Starting phenix.real_space_refine on Sat Jul 20 10:51:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/07_2024/7rpo_24618_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/07_2024/7rpo_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_24618/07_2024/7rpo_24618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/07_2024/7rpo_24618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/07_2024/7rpo_24618_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpo_24618/07_2024/7rpo_24618_neut.cif" } 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-dev-5388/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: 6.33, per 1000 atoms: 0.60 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: 4.69 Conformation dependent library (CDL) restraints added in 2.0 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... Secondary structure from input PDB file: 36 helices and 9 sheets defined 27.8% alpha, 21.5% beta 30 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 removed outlier: 3.600A pdb=" N PHE A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.929A pdb=" N ILE A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 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 161 through 165 removed outlier: 3.960A pdb=" N ASP A 164 " --> pdb=" O THR A 161 " (cutoff:3.500A) 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 10 through 20 Processing helix chain 'B' and resid 73 through 81 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 145 Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.896A pdb=" N LEU B 150 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY B 151 " --> pdb=" O SER B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'C' and resid 9 through 19 removed outlier: 3.935A pdb=" N ASP C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) 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 136 through 147 removed outlier: 3.843A pdb=" N LYS C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 141 " --> pdb=" O ASP C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.838A pdb=" N VAL C 204 " --> pdb=" O LEU C 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 removed outlier: 3.889A pdb=" N LYS E 12 " --> pdb=" O GLU E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 33 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 37 through 47 removed outlier: 3.893A pdb=" N GLN E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY E 47 " --> pdb=" O TYR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 75 removed outlier: 3.649A pdb=" N LEU E 66 " --> pdb=" O GLY E 62 " (cutoff:3.500A) 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 77 through 88 removed outlier: 3.727A pdb=" N THR E 87 " --> pdb=" O ASN E 83 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 97 removed outlier: 4.004A pdb=" N ARG E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 120 through 134 removed outlier: 3.583A pdb=" N LEU E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 153 removed outlier: 3.931A pdb=" N LEU E 142 " --> pdb=" O GLY E 138 " (cutoff:3.500A) 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 160 through 168 removed outlier: 3.924A pdb=" N ARG E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 187 Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 193 through 204 removed outlier: 4.138A pdb=" N ILE E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 218 Processing helix chain 'E' and resid 246 through 252 Processing helix chain 'E' and resid 290 through 293 removed outlier: 3.589A pdb=" N VAL E 293 " --> pdb=" O PRO E 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 290 through 293' Processing helix chain 'E' and resid 294 through 299 Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 339 through 343 Processing helix chain 'E' and resid 366 through 373 Processing helix chain 