Starting phenix.real_space_refine on Sat Apr 6 04:24:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gga_40000/04_2024/8gga_40000_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gga_40000/04_2024/8gga_40000.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/8gga_40000/04_2024/8gga_40000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gga_40000/04_2024/8gga_40000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gga_40000/04_2024/8gga_40000_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gga_40000/04_2024/8gga_40000_updated.pdb" } 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= 0.021 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 41 5.16 5 C 4438 2.51 5 N 1224 2.21 5 O 1289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6995 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2318 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 488 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 255 Chain: "B" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2454 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 113 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: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 1824 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 7, 'TRANS': 261} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 173 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: 4.35, per 1000 atoms: 0.62 Number of scatterers: 6995 At special positions: 0 Unit cell: (83.2992, 135.361, 102.389, 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 41 16.00 P 3 15.00 O 1289 8.00 N 1224 7.00 C 4438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.3 seconds 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1874 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 8 sheets defined 44.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.641A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 removed outlier: 3.642A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 110 removed outlier: 3.637A pdb=" N GLU A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.540A pdb=" N GLU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU A 153 " --> pdb=" O HIS A 149 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TRP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 removed outlier: 3.572A pdb=" N CYS A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 4.119A pdb=" N GLN A 176 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 177 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE A 178 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 179 " --> pdb=" O GLN A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 179' Processing helix chain 'A' and resid 233 through 236 removed outlier: 4.196A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.657A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.602A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 392 removed outlier: 4.679A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 removed outlier: 3.743A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'G' and resid 10 through 23 removed outlier: 3.693A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'R' and resid 32 through 60 removed outlier: 3.750A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL R 52 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 96 Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.515A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE R 133 " --> pdb=" O VAL R 129 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA R 134 " --> pdb=" O ASP R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 171 removed outlier: 3.658A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 4.268A 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 181 through 186 Processing helix chain 'R' and resid 197 through 236 removed outlier: 5.564A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.540A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 298 removed outlier: 3.945A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.931A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 325 removed outlier: 3.680A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 359 through 362 removed outlier: 7.415A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.730A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 103 removed outlier: 7.096A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.965A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.940A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.821A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.705A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.756A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 309 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: 1.90 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2299 1.34 - 1.46: 1053 1.46 - 1.57: 3719 1.57 - 1.69: 5 1.69 - 1.81: 56 Bond restraints: 7132 Sorted by residual: bond pdb=" N THR A 204 " pdb=" CA THR A 204 " ideal model delta sigma weight residual 1.457 