Starting phenix.real_space_refine on Sat Dec 9 09:17:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/12_2023/7rpo_24618_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/12_2023/7rpo_24618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/12_2023/7rpo_24618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/12_2023/7rpo_24618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/12_2023/7rpo_24618_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/12_2023/7rpo_24618_updated.pdb" } resolution = 4.16 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= 0.001 sd= 0.026 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: 6 Type Number sf(0) Gaussians Mn 4 7.51 5 P 63 5.49 5 S 25 5.16 5 C 6571 2.51 5 N 1753 2.21 5 O 2186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1953 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "B" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1922 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "C" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1941 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 5, 'TRANS': 239} Chain: "X" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 229 Classifications: {'DNA': 11} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 10} Chain: "Z" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "E" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3489 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 13, 'TRANS': 425} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MN': 2} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 6.29, per 1000 atoms: 0.59 Number of scatterers: 10602 At special positions: 0 Unit cell: (118.5, 109.5, 124.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 4 24.99 S 25 16.00 P 63 15.00 O 2186 8.00 N 1753 7.00 C 6571 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.27 Conformation dependent library (CDL) restraints added in 1.8 seconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2218 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 12 sheets defined 24.3% alpha, 21.0% beta 30 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 4.81 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 4.138A pdb=" N SER A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.679A pdb=" N SER A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.599A pdb=" N VAL A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 202 through 211 removed outlier: 3.538A pdb=" N GLY A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 21 removed outlier: 3.909A pdb=" N ASP B 21 " --> pdb=" O ARG B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.572A pdb=" N ASN B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 200 through 206 removed outlier: 3.801A pdb=" N THR B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 18 removed outlier: 3.851A pdb=" N ILE C 14 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 137 through 148 removed outlier: 3.662A pdb=" N SER C 141 " --> pdb=" O ASP C 137 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'E' and resid 4 through 13 removed outlier: 3.889A pdb=" N LYS E 12 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU E 13 " --> pdb=" O TYR E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.778A pdb=" N THR E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA E 27 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 removed outlier: 3.893A pdb=" N GLN E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 removed outlier: 4.117A pdb=" N ILE E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 87 removed outlier: 3.727A pdb=" N THR E 87 " --> pdb=" O ASN E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 94 No H-bonds generated for 'chain 'E' and resid 91 through 94' Processing helix chain 'E' and resid 97 through 99 No H-bonds generated for 'chain 'E' and resid 97 through 99' Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.583A pdb=" N LEU E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 153 removed outlier: 3.530A pdb=" N ARG E 145 " --> pdb=" O ASP E 141 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU E 151 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 167 removed outlier: 3.628A pdb=" N PHE E 161 " --> pdb=" O GLU E 158 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU E 162 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL E 163 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 188 Processing helix chain 'E' and resid 191 through 203 removed outlier: 4.039A pdb=" N GLU E 195 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE E 196 " --> pdb=" O ALA E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 291 through 293 No H-bonds generated for 'chain 'E' and resid 291 through 293' Processing helix chain 'E' and resid 295 through 298 No H-bonds generated for 'chain 'E' and resid 295 through 298' Processing helix chain 'E' and resid 324 through 329 removed outlier: 3.835A pdb=" N HIS E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 342 No H-bonds generated for 'chain 'E' and resid 340 through 342' Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'E' and