'E' and resid 392 through 406 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=AA1, 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) removed outlier: 3.853A pdb=" N LYS A 110 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU C 175 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing sheet with id=AA2, 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=AA3, first strand: chain 'A' and resid 176 through 181 removed outlier: 3.747A pdb=" N TYR A 177 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 170 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 168 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 166 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 169 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 158 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY A 171 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU A 156 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 61 removed outlier: 5.231A pdb=" N GLY B 59 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS B 5 " --> pdb=" O GLY B 59 " (cutoff:3.500A) 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=AA5, 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=AA6, 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) removed outlier: 3.637A pdb=" N THR B 173 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 175 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 108 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.714A pdb=" N PHE C 67 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE C 69 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA C 25 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU C 24 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU C 39 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL C 26 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL C 37 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 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=AA8, first strand: chain 'E' and resid 388 through 389 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=AA9, 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: 7.535A pdb=" N ILE E 306 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU E 352 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU E 308 " --> pdb=" O PHE E 350 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL E 312 " --> pdb=" O ASN E 346 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN E 346 " --> pdb=" O VAL E 312 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 849 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: 3.36 Time building geometry restraints manager: 5.13 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: 27 2.39 - 3.02: 5691 3.02 - 3.64: 14979 3.64 - 4.27: 21306 4.27 - 4.90: 35049 Nonbonded interactions: 77052 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 77047 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 33.870 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.640 ------------------------------------------------------------------------------- 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= 0.153 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 : 1.123 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: A 5 VAL cc_start: 0.7540 (t) cc_final: 0.7181 (m) REVERT: A 24 ASP cc_start: 0.5986 (t70) cc_final: 0.5304 (t0) REVERT: A 28 LEU cc_start: 0.7221 (mt) cc_final: 0.6808 (mp) REVERT: A 39 HIS cc_start: 0.7684 (t-90) cc_final: 0.7404 (t-90) REVERT: A 47 MET cc_start: 0.7688 (ttt) cc_final: 0.7285 (ttt) REVERT: A 57 LEU cc_start: 0.8144 (mt) cc_final: 0.7881 (mt) REVERT: A 59 GLU cc_start: 0.8294 (tp30) cc_final: 0.7918 (tp30) REVERT: A 77 LYS cc_start: 0.8708 (pttt) cc_final: 0.8505 (ptpt) REVERT: A 79 LEU cc_start: 0.7529 (mt) cc_final: 0.6939 (mt) REVERT: A 99 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8157 (mtpp) REVERT: A 101 ILE cc_start: 0.7816 (mt) cc_final: 0.7476 (mp) REVERT: A 110 LYS cc_start: 0.7390 (ttmt) cc_final: 0.7137 (ttmm) REVERT: A 136 PHE cc_start: 0.7173 (p90) cc_final: 0.6649 (p90) REVERT: A 156 GLU cc_start: 0.8103 (mp0) cc_final: 0.7807 (mp0) REVERT: A 159 ILE cc_start: 0.8047 (mt) cc_final: 0.7839 (mm) REVERT: A 190 LEU cc_start: 0.7604 (tp) cc_final: 0.7360 (mt) REVERT: A 212 LEU cc_start: 0.7787 (mt) cc_final: 0.7577 (tp) REVERT: A 213 ARG cc_start: 0.7061 (mtt90) cc_final: 0.6718 (mtt90) REVERT: A 221 VAL cc_start: 0.8086 (t) cc_final: 0.7727 (p) REVERT: A 231 ILE cc_start: 0.8109 (mt) cc_final: 0.7564 (tt) REVERT: A 233 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7489 (p) REVERT: B 30 VAL cc_start: 0.8305 (t) cc_final: 0.8098 (t) REVERT: B 78 ASP cc_start: 0.6720 (m-30) cc_final: 0.6407 (m-30) REVERT: B 81 LYS cc_start: 0.7912 (ttmm) cc_final: 0.7663 (ttpp) REVERT: B 156 ILE cc_start: 0.8086 (mm) cc_final: 0.7777 (mt) REVERT: B 162 LYS cc_start: 0.8349 (mttp) cc_final: 0.7958 (mmmt) REVERT: B 168 ILE cc_start: 0.8419 (tt) cc_final: 0.8152 (tt) REVERT: B 184 THR cc_start: 0.6611 (OUTLIER) cc_final: 0.6388 (p) REVERT: B 200 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6910 (tm-30) REVERT: C 2 LYS cc_start: 0.7911 (mttt) cc_final: 0.7638 (tppt) REVERT: C 3 VAL cc_start: 0.8648 (t) cc_final: 0.8389 (p) REVERT: C 6 ASP cc_start: 0.7991 (t0) cc_final: 0.7649 (t0) REVERT: C 7 ASP cc_start: 0.7609 (t70) cc_final: 0.7132 (t0) REVERT: C 23 ASP cc_start: 0.8016 (m-30) cc_final: 0.7815 (m-30) REVERT: C 30 LYS cc_start: 0.8021 (mptt) cc_final: 0.7562 (mmmm) REVERT: C 31 GLN cc_start: 0.8039 (mp10) cc_final: 0.7804 (mt0) REVERT: C 75 MET cc_start: 0.6836 (tmm) cc_final: 0.6633 (tpp) REVERT: C 139 PHE cc_start: 0.8027 (t80) cc_final: 0.7575 (t80) REVERT: C 140 LYS cc_start: 0.8082 (ttpt) cc_final: 0.7502 (tttm) REVERT: C 167 GLU cc_start: 0.7801 (pp20) cc_final: 0.7390 (pp20) REVERT: C 191 GLU cc_start: 0.7005 (mp0) cc_final: 0.6749 (mp0) REVERT: C 205 LEU cc_start: 0.8461 (mt) cc_final: 0.7855 (tp) REVERT: C 229 ASN cc_start: 0.7470 (t0) cc_final: 0.7201 (t0) REVERT: E 1 MET cc_start: 0.7067 (mmm) cc_final: 0.6704 (mmm) REVERT: E 2 GLU cc_start: 0.7234 (pm20) cc_final: 0.7029 (pm20) REVERT: E 11 ASP cc_start: 0.6648 (t70) cc_final: 0.6334 (t0) REVERT: E 13 LEU cc_start: 0.7464 (tp) cc_final: 0.7235 (tp) REVERT: E 36 THR cc_start: 0.7292 (p) cc_final: 0.6691 (p) REVERT: E 46 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7351 (tm-30) REVERT: E 48 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7854 (mmmm) REVERT: E 49 LEU cc_start: 0.7264 (mp) cc_final: 0.7025 (mt) REVERT: E 67 ILE cc_start: 0.8020 (mt) cc_final: 0.7668 (pt) REVERT: E 86 LYS cc_start: 0.7898 (tptp) cc_final: 0.7462 (mmmm) REVERT: E 101 LYS cc_start: 0.8699 (pttm) cc_final: 0.8184 (pttm) REVERT: E 111 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6243 (pp) REVERT: E 126 SER cc_start: 0.8510 (t) cc_final: 0.7909 (p) REVERT: E 169 ARG cc_start: 0.7185 (ptt180) cc_final: 0.6933 (ptt90) REVERT: E 174 ILE cc_start: 0.7888 (mm) cc_final: 0.7595 (tt) REVERT: E 197 ILE cc_start: 0.7992 (mm) cc_final: 0.7692 (tp) REVERT: E 203 LEU cc_start: 0.7947 (mt) cc_final: 0.7669 (mt) REVERT: E 206 ASP cc_start: 0.7730 (p0) cc_final: 0.7526 (p0) REVERT: E 212 LYS cc_start: 0.7262 (pttm) cc_final: 0.6989 (pttp) REVERT: E 236 MET cc_start: 0.7580 (ptp) cc_final: 0.7362 (ptp) REVERT: E 239 GLU cc_start: 0.7244 (tp30) cc_final: 0.6136 (mp0) REVERT: E 291 ASP cc_start: 0.7755 (p0) cc_final: 0.7513 (p0) REVERT: E 321 MET cc_start: 0.6543 (mmm) cc_final: 0.5649 (mmm) REVERT: E 325 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6995 (tp-100) REVERT: E 326 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7434 (tp30) REVERT: E 328 MET cc_start: 