Starting phenix.real_space_refine on Thu Nov 14 16:23:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gge_40004/11_2024/8gge_40004.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gge_40004/11_2024/8gge_40004.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/8gge_40004/11_2024/8gge_40004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gge_40004/11_2024/8gge_40004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gge_40004/11_2024/8gge_40004.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gge_40004/11_2024/8gge_40004.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= 0.019 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 32 5.16 5 C 4236 2.51 5 N 1204 2.21 5 O 1233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6708 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2526 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 13, 'TRANS': 347} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 476 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 378 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 19, 'PHE:plan': 5, 'GLU:plan': 23, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 304 Chain: "B" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2408 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 8, 'ARG:plan': 9, 'ASN:plan1': 4, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 143 Chain: "G" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 340 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 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: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1387 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 505 Unresolved non-hydrogen angles: 664 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 9, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 252 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: 5.00, per 1000 atoms: 0.75 Number of scatterers: 6708 At special positions: 0 Unit cell: (84.1669, 136.229, 103.256, 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 32 16.00 P 3 15.00 O 1233 8.00 N 1204 7.00 C 4236 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: 1.84 Conformation dependent library (CDL) restraints added in 1.0 seconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1870 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 47.1% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.938A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.704A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 113 removed outlier: 3.600A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 136 removed outlier: 4.135A pdb=" N TYR A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 155 removed outlier: 4.021A pdb=" N TYR A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 175 through 181 removed outlier: 3.673A pdb=" N LYS A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.995A 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: 4.069A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.009A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.610A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 389 removed outlier: 3.843A pdb=" N ILE A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASN A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE A 383 " --> pdb=" O CYS A 379 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLN A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 removed outlier: 4.054A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.826A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.731A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.756A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.659A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 54 removed outlier: 4.223A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 78 removed outlier: 4.259A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 94 removed outlier: 4.065A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.706A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP R 113 " --> pdb=" O TRP R 109 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 171 removed outlier: 3.633A pdb=" N MET R 156 " --> pdb=" O VAL R 152 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.870A 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 178 through 187 Processing helix chain 'R' and resid 198 through 208 Processing helix chain 'R' and resid 208 through 230 removed outlier: 4.170A pdb=" N LEU R 212 " --> pdb=" O PHE R 208 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL R 216 " --> pdb=" O LEU R 212 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE R 217 " --> pdb=" O VAL R 213 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR R 219 " --> pdb=" O MET R 215 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER R 220 " --> pdb=" O VAL R 216 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL R 222 " --> pdb=" O VAL R 218 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS R 227 " --> pdb=" O PHE R 223 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG R 228 " --> pdb=" O GLN R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 287 removed outlier: 3.641A pdb=" N GLY R 276 " --> pdb=" O LEU R 272 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE R 277 " --> pdb=" O LYS R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 299 removed outlier: 3.733A pdb=" N ILE R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 314 Processing helix chain 'R' and resid 317 through 326 Proline residue: R 323 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 3.952A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 9.475A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.937A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.856A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.508A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.902A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.820A 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: 6.723A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.595A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.756A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 909 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: 2.04 Time building geometry restraints manager: 2.11 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: 1797 1.33 - 1.45: 1256 1.45 - 1.57: 3726 1.57 - 1.69: 6 1.69 - 1.81: 44 Bond restraints: 6829 Sorted by residual: bond pdb=" CA GLN A 384 " pdb=" C GLN A 384 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.32e-02 5.74e+03 3.86e+01 bond pdb=" N ARG A 385 " pdb=" CA ARG A 385 " ideal model delta sigma weight residual 1.459 1.408 0.051 1.19e-02 7.06e+03 1.85e+01 bond pdb=" CA PHE A 376 " pdb=" C PHE A 376 " ideal model delta sigma weight residual 1.526 1.474 0.052 1.39e-02 5.18e+03 1.40e+01 bond pdb=" CA LEU A 388 " pdb=" C LEU A 388 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" CA ASP A 381 " pdb=" C ASP A 381 " ideal model delta sigma weight residual 1.527 1.481 0.046 1.30e-02 5.92e+03 1.26e+01 ... (remaining 6824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 9247 2.17 - 4.35: 84 4.35 - 6.52: 18 6.52 - 8.69: 4 8.69 - 10.87: 4 Bond angle restraints: 9357 Sorted by residual: angle pdb=" N HIS A 387 " pdb=" CA HIS A 387 " pdb=" C HIS A 387 " ideal model delta sigma weight residual 111.14 121.58 -10.44 1.08e+00 8.57e-01 9.34e+01 angle pdb=" N TYR A 391 " pdb=" CA TYR A 391 " pdb=" C TYR A 391 " ideal model delta sigma weight residual 113.43 102.56 10.87 1.26e+00 6.30e-01 7.44e+01 angle pdb=" N ASP A 381 " pdb=" CA ASP A 381 " pdb=" C ASP A 381 " ideal model delta sigma weight residual 111.39 102.62 8.77 1.38e+00 5.25e-01 4.04e+01 angle pdb=" N PHE A 376 " pdb=" CA PHE A 376 " pdb=" C PHE A 376 " ideal model delta sigma weight residual 111.90 103.54 8.36 1.32e+00 5.74e-01 4.01e+01 angle pdb=" N CYS A 379 " pdb=" CA CYS A 379 " pdb=" C CYS A 379 " ideal model delta sigma weight residual 111.52 102.69 8.83 1.40e+00 5.10e-01 3.98e+01 ... (remaining 9352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 3667 17.57 - 35.15: 239 35.15 - 52.72: 41 52.72 - 70.29: 4 70.29 - 87.86: 3 Dihedral angle restraints: 3954 sinusoidal: 1088 harmonic: 2866 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 18.88 85.71 1 2.00e+01 2.50e-03 2.22e+01 dihedral pdb=" CA GLU A 259 " pdb=" C GLU A 259 " pdb=" N ASP A 260 " pdb=" CA ASP A 260 " ideal model delta harmonic sigma weight residual 180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CB LYS B 89 " pdb=" CG LYS B 89 " pdb=" CD LYS B 89 " pdb=" CE LYS B 89 " ideal model delta sinusoidal sigma weight residual -60.00 -109.82 49.82 3 1.50e+01 4.44e-03 8.82e+00 ... (remaining 3951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 916 0.051 - 0.103: 176 0.103 - 0.154: 34 0.154 - 0.205: 2 0.205 - 0.257: 1 Chirality restraints: 1129 Sorted by residual: chirality pdb=" CA HIS A 387 " pdb=" N HIS A 387 " pdb=" C HIS A 387 " pdb=" CB HIS A 387 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA GLU A 392 " pdb=" N GLU A 392 " pdb=" C GLU A 392 " pdb=" CB GLU