1.497 -0.041 1.24e-02 6.50e+03 1.08e+01 bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.65e+00 bond pdb=" N ILE A 207 " pdb=" CA ILE A 207 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.25e-02 6.40e+03 8.39e+00 bond pdb=" N SER A 205 " pdb=" CA SER A 205 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.27e+00 bond pdb=" N PHE R 133 " pdb=" CA PHE R 133 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.21e-02 6.83e+03 8.13e+00 ... (remaining 7127 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.08: 163 107.08 - 113.83: 4039 113.83 - 120.58: 2890 120.58 - 127.33: 2595 127.33 - 134.08: 75 Bond angle restraints: 9762 Sorted by residual: angle pdb=" C ASP A 223 " pdb=" CA ASP A 223 " pdb=" CB ASP A 223 " ideal model delta sigma weight residual 110.62 101.55 9.07 1.51e+00 4.39e-01 3.60e+01 angle pdb=" N ARG A 231 " pdb=" CA ARG A 231 " pdb=" C ARG A 231 " ideal model delta sigma weight residual 113.43 107.03 6.40 1.26e+00 6.30e-01 2.58e+01 angle pdb=" CA LEU A 203 " pdb=" C LEU A 203 " pdb=" O LEU A 203 " ideal model delta sigma weight residual 121.28 116.55 4.73 1.18e+00 7.18e-01 1.61e+01 angle pdb=" CA GLY A 206 " pdb=" C GLY A 206 " pdb=" O GLY A 206 " ideal model delta sigma weight residual 121.58 118.00 3.58 9.00e-01 1.23e+00 1.58e+01 angle pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sigma weight residual 120.50 132.34 -11.84 3.00e+00 1.11e-01 1.56e+01 ... (remaining 9757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.13: 4009 28.13 - 56.25: 127 56.25 - 84.38: 8 84.38 - 112.51: 2 112.51 - 140.64: 3 Dihedral angle restraints: 4149 sinusoidal: 1269 harmonic: 2880 Sorted by residual: 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 303.79 163.16 140.64 1 2.00e+01 2.50e-03 4.26e+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 -158.46 -132.27 1 2.00e+01 2.50e-03 4.01e+01 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 -65.39 -117.31 1 2.00e+01 2.50e-03 3.50e+01 ... (remaining 4146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 892 0.047 - 0.094: 203 0.094 - 0.140: 65 0.140 - 0.187: 7 0.187 - 0.234: 2 Chirality restraints: 1169 Sorted by residual: chirality pdb=" CA ASP A 223 " pdb=" N ASP A 223 " pdb=" C ASP A 223 " pdb=" CB ASP A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA VAL A 202 " pdb=" N VAL A 202 " pdb=" C VAL A 202 " pdb=" CB VAL A 202 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA ARG A 201 " pdb=" N ARG A 201 " pdb=" C ARG A 201 " pdb=" CB ARG A 201 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1166 not shown) Planarity restraints: 1247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 131 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C ARG R 131 " -0.066 2.00e-02 2.50e+03 pdb=" O ARG R 131 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR R 132 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 198 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C LEU A 198 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 198 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A 199 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO R 168 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.026 5.00e-02 4.00e+02 ... (remaining 1244 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 945 2.75 - 3.29: 6614 3.29 - 3.83: 10825 3.83 - 4.36: 11779 4.36 - 4.90: 21600 Nonbonded interactions: 51763 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.215 2.440 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.312 2.440 nonbonded pdb=" O PHE R 133 " pdb=" N SER R 137 " model vdw 2.353 2.520 nonbonded pdb=" ND2 ASN R 51 " pdb=" O ALA R 76 " model vdw 2.355 2.520 nonbonded pdb=" ND2 ASN A 23 " pdb=" OD1 ASN B 88 " model vdw 2.359 2.520 ... (remaining 51758 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.720 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.050 Find NCS groups from input model: 0.240 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.004 0.055 7132 Z= 0.259 Angle : 0.667 11.840 9762 Z= 0.378 Chirality : 0.045 0.234 1169 Planarity : 0.005 0.073 1247 Dihedral : 14.504 140.637 2275 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -0.34 (0.27), residues: 968 helix: 1.15 (0.26), residues: 416 sheet: -1.14 (0.44), residues: 163 loop : -1.29 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.010 0.001 HIS R 296 PHE 0.010 0.001 PHE B 235 TYR 0.012 0.001 TYR R 132 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.862 Fit side-chains REVERT: A 177 TYR cc_start: 0.7961 (t80) cc_final: 0.7056 (t80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1806 time to fit residues: 21.2778 Evaluate side-chains 64 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7132 Z= 0.319 Angle : 0.543 6.132 9762 Z= 0.296 Chirality : 0.044 0.139 1169 Planarity : 0.004 0.040 1247 Dihedral : 8.332 125.602 1073 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.66 % Allowed : 10.28 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.27), residues: 968 helix: 1.47 (0.25), residues: 419 sheet: -1.10 (0.43), residues: 163 loop : -1.36 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.012 0.002 HIS R 296 PHE 0.019 0.002 PHE B 235 TYR 0.016 0.001 TYR B 105 ARG 0.003 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.762 Fit side-chains REVERT: A 177 TYR cc_start: 0.7922 (t80) cc_final: 0.7019 (t80) REVERT: B 59 TYR cc_start: 0.8612 (m-80) cc_final: 0.8359 (m-80) REVERT: B 75 GLN cc_start: 0.8487 (mt0) cc_final: 0.8023 (mt0) REVERT: R 294 ILE cc_start: 0.7490 (mm) cc_final: 0.7262 (mm) outliers start: 10 outliers final: 10 residues processed: 73 average time/residue: 0.1700 time to fit residues: 17.6031 Evaluate side-chains 72 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 131 ARG Chi-restraints excluded: chain R residue 136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 0.0470 chunk 94 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 7132 Z= 0.154 Angle : 0.441 6.362 9762 Z= 0.238 Chirality : 0.040 0.137 1169 Planarity : 0.003 0.036 1247 Dihedral : 7.260 125.714 1073 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.16 % Allowed : 13.93 % Favored : 84.91 % 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: 0.20 (0.27), residues: 968 helix: 1.85 (0.26), residues: 422 sheet: -0.91 (0.42), residues: 164 loop : -1.36 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.009 0.001 HIS R 296 PHE 0.010 0.001 PHE R 223 TYR 0.008 0.001 TYR R 308 ARG 0.002 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.847 Fit side-chains REVERT: A 177 TYR cc_start: 0.7925 (t80) cc_final: 0.7048 (t80) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.1501 time to fit residues: 16.0979 Evaluate side-chains 69 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 115 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 0.0070 chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7132 Z= 0.254 Angle : 0.493 6.702 9762 Z= 0.266 Chirality : 0.042 0.132 1169 Planarity : 0.003 0.037 1247 Dihedral : 6.951 124.703 1073 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.99 % Allowed : 16.42 % Favored : 81.59 % 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: 968 helix: 1.81 (0.26), residues: 425 sheet: -0.90 (0.42), residues: 163 loop : -1.43 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.007 0.001 HIS R 296 PHE 0.016 0.002 PHE B 235 TYR 0.013 0.001 TYR R 308 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.827 Fit side-chains REVERT: A 177 TYR cc_start: 0.7958 (t80) cc_final: 0.7056 (t80) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 0.1554 time to fit residues: 15.9096 Evaluate side-chains 73 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 201 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7132 Z= 0.167 Angle : 0.445 6.791 9762 Z= 0.238 Chirality : 0.041 0.132 1169 Planarity : 0.003 0.036 1247 Dihedral : 6.818 127.230 1073 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.32 % Allowed : 17.08 % Favored : 80.60 % 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: 0.33 (0.28), residues: 968 helix: 2.01 (0.26), residues: 422 sheet: -0.82 (0.41), residues: 163 loop : -1.39 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.007 0.001 HIS R 296 PHE 0.010 0.001 PHE B 199 TYR 0.014 0.001 TYR R 174 ARG 0.001 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.955 Fit side-chains REVERT: A 177 TYR cc_start: 0.7934 (t80) cc_final: 0.7075 (t80) outliers start: 14 outliers final: 9 residues processed: 73 average time/residue: 0.1616 time to fit residues: 17.5965 Evaluate side-chains 73 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 282 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 0.0770 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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: 0.8039 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7132 Z= 0.154 Angle : 0.436 6.721 9762 Z= 0.233 Chirality : 0.041 0.130 1169 Planarity : 0.003 0.034 1247 Dihedral : 6.672 124.666 1073 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.16 % Allowed : 18.57 % Favored : 79.27 % 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: 0.42 (0.28), residues: 968 helix: 2.11 (0.26), residues: 422 sheet: -0.83 (0.41), residues: 164 loop : -1.34 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.008 0.001 HIS R 296 PHE 0.011 0.001 PHE B 199 TYR 0.014 0.001 TYR R 174 ARG 0.001 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.794 Fit side-chains REVERT: A 177 TYR cc_start: 0.7937 (t80) cc_final: 0.7082 (t80) outliers start: 13 outliers final: 11 residues processed: 70 average time/residue: 0.1551 time to fit residues: 15.9527 Evaluate side-chains 74 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 0.0010 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 0.0470 overall best weight: 0.5084 ------------------------------------------------------------------------------- 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: 0.8013 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7132 Z= 0.127 Angle : 0.423 6.941 9762 Z= 0.224 Chirality : 0.040 0.131 1169 