0.7739 (mtm) cc_final: 0.7095 (mtm) REVERT: E 336 ILE cc_start: 0.7362 (mt) cc_final: 0.6787 (mm) REVERT: E 360 TYR cc_start: 0.7426 (m-80) cc_final: 0.6726 (m-80) REVERT: E 373 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7817 (mm-30) REVERT: E 397 LYS cc_start: 0.7841 (mmmt) cc_final: 0.7605 (mmtp) REVERT: E 434 LEU cc_start: 0.8334 (tp) cc_final: 0.7901 (pt) outliers start: 17 outliers final: 4 residues processed: 410 average time/residue: 0.2756 time to fit residues: 148.3076 Evaluate side-chains 350 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 343 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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: 5.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10899 Z= 0.303 Angle : 0.640 7.921 14963 Z= 0.353 Chirality : 0.045 0.187 1723 Planarity : 0.004 0.054 1683 Dihedral : 20.944 154.970 1931 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.25 % Favored : 89.67 % Rotamer: Outliers : 0.10 % Allowed : 3.09 % Favored : 96.81 % 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: -2.27 (0.24), residues: 1171 helix: -0.37 (0.31), residues: 297 sheet: -0.21 (0.31), residues: 322 loop : -3.07 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 50 HIS 0.005 0.001 HIS A 240 PHE 0.025 0.002 PHE C 228 TYR 0.016 0.002 TYR A 177 ARG 0.003 0.001 ARG E 280 *********************** 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 362 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 1.120 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: A 24 ASP cc_start: 0.5564 (t70) cc_final: 0.5302 (t0) REVERT: A 39 HIS cc_start: 0.7605 (t-90) cc_final: 0.7258 (t-90) REVERT: A 57 LEU cc_start: 0.8289 (mt) cc_final: 0.7976 (mt) REVERT: A 59 GLU cc_start: 0.8400 (tp30) cc_final: 0.8118 (tp30) REVERT: A 70 LEU cc_start: 0.7525 (mt) cc_final: 0.7182 (mt) REVERT: A 99 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7970 (mtpp) REVERT: A 110 LYS cc_start: 0.7269 (ttmt) cc_final: 0.7066 (ttmm) REVERT: A 116 LYS cc_start: 0.8037 (mtmm) cc_final: 0.7664 (tptt) REVERT: A 156 GLU cc_start: 0.8053 (mp0) cc_final: 0.7844 (mp0) REVERT: A 213 ARG cc_start: 0.6954 (mtt90) cc_final: 0.6623 (mtt90) REVERT: A 229 MET cc_start: 0.6459 (ttt) cc_final: 0.5984 (ttt) REVERT: A 231 ILE cc_start: 0.7974 (mt) cc_final: 0.7611 (tt) REVERT: B 21 ASP cc_start: 0.7328 (t0) cc_final: 0.6528 (t0) REVERT: B 33 GLU cc_start: 0.7647 (pm20) cc_final: 0.7327 (pm20) REVERT: B 40 ILE cc_start: 0.8901 (tp) cc_final: 0.8507 (tp) REVERT: B 73 LEU cc_start: 0.7216 (tp) cc_final: 0.6885 (tp) REVERT: B 132 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8069 (ttmm) REVERT: C 3 VAL cc_start: 0.8588 (t) cc_final: 0.8206 (p) REVERT: C 6 ASP cc_start: 0.7579 (t0) cc_final: 0.7346 (t0) REVERT: C 7 ASP cc_start: 0.7777 (t70) cc_final: 0.7308 (t0) REVERT: C 30 LYS cc_start: 0.7907 (mptt) cc_final: 0.7587 (mmmm) REVERT: C 31 GLN cc_start: 0.8025 (mp10) cc_final: 0.7793 (mt0) REVERT: C 75 MET cc_start: 0.7063 (tmm) cc_final: 0.6783 (tpp) REVERT: C 76 LYS cc_start: 0.8354 (ttpt) cc_final: 0.8065 (ttpt) REVERT: C 95 ASP cc_start: 0.8280 (t70) cc_final: 0.7690 (t70) REVERT: C 100 ASN cc_start: 0.7708 (m-40) cc_final: 0.7355 (m-40) REVERT: C 108 GLU cc_start: 0.7049 (pp20) cc_final: 0.6699 (tm-30) REVERT: C 112 ARG cc_start: 0.8283 (tpp80) cc_final: 0.7961 (tpp80) REVERT: C 140 LYS cc_start: 0.8313 (ttpt) cc_final: 0.7827 (tttm) REVERT: C 165 LYS cc_start: 0.7851 (pttp) cc_final: 0.7165 (ptpt) REVERT: C 171 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7142 (mm-30) REVERT: C 205 LEU cc_start: 0.8344 (mt) cc_final: 0.8125 (tp) REVERT: C 209 LYS cc_start: 0.8215 (ptmm) cc_final: 0.7766 (ptmm) REVERT: C 215 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7798 (ttmm) REVERT: C 229 ASN cc_start: 0.7522 (t0) cc_final: 0.7313 (t0) REVERT: C 230 MET cc_start: 0.5453 (mtm) cc_final: 0.4876 (mtm) REVERT: E 6 ILE cc_start: 0.6509 (tp) cc_final: 0.6205 (tp) REVERT: E 46 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7435 (tm-30) REVERT: E 48 LYS cc_start: 0.8005 (mmtm) cc_final: 0.7725 (mmmm) REVERT: E 52 ASP cc_start: 0.7457 (m-30) cc_final: 0.7191 (t70) REVERT: E 86 LYS cc_start: 0.7790 (tppt) cc_final: 0.7496 (mmmm) REVERT: E 101 LYS cc_start: 0.8616 (pttm) cc_final: 0.8056 (pttm) REVERT: E 117 GLU cc_start: 0.5075 (mp0) cc_final: 0.4750 (mp0) REVERT: E 126 SER cc_start: 0.8348 (t) cc_final: 0.7835 (p) REVERT: E 127 THR cc_start: 0.8070 (m) cc_final: 0.7785 (m) REVERT: E 135 THR cc_start: 0.8059 (m) cc_final: 0.7772 (p) REVERT: E 174 ILE cc_start: 0.7890 (mm) cc_final: 0.7637 (tt) REVERT: E 197 ILE cc_start: 0.8043 (mm) cc_final: 0.7743 (tp) REVERT: E 206 ASP cc_start: 0.7849 (p0) cc_final: 0.7562 (p0) REVERT: E 216 GLU cc_start: 0.7148 (tp30) cc_final: 0.6898 (mm-30) REVERT: E 223 LYS cc_start: 0.7780 (mmtp) cc_final: 0.7511 (mmtm) REVERT: E 239 GLU cc_start: 0.7459 (tp30) cc_final: 0.6278 (mp0) REVERT: E 248 LEU cc_start: 0.6804 (mp) cc_final: 0.6562 (mp) REVERT: E 265 ARG cc_start: 0.7600 (mtp180) cc_final: 0.7283 (mtm180) REVERT: E 274 LYS cc_start: 0.7076 (mppt) cc_final: 0.6662 (mppt) REVERT: E 290 PRO cc_start: 0.8054 (Cg_endo) cc_final: 0.7674 (Cg_exo) REVERT: E 324 PHE cc_start: 0.7490 (t80) cc_final: 0.7226 (t80) REVERT: E 325 GLN cc_start: 0.7379 (mm-40) cc_final: 0.7021 (tp-100) REVERT: E 326 GLU cc_start: 0.7698 (tp30) cc_final: 0.7002 (tp30) REVERT: E 328 MET cc_start: 0.7660 (mtm) cc_final: 0.7253 (mtm) REVERT: E 329 HIS cc_start: 0.7231 (m90) cc_final: 0.5826 (m90) REVERT: E 336 ILE cc_start: 0.7316 (mt) cc_final: 0.7060 (mm) REVERT: E 360 TYR cc_start: 0.7584 (m-80) cc_final: 0.6724 (m-80) REVERT: E 363 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8238 (mmtp) REVERT: E 397 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7625 (mmtp) REVERT: E 434 LEU cc_start: 0.8394 (tp) cc_final: 0.8001 (pt) outliers start: 1 outliers final: 0 residues processed: 362 average time/residue: 0.2785 time to fit residues: 132.0800 Evaluate side-chains 321 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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: 0.2980 chunk 34 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 0.0570 chunk 110 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 37 optimal weight: 0.0570 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 overall best weight: 0.2816 ------------------------------------------------------------------------------- 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 ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10899 Z= 0.157 Angle : 0.563 8.699 14963 Z= 0.304 Chirality : 0.043 0.162 1723 Planarity : 0.004 0.058 1683 Dihedral : 20.818 150.748 1931 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: -2.03 (0.24), residues: 1171 helix: -0.32 (0.31), residues: 305 sheet: 0.32 (0.33), residues: 297 loop : -3.00 (0.22), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 50 HIS 0.003 0.001 HIS A 39 PHE 0.027 0.002 PHE A 30 TYR 0.015 0.001 TYR C 59 ARG 0.007 0.000 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 354 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 1.046 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: A 24 ASP cc_start: 0.5588 (t70) cc_final: 0.5285 (t0) REVERT: A 57 LEU cc_start: 0.8237 (mt) cc_final: 0.8022 (mt) REVERT: A 59 GLU cc_start: 0.8384 (tp30) cc_final: 0.8028 (tp30) REVERT: A 110 LYS cc_start: 0.7147 (ttmt) cc_final: 0.6836 (ttmm) REVERT: A 116 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7725 (tptt) REVERT: A 119 LYS cc_start: 0.7227 (mppt) cc_final: 0.6865 (mppt) REVERT: A 136 PHE cc_start: 0.7151 (p90) cc_final: 0.6913 (p90) REVERT: A 156 GLU