A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.56 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 1126 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 375 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C VAL A 375 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 375 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 376 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 393 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C LEU A 393 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A 393 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 394 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO G 49 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.023 5.00e-02 4.00e+02 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1249 2.77 - 3.30: 6258 3.30 - 3.83: 10166 3.83 - 4.37: 10536 4.37 - 4.90: 19574 Nonbonded interactions: 47783 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.232 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.259 3.040 nonbonded pdb=" NZ LYS A 53 " pdb=" O1G GTP A 401 " model vdw 2.265 3.120 nonbonded pdb=" O VAL A 375 " pdb=" N ASP A 378 " model vdw 2.286 3.120 nonbonded pdb=" O MET R 171 " pdb=" ND1 HIS R 172 " model vdw 2.287 3.120 ... (remaining 47778 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: 1.810 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.080 Find NCS groups from input model: 0.080 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6829 Z= 0.231 Angle : 0.593 10.867 9357 Z= 0.358 Chirality : 0.042 0.257 1129 Planarity : 0.003 0.041 1203 Dihedral : 12.439 87.864 2084 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.28), residues: 954 helix: 1.70 (0.28), residues: 377 sheet: -1.02 (0.40), residues: 184 loop : -1.17 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 286 HIS 0.006 0.001 HIS A 387 PHE 0.021 0.001 PHE R 289 TYR 0.009 0.001 TYR R 174 ARG 0.007 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.760 Fit side-chains REVERT: A 331 ASP cc_start: 0.8236 (t0) cc_final: 0.7971 (t70) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1482 time to fit residues: 19.4883 Evaluate side-chains 73 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 76 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 384 GLN B 88 ASN B 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6829 Z= 0.327 Angle : 0.559 6.033 9357 Z= 0.307 Chirality : 0.044 0.151 1129 Planarity : 0.004 0.050 1203 Dihedral : 5.394 87.099 1059 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.57 % Allowed : 12.77 % Favored : 85.66 % 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: -0.10 (0.28), residues: 954 helix: 1.58 (0.27), residues: 400 sheet: -1.06 (0.40), residues: 181 loop : -1.35 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 99 HIS 0.007 0.002 HIS A 387 PHE 0.029 0.002 PHE B 234 TYR 0.019 0.002 TYR R 174 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.825 Fit side-chains REVERT: A 154 TRP cc_start: 0.7889 (t-100) cc_final: 0.7174 (t-100) REVERT: A 331 ASP cc_start: 0.7602 (t0) cc_final: 0.7358 (t70) outliers start: 8 outliers final: 6 residues processed: 82 average time/residue: 0.1373 time to fit residues: 17.0235 Evaluate side-chains 77 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 95 optimal weight: 0.0170 chunk 78 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6829 Z= 0.139 Angle : 0.455 6.207 9357 Z= 0.247 Chirality : 0.041 0.162 1129 Planarity : 0.003 0.043 1203 Dihedral : 4.963 84.357 1059 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.18 % Allowed : 17.09 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.28), residues: 954 helix: 1.78 (0.27), residues: 411 sheet: -0.75 (0.40), residues: 183 loop : -1.34 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 99 HIS 0.007 0.001 HIS A 387 PHE 0.021 0.001 PHE R 282 TYR 0.011 0.001 TYR R 174 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.715 Fit side-chains REVERT: A 154 TRP cc_start: 0.7838 (t-100) cc_final: 0.7143 (t-100) REVERT: A 211 LYS cc_start: 0.8980 (mmtm) cc_final: 0.8702 (mmtm) REVERT: A 331 ASP cc_start: 0.7422 (t0) cc_final: 0.7060 (t70) REVERT: A 368 ASP cc_start: 0.7952 (t0) cc_final: 0.7692 (t0) outliers start: 6 outliers final: 2 residues processed: 85 average time/residue: 0.1338 time to fit residues: 17.0377 Evaluate side-chains 73 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6829 Z= 0.152 Angle : 0.451 6.205 9357 Z= 0.246 Chirality : 0.041 0.150 1129 Planarity : 0.003 0.044 1203 Dihedral : 4.888 84.107 1059 