8309 (mm110) cc_final: 0.8061 (tp40) REVERT: A 393 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7025 (mp) outliers start: 12 outliers final: 10 residues processed: 92 average time/residue: 0.1526 time to fit residues: 20.1721 Evaluate side-chains 90 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6903 Z= 0.152 Angle : 0.450 7.945 9447 Z= 0.236 Chirality : 0.041 0.176 1127 Planarity : 0.003 0.030 1214 Dihedral : 7.261 137.052 1049 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.14 % Allowed : 16.07 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.28), residues: 942 helix: 2.33 (0.26), residues: 429 sheet: -0.62 (0.42), residues: 164 loop : -1.04 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 PHE 0.017 0.001 PHE B 292 TYR 0.005 0.001 TYR A 339 ARG 0.004 0.000 ARG A 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.879 Fit side-chains REVERT: A 59 GLN cc_start: 0.8317 (mm110) cc_final: 0.8073 (tp40) REVERT: A 393 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7049 (mp) REVERT: R 279 MET cc_start: 0.7498 (mmt) cc_final: 0.6997 (mmt) outliers start: 12 outliers final: 11 residues processed: 86 average time/residue: 0.1777 time to fit residues: 22.0050 Evaluate side-chains 90 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 8.9990 chunk 11 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118067 restraints weight = 10278.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.117316 restraints weight = 7372.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118467 restraints weight = 6880.495| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6903 Z= 0.146 Angle : 0.443 7.915 9447 Z= 0.232 Chirality : 0.041 0.179 1127 Planarity : 0.003 0.030 1214 Dihedral : 7.149 136.431 1049 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.14 % Allowed : 16.25 % Favored : 81.61 % 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: 0.93 (0.28), residues: 942 helix: 2.36 (0.26), residues: 428 sheet: -0.59 (0.42), residues: 164 loop : -1.00 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE B 292 TYR 0.005 0.001 TYR B 105 ARG 0.004 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1561.19 seconds wall clock time: 33 minutes 12.02 seconds (1992.02 seconds total)