resid 393 through 405 removed outlier: 3.582A pdb=" N LYS E 397 " --> pdb=" O VAL E 393 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N SER E 398 " --> pdb=" O GLU E 394 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.520A pdb=" N ILE A 101 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 100 " --> pdb=" O ILE A 113 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 66 through 71 removed outlier: 3.816A pdb=" N THR A 66 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N SER A 25 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU A 40 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE A 27 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG A 38 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 29 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 36 " --> pdb=" O ASN A 29 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 31 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 35 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 50 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS A 39 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 48 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 51 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 241 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 233 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 231 " --> pdb=" O PHE A 243 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 135 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 191 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 137 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU A 189 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 157 through 160 removed outlier: 3.653A pdb=" N ARG A 158 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 169 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 166 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 168 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 170 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 177 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.652A pdb=" N SER B 92 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 99 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 68 through 72 removed outlier: 3.948A pdb=" N PHE B 71 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 26 " --> pdb=" O PHE B 71 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLU B 25 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN B 27 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER B 38 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 36 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 35 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 48 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 49 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR B 236 " --> pdb=" O PHE B 51 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B 228 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B 214 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 194 through 197 removed outlier: 3.839A pdb=" N LEU B 163 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 178 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 2 through 5 removed outlier: 4.161A pdb=" N ALA C 86 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE C 102 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 24 through 28 removed outlier: 4.225A pdb=" N ALA C 25 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE C 69 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE C 67 " --> pdb=" O LEU C 27 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 33 through 39 removed outlier: 3.671A pdb=" N ALA C 38 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE C 47 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 46 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER C 48 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS C 235 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 236 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 228 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 238 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 226 " --> pdb=" O TYR C 238 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 193 through 197 Processing sheet with id= K, first strand: chain 'E' and resid 257 through 260 removed outlier: 3.956A pdb=" N GLY E 410 " --> pdb=" O LYS E 260 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL E 411 " --> pdb=" O LEU E 434 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 434 " --> pdb=" O VAL E 411 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 432 " --> pdb=" O VAL E 413 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 275 through 278 removed outlier: 3.626A pdb=" N GLY E 309 " --> pdb=" O ALA E 266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS E 270 " --> pdb=" O PHE E 305 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP E 351 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU E 310 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU E 349 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL E 312 