cc_start: 0.8002 (mp0) cc_final: 0.7785 (mm-30) REVERT: A 213 ARG cc_start: 0.6996 (mtt90) cc_final: 0.6756 (mtt90) REVERT: A 220 MET cc_start: 0.7586 (tmm) cc_final: 0.7184 (ttp) REVERT: A 229 MET cc_start: 0.6391 (ttt) cc_final: 0.6133 (ttt) REVERT: B 21 ASP cc_start: 0.7486 (t0) cc_final: 0.6739 (t0) REVERT: B 62 VAL cc_start: 0.6411 (m) cc_final: 0.6160 (m) REVERT: B 103 ASP cc_start: 0.6915 (m-30) cc_final: 0.6710 (m-30) REVERT: B 107 THR cc_start: 0.8052 (p) cc_final: 0.7758 (t) REVERT: B 132 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7802 (ttmm) REVERT: B 145 ASP cc_start: 0.6098 (m-30) cc_final: 0.5735 (t70) REVERT: B 153 VAL cc_start: 0.7889 (t) cc_final: 0.7577 (p) REVERT: B 155 ASN cc_start: 0.7614 (t0) cc_final: 0.7206 (t0) REVERT: C 2 LYS cc_start: 0.7564 (tppt) cc_final: 0.7234 (tppt) REVERT: C 3 VAL cc_start: 0.8318 (t) cc_final: 0.7772 (p) REVERT: C 6 ASP cc_start: 0.7425 (t0) cc_final: 0.7149 (t0) REVERT: C 7 ASP cc_start: 0.7759 (t70) cc_final: 0.7348 (t0) REVERT: C 76 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7820 (ttpt) REVERT: C 77 ILE cc_start: 0.8263 (pt) cc_final: 0.8013 (tt) REVERT: C 108 GLU cc_start: 0.7143 (pp20) cc_final: 0.6900 (tm-30) REVERT: C 112 ARG cc_start: 0.8211 (tpp80) cc_final: 0.7872 (tpp80) REVERT: C 165 LYS cc_start: 0.7945 (pttp) cc_final: 0.7322 (ptpt) REVERT: C 171 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7125 (mm-30) REVERT: C 205 LEU cc_start: 0.8260 (mt) cc_final: 0.7852 (tp) REVERT: C 209 LYS cc_start: 0.8087 (ptmm) cc_final: 0.7584 (ptmm) REVERT: C 215 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7818 (ttmm) REVERT: C 229 ASN cc_start: 0.7420 (t0) cc_final: 0.7170 (t0) REVERT: C 230 MET cc_start: 0.5510 (mtm) cc_final: 0.5173 (mtm) REVERT: E 6 ILE cc_start: 0.6759 (tp) cc_final: 0.6401 (tp) REVERT: E 13 LEU cc_start: 0.7284 (tp) cc_final: 0.7057 (tp) REVERT: E 15 LYS cc_start: 0.8410 (mtmt) cc_final: 0.8083 (mmtm) REVERT: E 36 THR cc_start: 0.7955 (p) cc_final: 0.7496 (p) REVERT: E 101 LYS cc_start: 0.8660 (pttm) cc_final: 0.8182 (pttm) REVERT: E 117 GLU cc_start: 0.4991 (mp0) cc_final: 0.4665 (mp0) REVERT: E 126 SER cc_start: 0.8273 (t) cc_final: 0.7805 (p) REVERT: E 135 THR cc_start: 0.7844 (m) cc_final: 0.7602 (p) REVERT: E 174 ILE cc_start: 0.7935 (mm) cc_final: 0.7553 (tt) REVERT: E 197 ILE cc_start: 0.7847 (mm) cc_final: 0.7590 (tp) REVERT: E 203 LEU cc_start: 0.7744 (mt) cc_final: 0.7520 (mt) REVERT: E 236 MET cc_start: 0.7595 (ptp) cc_final: 0.7369 (ptp) REVERT: E 239 GLU cc_start: 0.7541 (tp30) cc_final: 0.6422 (mp0) REVERT: E 265 ARG cc_start: 0.7626 (mtp180) cc_final: 0.7234 (mtm180) REVERT: E 274 LYS cc_start: 0.7023 (mppt) cc_final: 0.6551 (mppt) REVERT: E 290 PRO cc_start: 0.8032 (Cg_endo) cc_final: 0.7722 (Cg_exo) REVERT: E 326 GLU cc_start: 0.7647 (tp30) cc_final: 0.6719 (tp30) REVERT: E 328 MET cc_start: 0.7517 (mtm) cc_final: 0.7129 (mmp) REVERT: E 329 HIS cc_start: 0.7217 (m90) cc_final: 0.5725 (m90) REVERT: E 363 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8175 (mmtp) REVERT: E 397 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7422 (mmtp) REVERT: E 434 LEU cc_start: 0.8339 (tp) cc_final: 0.7889 (pt) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.2870 time to fit residues: 132.6874 Evaluate side-chains 326 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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: 0.7980 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** B 116 GLN ** 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: 0.7024 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 10899 Z= 0.301 Angle : 0.655 10.251 14963 Z= 0.356 Chirality : 0.045 0.157 1723 Planarity : 0.005 0.062 1683 Dihedral : 21.075 154.388 1931 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.27 % Favored : 88.64 