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.57 % Allowed : 17.88 % Favored : 80.55 % 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: 0.30 (0.28), residues: 954 helix: 1.90 (0.27), residues: 411 sheet: -0.61 (0.40), residues: 179 loop : -1.36 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 99 HIS 0.007 0.001 HIS A 387 PHE 0.024 0.001 PHE R 282 TYR 0.010 0.001 TYR A 130 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.800 Fit side-chains REVERT: A 154 TRP cc_start: 0.7813 (t-100) cc_final: 0.7136 (t-100) REVERT: A 211 LYS cc_start: 0.8952 (mmtm) cc_final: 0.8569 (mmtm) REVERT: A 331 ASP cc_start: 0.7308 (t0) cc_final: 0.6873 (t70) REVERT: A 368 ASP cc_start: 0.7958 (t0) cc_final: 0.7598 (t0) REVERT: B 262 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7970 (mpp) REVERT: R 215 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6351 (mmm) outliers start: 8 outliers final: 4 residues processed: 77 average time/residue: 0.1310 time to fit residues: 15.5013 Evaluate side-chains 77 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6829 Z= 0.377 Angle : 0.559 6.008 9357 Z= 0.306 Chirality : 0.045 0.164 1129 Planarity : 0.004 0.050 1203 Dihedral : 5.457 86.814 1059 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.55 % Allowed : 19.25 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.28), residues: 954 helix: 1.70 (0.27), residues: 410 sheet: -0.80 (0.40), residues: 176 loop : -1.51 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 63 HIS 0.007 0.002 HIS B 142 PHE 0.027 0.002 PHE R 282 TYR 0.012 0.001 TYR A 360 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.767 Fit side-chains REVERT: A 154 TRP cc_start: 0.7909 (t-100) cc_final: 0.7180 (t-100) REVERT: A 211 LYS cc_start: 0.8983 (mmtm) cc_final: 0.8602 (mmtm) REVERT: A 331 ASP cc_start: 0.7563 (t0) cc_final: 0.7297 (t70) REVERT: A 368 ASP cc_start: 0.8329 (t0) cc_final: 0.7981 (t0) REVERT: R 215 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6663 (mtm) outliers start: 13 outliers final: 11 residues processed: 80 average time/residue: 0.1450 time to fit residues: 17.2498 Evaluate side-chains 82 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6829 Z= 0.185 Angle : 0.479 6.117 9357 Z= 0.262 Chirality : 0.042 0.155 1129 Planarity : 0.003 0.047 1203 Dihedral : 5.186 85.793 1059 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.55 % Allowed : 19.45 % Favored : 78.00 % 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: 0.15 (0.28), residues: 954 helix: 1.83 (0.27), residues: 411 sheet: -0.73 (0.40), residues: 181 loop : -1.51 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 99 HIS 0.007 0.001 HIS A 387 PHE 0.025 0.001 PHE R 282 TYR 0.009 0.001 TYR R 174 ARG 0.006 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.785 Fit side-chains REVERT: A 154 TRP cc_start: 0.7852 (t-100) cc_final: 0.7164 (t-100) REVERT: A 211 LYS cc_start: 0.8999 (mmtm) cc_final: 0.8596 (mmtm) REVERT: A 331 ASP cc_start: 0.7470 (t0) cc_final: 0.7235 (t70) REVERT: A 368 ASP cc_start: 0.8233 (t0) cc_final: 0.7863 (t0) REVERT: R 215 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6223 (mmm) outliers start: 13 outliers final: 9 residues processed: 86 average time/residue: 0.1347 time to fit residues: 17.9255 Evaluate side-chains 84 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 52 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 chunk 58 optimal weight: 0.0770 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 6829 Z= 0.133 Angle : 0.450 6.196 9357 Z= 0.244 Chirality : 0.041 0.139 1129 Planarity : 0.003 0.046 1203 Dihedral : 4.890 83.826 1059 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.16 % Allowed : 20.24 % Favored : 77.60 % 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: 0.39 (0.28), residues: 954 helix: 2.05 (0.27), residues: 411 sheet: -0.56 (0.41), residues: 174 loop : -1.43 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 99 HIS 0.007 0.001 HIS R 172 PHE 0.023 0.001 PHE R 282 TYR 0.010 0.001 TYR A 391 ARG 0.006 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.856 Fit side-chains REVERT: A 211 LYS cc_start: 0.9035 (mmtm) cc_final: 0.8641 (mmtm) REVERT: A 331 ASP cc_start: 0.7294 (t0) cc_final: 0.6969 (t70) REVERT: A 368 ASP cc_start: 0.8094 (t0) cc_final: 0.7627 (t0) REVERT: B 292 PHE cc_start: 0.8890 (m-80) cc_final: 0.8385 (m-80) REVERT: R 215 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6249 (mmm) outliers start: 11 outliers final: 6 residues processed: 81 average time/residue: 0.1362 time to fit residues: 16.9972 