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL E 347 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE E 314 " --> pdb=" O VAL E 345 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL E 345 " --> pdb=" O ILE E 314 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2890 1.33 - 1.45: 1884 1.45 - 1.57: 5953 1.57 - 1.69: 122 1.69 - 1.80: 50 Bond restraints: 10899 Sorted by residual: bond pdb=" C4' AMP E 701 " pdb=" O4' AMP E 701 " ideal model delta sigma weight residual 1.454 1.429 0.025 1.50e-02 4.44e+03 2.72e+00 bond pdb=" CA LYS C 178 " pdb=" C LYS C 178 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.72e-02 3.38e+03 1.77e+00 bond pdb=" N GLY E 309 " pdb=" CA GLY E 309 " ideal model delta sigma weight residual 1.453 1.442 0.011 8.60e-03 1.35e+04 1.65e+00 bond pdb=" C3' DA Z 22 " pdb=" O3' DA Z 22 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" C3' DT Z 30 " pdb=" O3' DT Z 30 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.45e+00 ... (remaining 10894 not shown) Histogram of bond angle deviations from ideal: 98.82 - 106.23: 545 106.23 - 113.64: 6114 113.64 - 121.06: 5141 121.06 - 128.47: 3090 128.47 - 135.88: 73 Bond angle restraints: 14963 Sorted by residual: angle pdb=" C LEU A 249 " pdb=" CA LEU A 249 " pdb=" CB LEU A 249 " ideal model delta sigma weight residual 117.23 109.96 7.27 1.36e+00 5.41e-01 2.86e+01 angle pdb=" C1' AMP E 701 " pdb=" C2' AMP E 701 " pdb=" C3' AMP E 701 " ideal model delta sigma weight residual 101.50 105.65 -4.15 1.00e+00 1.00e+00 1.73e+01 angle pdb=" CA LEU A 249 " pdb=" C LEU A 249 " pdb=" N LEU A 250 " ideal model delta sigma weight residual 119.98 116.82 3.16 8.50e-01 1.38e+00 1.38e+01 angle pdb=" C2' AMP E 701 " pdb=" C3' AMP E 701 " pdb=" C4' AMP E 701 " ideal model delta sigma weight residual 102.60 106.06 -3.46 1.00e+00 1.00e+00 1.20e+01 angle pdb=" C3' AMP E 701 " pdb=" C4' AMP E 701 " pdb=" C5' AMP E 701 " ideal model delta sigma weight residual 115.20 110.34 4.86 1.50e+00 4.44e-01 1.05e+01 ... (remaining 14958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.40: 6078 30.40 - 60.80: 380 60.80 - 91.19: 4 91.19 - 121.59: 0 121.59 - 151.99: 5 Dihedral angle restraints: 6467 sinusoidal: 3035 harmonic: 3432 Sorted by residual: dihedral pdb=" C4' DT Z 30 " pdb=" C3' DT Z 30 " pdb=" O3' DT Z 30 " pdb=" P DC Z 31 " ideal model delta sinusoidal sigma weight residual 220.00 68.01 151.99 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" C4' DA Z 22 " pdb=" C3' DA Z 22 " pdb=" O3' DA Z 22 " pdb=" P DC Z 23 " ideal model delta sinusoidal sigma weight residual 220.00 70.14 149.86 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C4' DC Z 26 " pdb=" C3' DC Z 26 " pdb=" O3' DC Z 26 " pdb=" P DG Z 27 " ideal model delta sinusoidal sigma weight residual 220.00 71.90 148.10 1 3.50e+01 8.16e-04 1.45e+01 ... (remaining 6464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1111 0.030 - 0.060: 401 0.060 - 0.089: 100 0.089 - 0.119: 96 0.119 - 0.149: 15 Chirality restraints: 1723 Sorted by residual: chirality pdb=" C3' AMP E 701 " pdb=" C2' AMP E 701 " pdb=" C4' AMP E 701 " pdb=" O3' AMP E 701 " both_signs ideal model delta sigma weight residual False -2.74 -2.60 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE E 306 " pdb=" N ILE E 306 " pdb=" C ILE E 306 " pdb=" CB ILE E 306 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE B 68 " pdb=" N ILE B 68 " pdb=" C ILE B 68 " pdb=" CB ILE B 68 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1720 not shown) Planarity restraints: 1683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 93 " 0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO C 94 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 94 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 94 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 121 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO C 122 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 122 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 122 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 227 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO A 228 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " -0.018 5.00e-02 4.00e+02 ... (remaining 1680 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 28 2.39 - 3.02: 5717 3.02 - 3.64: 15002 3.64 - 4.27: 21396 4.27 - 4.90: 35089 Nonbonded interactions: 77232 Sorted by model distance: nonbonded pdb=" O1P AMP E 701 " pdb="MN MN E 703 " model vdw 1.759 2.320 nonbonded pdb=" O GLY E 60 " pdb="MN MN X 101 " model vdw 1.776 2.320 nonbonded pdb=" OE2 GLU E 409 " pdb="MN MN E 703 " model vdw 1.815 2.320 nonbonded pdb=" O3' DG X 20 " pdb="MN MN X 101 " model vdw 2.187 2.320 nonbonded pdb=" OG SER C 211 " pdb=" O ASN C 229 " model vdw 2.192 2.440 ... (remaining 77227 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=0.50 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: 0.350 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: 1.970 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 33.970 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 