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % 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: -2.34 (0.24), residues: 1171 helix: -0.65 (0.30), residues: 306 sheet: -0.14 (0.31), residues: 327 loop : -3.11 (0.23), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 50 HIS 0.003 0.001 HIS A 39 PHE 0.024 0.003 PHE C 228 TYR 0.027 0.002 TYR C 59 ARG 0.007 0.001 ARG E 234 *********************** 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 349 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 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: A 3 LYS cc_start: 0.8065 (ttpp) cc_final: 0.7824 (ttpp) REVERT: A 24 ASP cc_start: 0.5736 (t70) cc_final: 0.5279 (t0) REVERT: A 57 LEU cc_start: 0.8210 (mt) cc_final: 0.7940 (mt) REVERT: A 69 LYS cc_start: 0.7570 (pttp) cc_final: 0.7335 (mptt) REVERT: A 93 GLU cc_start: 0.8755 (pp20) cc_final: 0.8252 (pp20) REVERT: A 99 LYS cc_start: 0.7744 (tptt) cc_final: 0.7480 (ttmm) REVERT: A 116 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7676 (tptt) REVERT: A 119 LYS cc_start: 0.7233 (mppt) cc_final: 0.6960 (mppt) REVERT: A 136 PHE cc_start: 0.7215 (p90) cc_final: 0.6928 (p90) REVERT: A 206 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7832 (ttmm) REVERT: A 213 ARG cc_start: 0.7078 (mtt90) cc_final: 0.6812 (mtt90) REVERT: A 229 MET cc_start: 0.6374 (ttt) cc_final: 0.6093 (ttt) REVERT: B 11 SER cc_start: 0.8160 (m) cc_final: 0.7635 (p) REVERT: B 21 ASP cc_start: 0.7479 (t0) cc_final: 0.6603 (t0) REVERT: B 107 THR cc_start: 0.8061 (p) cc_final: 0.7790 (t) REVERT: B 132 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7860 (ttmm) REVERT: B 155 ASN cc_start: 0.7583 (t0) cc_final: 0.7286 (t0) REVERT: B 159 LYS cc_start: 0.7962 (ttmm) cc_final: 0.7739 (ttmm) REVERT: C 3 VAL cc_start: 0.8702 (t) cc_final: 0.8341 (p) REVERT: C 6 ASP cc_start: 0.7592 (t0) cc_final: 0.7377 (t0) REVERT: C 7 ASP cc_start: 0.7825 (t70) cc_final: 0.7387 (t0) REVERT: C 33 SER cc_start: 0.7831 (m) cc_final: 0.7046 (m) REVERT: C 35 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6882 (mm-30) REVERT: C 75 MET cc_start: 0.7803 (tpp) cc_final: 0.7462 (tpp) REVERT: C 85 GLU cc_start: 0.7371 (mp0) cc_final: 0.6958 (mp0) REVERT: C 112 ARG cc_start: 0.8181 (tpp80) cc_final: 0.7979 (tpp80) REVERT: C 154 VAL cc_start: 0.8017 (t) cc_final: 0.7629 (p) REVERT: C 165 LYS cc_start: 0.8027 (pttp) cc_final: 0.7228 (ptpt) REVERT: C 171 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7188 (mm-30) REVERT: C 205 LEU cc_start: 0.8453 (mt) cc_final: 0.8138 (tp) REVERT: C 209 LYS cc_start: 0.8289 (ptmm) cc_final: 0.8023 (ptmm) REVERT: C 215 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7744 (ttmm) REVERT: C 229 ASN cc_start: 0.7441 (t0) cc_final: 0.7193 (t0) REVERT: C 230 MET cc_start: 0.5703 (mtm) cc_final: 0.5327 (mtm) REVERT: E 1 MET cc_start: 0.7243 (mtm) cc_final: 0.7041 (mtm) REVERT: E 6 ILE cc_start: 0.6701 (tp) cc_final: 0.6352 (tp) REVERT: E 36 THR cc_start: 0.7729 (p) cc_final: 0.7239 (p) REVERT: E 49 LEU cc_start: 0.7373 (mt) cc_final: 0.7172 (mt) REVERT: E 86 LYS cc_start: 0.7888 (tptm) cc_final: 0.7604 (mmmm) REVERT: E 101 LYS cc_start: 0.8681 (pttm) cc_final: 0.8045 (pttm) REVERT: E 110 PHE cc_start: 0.6011 (m-10) cc_final: 0.5741 (m-10) REVERT: E 117 GLU cc_start: 0.4936 (mp0) cc_final: 0.4642 (mp0) REVERT: E 126 SER cc_start: 0.8387 (t) cc_final: 0.7868 (p) REVERT: E 127 THR cc_start: 0.8054 (m) cc_final: 0.7800 (m) REVERT: E 135 THR cc_start: 0.8403 (m) cc_final: 0.8073 (p) REVERT: E 141 ASP cc_start: 0.7260 (m-30) cc_final: 0.6926 (m-30) REVERT: E 174 ILE cc_start: 0.7950 (mm) cc_final: 0.7649 (tp) REVERT: E 194 SER cc_start: 0.7996 (p) cc_final: 0.7650 (p) REVERT: E 197 ILE cc_start: 0.7961 (mm) cc_final: 0.7564 (tp) REVERT: E 239 GLU cc_start: 0.7318 (tp30) cc_final: 0.6728 (mp0) REVERT: E 248 LEU cc_start: 0.6795 (mp) cc_final: 