Evaluate side-chains 79 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.0570 chunk 28 optimal weight: 0.0870 chunk 18 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6829 Z= 0.112 Angle : 0.438 7.545 9357 Z= 0.237 Chirality : 0.040 0.146 1129 Planarity : 0.003 0.045 1203 Dihedral : 4.688 81.938 1059 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.77 % Allowed : 20.63 % Favored : 77.60 % 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: 0.63 (0.29), residues: 954 helix: 2.22 (0.27), residues: 409 sheet: -0.30 (0.41), residues: 173 loop : -1.32 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.006 0.001 HIS A 387 PHE 0.023 0.001 PHE R 282 TYR 0.016 0.001 TYR A 391 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.835 Fit side-chains REVERT: A 211 LYS cc_start: 0.9031 (mmtm) cc_final: 0.8659 (mmtm) REVERT: A 331 ASP cc_start: 0.7166 (t0) cc_final: 0.6925 (t70) REVERT: B 292 PHE cc_start: 0.8837 (m-80) cc_final: 0.8341 (m-80) REVERT: R 215 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.6100 (mmm) outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 0.1263 time to fit residues: 15.9534 Evaluate side-chains 79 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 4.9990 chunk 89 optimal weight: 0.0470 chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6829 Z= 0.209 Angle : 0.488 6.761 9357 Z= 0.263 Chirality : 0.042 0.170 1129 Planarity : 0.003 0.046 1203 Dihedral : 4.901 83.131 1059 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.16 % Allowed : 21.81 % Favored : 76.03 % 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: 0.54 (0.29), residues: 954 helix: 2.16 (0.27), residues: 410 sheet: -0.46 (0.42), residues: 176 loop : -1.34 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.006 0.001 HIS R 172 PHE 0.023 0.001 PHE R 282 TYR 0.016 0.001 TYR A 391 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.813 Fit side-chains REVERT: A 211 LYS cc_start: 0.9041 (mmtm) cc_final: 0.8660 (mmtm) REVERT: A 331 ASP cc_start: 0.7237 (t0) cc_final: 0.6896 (t70) REVERT: R 215 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6048 (mmm) outliers start: 11 outliers final: 8 residues processed: 79 average time/residue: 0.1230 time to fit residues: 14.9969 Evaluate side-chains 80 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 76 optimal weight: 0.2980 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6829 Z= 0.157 Angle : 0.471 8.044 9357 Z= 0.252 Chirality : 0.041 0.163 1129 Planarity : 0.003 0.045 1203 Dihedral : 4.859 83.027 1059 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.96 % Allowed : 21.41 % Favored : 76.62 % 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 (0.29), residues: 954 helix: 2.17 (0.27), residues: 410 sheet: -0.38 (0.42), residues: 176 loop : -1.40 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 339 HIS 0.007 0.001 HIS R 172 PHE 0.023 0.001 PHE R 282 TYR 0.020 0.001 TYR A 391 ARG 0.005 0.000 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.780 Fit side-chains REVERT: A 211 LYS cc_start: 0.9043 (mmtm) cc_final: 0.8612 (mmtm) REVERT: A 331 ASP cc_start: 0.7211 (t0) cc_final: 0.6921 (t70) REVERT: A 368 ASP cc_start: 0.7771 (t70) cc_final: 0.6978 (t0) REVERT: B 292 PHE cc_start: 0.8823 (m-80) cc_final: 0.8281 (m-80) REVERT: R 215 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.5985 (mmm) outliers start: 10 outliers final: 8 residues processed: 78 average time/residue: 0.1282 time to fit residues: 15.3689 Evaluate side-chains 81 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.140317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.103999 restraints weight = 11816.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.106875 restraints weight = 6535.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108819 restraints weight = 4633.477| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6829 Z= 0.148 Angle : 0.470 7.880 9357 Z= 0.250 Chirality : 0.041 0.160 1129 Planarity : 0.003 0.045 1203 Dihedral : 4.818 82.840 1059 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.16 % Allowed : 21.22 % Favored : 76.62 % 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: 0.60 (0.29), residues: 954 helix: 2.22 (0.27), residues: 408 sheet: -0.33 (0.42), residues: 175 loop : -1.34 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 339 HIS 0.007 0.001 HIS R 172 PHE 0.023 0.001 PHE R 282 TYR 0.017 0.001 TYR A 391 ARG 0.004 0.000 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1556.72 seconds wall clock time: 29 minutes 8.10 seconds (1748.10 seconds total)