Planarity : 0.003 0.034 1247 Dihedral : 6.556 123.557 1073 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.16 % Allowed : 18.57 % Favored : 79.27 % 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: 0.58 (0.28), residues: 968 helix: 2.24 (0.26), residues: 419 sheet: -0.63 (0.41), residues: 165 loop : -1.29 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.008 0.001 HIS R 296 PHE 0.014 0.001 PHE A 376 TYR 0.014 0.001 TYR R 174 ARG 0.001 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.761 Fit side-chains REVERT: A 177 TYR cc_start: 0.7977 (t80) cc_final: 0.7105 (t80) outliers start: 13 outliers final: 9 residues processed: 77 average time/residue: 0.1836 time to fit residues: 20.8538 Evaluate side-chains 75 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 0.0070 chunk 8 optimal weight: 30.0000 chunk 72 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 0.0040 overall best weight: 0.6814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7132 Z= 0.149 Angle : 0.438 6.749 9762 Z= 0.232 Chirality : 0.040 0.127 1169 Planarity : 0.003 0.034 1247 Dihedral : 6.513 121.155 1073 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.32 % Allowed : 18.08 % Favored : 79.60 % 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: 0.56 (0.28), residues: 968 helix: 2.22 (0.26), residues: 421 sheet: -0.58 (0.42), residues: 165 loop : -1.35 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.008 0.001 HIS R 296 PHE 0.012 0.001 PHE A 376 TYR 0.013 0.001 TYR R 174 ARG 0.001 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.804 Fit side-chains REVERT: A 177 TYR cc_start: 0.7995 (t80) cc_final: 0.7101 (t80) REVERT: R 79 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7870 (t0) outliers start: 14 outliers final: 12 residues processed: 74 average time/residue: 0.1646 time to fit residues: 17.9761 Evaluate side-chains 78 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 282 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 85 optimal weight: 0.0370 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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: 0.8021 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7132 Z= 0.141 Angle : 0.432 7.223 9762 Z= 0.228 Chirality : 0.040 0.128 1169 Planarity : 0.002 0.034 1247 Dihedral : 6.461 119.437 1073 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.82 % Allowed : 18.08 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.28), residues: 968 helix: 2.29 (0.26), residues: 414 sheet: -0.55 (0.41), residues: 169 loop : -1.35 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.008 0.001 HIS R 296 PHE 0.012 0.001 PHE A 376 TYR 0.012 0.001 TYR R 174 ARG 0.001 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 0.998 Fit side-chains REVERT: A 177 TYR cc_start: 0.8045 (t80) cc_final: 0.7106 (t80) REVERT: R 79 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7903 (t0) outliers start: 17 outliers final: 14 residues processed: 78 average time/residue: 0.1724 time to fit residues: 19.6327 Evaluate side-chains 80 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 40.0000 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8025 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7132 Z= 0.154 Angle : 0.442 7.048 9762 Z= 0.234 Chirality : 0.041 0.137 1169 Planarity : 0.003 0.034 1247 Dihedral : 6.440 117.651 1073 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.32 % Allowed : 18.41 % Favored : 79.27 % 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 (0.28), residues: 968 helix: 2.31 (0.26), residues: 419 sheet: -0.54 (0.42), residues: 167 loop : -1.33 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.008 0.001 HIS R 296 PHE 0.015 0.001 PHE A 376 TYR 0.012 0.001 TYR R 174 ARG 0.001 0.000 ARG A 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.819 Fit side-chains REVERT: A 177 TYR cc_start: 0.8044 (t80) cc_final: 0.7112 (t80) outliers start: 14 outliers final: 13 residues processed: 73 average time/residue: 0.1531 time to fit residues: 16.4628 Evaluate side-chains 75 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114773 restraints weight = 10448.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114096 restraints weight = 9339.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115565 restraints weight = 8268.555| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7132 Z= 0.287 Angle : 0.503 6.647 9762 Z= 0.269 Chirality : 0.042 0.132 1169 Planarity : 0.003 0.034 1247 Dihedral : 6.652 115.203 1073 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.16 % Allowed : 18.57 % Favored : 79.27 % 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: 0.43 (0.27), residues: 968 helix: 2.10 (0.26), residues: 420 sheet: -0.62 (0.42), residues: 161 loop : -1.39 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.007 0.001 HIS R 296 PHE 0.016 0.002 PHE B 199 TYR 0.013 0.001 TYR R 308 ARG 0.002 0.000 ARG A 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1552.26 seconds wall clock time: 29 minutes 4.94 seconds (1744.94 seconds total)