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 0.044 10899 Z= 0.155 Angle : 0.505 7.267 14963 Z= 0.288 Chirality : 0.040 0.149 1723 Planarity : 0.003 0.034 1683 Dihedral : 16.976 151.990 4249 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 1.64 % Allowed : 9.76 % Favored : 88.60 % 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: -2.01 (0.25), residues: 1171 helix: -0.03 (0.33), residues: 294 sheet: -0.27 (0.32), residues: 303 loop : -2.74 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 50 HIS 0.002 0.001 HIS A 39 PHE 0.010 0.001 PHE C 228 TYR 0.008 0.001 TYR A 177 ARG 0.002 0.000 ARG E 330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 397 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 410 average time/residue: 0.2805 time to fit residues: 151.7669 Evaluate side-chains 319 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 315 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2475 time to fit residues: 2.8802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 95 optimal weight: 0.0060 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.0050 chunk 110 optimal weight: 7.9990 overall best weight: 0.3770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN B 116 GLN E 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10899 Z= 0.169 Angle : 0.576 8.117 14963 Z= 0.313 Chirality : 0.043 0.178 1723 Planarity : 0.004 0.053 1683 Dihedral : 20.726 149.590 1931 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: -1.92 (0.24), residues: 1171 helix: -0.03 (0.33), residues: 275 sheet: 0.17 (0.32), residues: 305 loop : -2.81 (0.22), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 50 HIS 0.002 0.001 HIS A 39 PHE 0.021 0.002 PHE E 10 TYR 0.009 0.001 TYR E 299 ARG 0.004 0.000 ARG E 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.2961 time to fit residues: 131.6410 Evaluate side-chains 297 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 75 ASN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 10899 Z= 0.411 Angle : 0.747 10.911 14963 Z= 0.407 Chirality : 0.048 0.173 1723 Planarity : 0.005 0.055 1683 Dihedral : 21.230 157.313 1931 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.13 % Favored : 87.79 % Rotamer: Outliers : 0.10 % Allowed : 4.73 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.23), residues: 1171 helix: -1.03 (0.30), residues: 285 sheet: -0.48 (0.31), residues: 299 loop : -3.00 (0.22), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP E 50 HIS 0.004 0.001 HIS E 269 PHE 0.025 0.003 PHE C 228 TYR 0.035 0.003 TYR C 59 ARG 0.011 0.001 ARG E 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 348 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 349 average time/residue: 0.2901 time to fit residues: 131.8835 Evaluate side-chains 300 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.169 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 0.0030 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10899 Z= 0.236 Angle : 0.632 8.107 14963 Z= 0.342 Chirality : 0.045 0.163 1723 Planarity : 0.005 0.058 1683 Dihedral : 21.102 153.605 1931 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: -2.49 (0.24), residues: 1171 helix: -0.80 (0.31), residues: 280 sheet: -0.17 (0.32), residues: 299 loop : -3.01 (0.22), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 50 HIS 0.003 0.001 HIS A 39 PHE 0.029 0.002 PHE E 324 TYR 0.020 0.001 TYR C 59 ARG 0.005 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.3093 time to fit residues: 139.4763 Evaluate side-chains 301 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN B 157 HIS ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10899 Z= 0.276 Angle : 0.663 8.723 14963 Z= 0.357 Chirality : 0.045 0.183 1723 Planarity : 0.005 0.057 1683 Dihedral : 21.149 155.559 1931 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.47 % Favored : 87.53 % Rotamer: Outliers : 0.10 % Allowed : 2.90 % Favored : 97.00 % 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: -2.60 (0.23), residues: 1171 helix: -0.92 (0.31), residues: 281 sheet: -0.24 (0.32), residues: 301 loop : -3.07 (0.22), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 50 HIS 0.008 0.001 HIS B 157 PHE 0.025 0.002 PHE C 139 TYR 0.019 0.002 TYR C 59 ARG 0.006 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 342 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 342 average time/residue: 0.2971 time to fit residues: 132.4170 Evaluate side-chains 290 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1120 time to fit residues: 2.0504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN B 116 GLN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10899 Z= 0.220 Angle : 0.634 11.373 14963 Z= 0.341 Chirality : 0.045 0.172 1723 Planarity : 0.005 0.063 1683 Dihedral : 21.110 154.129 1931 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 0.10 % Allowed : 1.74 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.24), residues: 1171 helix: -0.77 (0.31), residues: 278 sheet: -0.00 (0.32), residues: 291 loop : -3.03 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 50 HIS 0.003 0.001 HIS E 386 PHE 0.029 0.002 PHE E 324 TYR 0.019 0.001 TYR C 59 ARG 0.009 0.001 ARG E 234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.2962 time to fit residues: 130.6359 Evaluate side-chains 294 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 0.1980 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 0.0970 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN E 228 GLN ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10899 Z= 0.184 Angle : 0.632 12.520 14963 Z= 0.335 Chirality : 0.044 0.160 1723 Planarity : 0.004 0.063 1683 Dihedral : 21.077 152.281 1931 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 0.10 % Allowed : 1.55 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.24), residues: 1171 helix: -0.55 (0.32), residues: 276 sheet: 0.08 (0.32), residues: 289 loop : -2.94 (0.22), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 50 HIS 0.003 0.001 HIS A 39 PHE 0.023 0.002 PHE E 10 TYR 0.018 0.001 TYR C 59 ARG 0.006 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 317 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 318 average time/residue: 0.2959 time to fit residues: 122.3328 Evaluate side-chains 281 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 92 optimal weight: 0.0010 chunk 106 optimal weight: 2.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 116 GLN B 155 ASN B 157 HIS C 72 GLN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10899 Z= 0.288 Angle : 0.692 14.684 14963 Z= 0.367 Chirality : 0.046 0.192 1723 Planarity : 0.005 0.069 1683 Dihedral : 21.239 155.778 1931 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 0.19 % Allowed : 1.26 % Favored : 98.55 % 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: -2.41 (0.24), residues: 1171 helix: -0.70 (0.31), residues: 278 sheet: -0.07 (0.32), residues: 298 loop : -3.00 (0.22), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 50 HIS 0.008 0.001 HIS B 157 PHE 0.032 0.002 PHE E 324 TYR 0.025 0.002 TYR C 59 ARG 0.006 0.001 ARG E 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 319 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 319 average time/residue: 0.2965 time to fit residues: 124.4475 Evaluate side-chains 273 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 272 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1097 time to fit residues: 1.7445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 65 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN E 75 ASN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10899 Z= 0.191 Angle : 0.642 10.209 14963 Z= 0.339 Chirality : 0.044 0.163 1723 Planarity : 0.005 0.066 1683 Dihedral : 21.134 152.547 1931 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.24), residues: 1171 helix: -0.54 (0.32), residues: 268 sheet: 0.01 (0.32), residues: 300 loop : -2.81 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP E 50 HIS 0.003 0.001 HIS A 39 PHE 0.021 0.002 PHE C 218 TYR 0.014 0.001 TYR C 59 ARG 0.006 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.2932 time to fit residues: 125.6573 Evaluate side-chains 293 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.0270 chunk 54 optimal weight: 0.0050 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.4980 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.4452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN B 116 GLN B 157 HIS E 75 ASN ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10899 Z= 0.180 Angle : 0.646 9.907 14963 Z= 0.342 Chirality : 0.044 0.175 1723 Planarity : 0.005 0.071 1683 Dihedral : 21.095 149.957 1931 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.24), residues: 1171 helix: -0.58 (0.32), residues: 276 sheet: 0.11 (0.32), residues: 302 loop : -2.85 (0.22), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 50 HIS 0.008 0.001 HIS B 157 PHE 0.035 0.002 PHE E 324 TYR 0.015 0.001 TYR E 354 ARG 0.007 0.000 ARG A 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.3237 time to fit residues: 137.1732 Evaluate side-chains 293 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.249 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.0030 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN E 75 ASN ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.138693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.115801 restraints weight = 19189.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118597 restraints weight = 12208.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120530 restraints weight = 8767.613| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10899 Z= 0.194 Angle : 0.647 10.063 14963 Z= 0.341 Chirality : 0.044 0.155 1723 Planarity : 0.005 0.072 1683 Dihedral : 21.119 150.344 1931 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.24), residues: 1171 helix: -0.51 (0.32), residues: 275 sheet: 0.06 (0.32), residues: 302 loop : -2.84 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 50 HIS 0.004 0.001 HIS E 329 PHE 0.025 0.002 PHE E 10 TYR 0.013 0.001 TYR C 59 ARG 0.006 0.000 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2967.48 seconds wall clock time: 54 minutes 7.78 seconds (3247.78 seconds total)