0.6536 (mp) REVERT: E 265 ARG cc_start: 0.7610 (mtp180) cc_final: 0.7245 (mtm180) REVERT: E 274 LYS cc_start: 0.7177 (mppt) cc_final: 0.6315 (mppt) REVERT: E 281 ARG cc_start: 0.6709 (mtm180) cc_final: 0.6341 (mtm180) REVERT: E 290 PRO cc_start: 0.7993 (Cg_endo) cc_final: 0.7514 (Cg_exo) REVERT: E 294 ASP cc_start: 0.8619 (p0) cc_final: 0.8314 (p0) REVERT: E 325 GLN cc_start: 0.7431 (tp40) cc_final: 0.7158 (tp-100) REVERT: E 363 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8250 (mmtp) REVERT: E 397 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7482 (mmtp) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2835 time to fit residues: 129.7597 Evaluate side-chains 323 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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: 0.7980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 39 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: B 116 GLN E 75 ASN ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3599 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= 0.215 Angle : 0.614 10.252 14963 Z= 0.332 Chirality : 0.044 0.159 1723 Planarity : 0.004 0.060 1683 Dihedral : 21.025 151.728 1931 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % 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: -2.26 (0.24), residues: 1171 helix: -0.57 (0.31), residues: 305 sheet: -0.08 (0.31), residues: 321 loop : -3.05 (0.23), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 50 HIS 0.003 0.001 HIS A 39 PHE 0.022 0.002 PHE E 324 TYR 0.017 0.002 TYR B 218 ARG 0.005 0.000 ARG E 234 *********************** 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 355 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 1.101 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: A 3 LYS cc_start: 0.7994 (ttpp) cc_final: 0.7793 (ttpp) REVERT: A 24 ASP cc_start: 0.5741 (t70) cc_final: 0.5374 (t0) REVERT: A 57 LEU cc_start: 0.8203 (mt) cc_final: 0.7917 (mt) REVERT: A 65 PRO cc_start: 0.6685 (Cg_exo) cc_final: 0.6320 (Cg_endo) REVERT: A 91 LEU cc_start: 0.7737 (tp) cc_final: 0.7440 (tt) REVERT: A 116 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7705 (tptt) REVERT: A 119 LYS cc_start: 0.7256 (mppt) cc_final: 0.6767 (mppt) REVERT: A 136 PHE cc_start: 0.7180 (p90) cc_final: 0.6925 (p90) REVERT: A 213 ARG cc_start: 0.6952 (mtt90) cc_final: 0.6619 (mtt90) REVERT: A 229 MET cc_start: 0.6257 (ttt) cc_final: 0.6040 (ttt) REVERT: B 21 ASP cc_start: 0.7538 (t0) cc_final: 0.6629 (t0) REVERT: B 22 PHE cc_start: 0.7570 (m-10) cc_final: 0.7359 (m-10) REVERT: B 66 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7753 (mmmt) REVERT: B 67 GLU cc_start: 0.6404 (mt-10) cc_final: 0.6138 (mp0) REVERT: B 132 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7849 (ttmm) REVERT: B 155 ASN cc_start: 0.7433 (t0) cc_final: 0.7027 (t0) REVERT: B 162 LYS cc_start: 0.8177 (mttp) cc_final: 0.7751 (mttp) REVERT: B 216 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6813 (mm-30) REVERT: C 3 VAL cc_start: 0.8621 (t) cc_final: 0.8091 (p) REVERT: C 6 ASP cc_start: 0.7497 (t0) cc_final: 0.7257 (t0) REVERT: C 7 ASP cc_start: 0.7796 (t70) cc_final: 0.7406 (t0) REVERT: C 75 MET cc_start: 0.7674 (tpp) cc_final: 0.7411 (tpp) REVERT: C 76 LYS cc_start: 0.8365 (ttmt) cc_final: 0.8114 (ttmt) REVERT: C 85 GLU cc_start: 0.7377 (mp0) cc_final: 0.7138 (mp0) REVERT: C 88 GLU cc_start: 0.7338 (pp20) cc_final: 0.6899 (pp20) REVERT: C 98 ILE cc_start: 0.7603 (mm) cc_final: 0.7375 (mm) REVERT: C 112 ARG cc_start: 0.8214 (tpp80) cc_final: 0.7998 (tpp80) REVERT: C 165 LYS cc_start: 0.7961 (pttp) cc_final: 0.7369 (ptpt) REVERT: C 171 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7207 (mm-30) REVERT: C 195 SER cc_start: 0.8511 (m) cc_final: 0.8200 (p) REVERT: C 205 LEU cc_start: 0.8291 (mt) cc_final: 0.7901 (tp) REVERT: C 209 LYS cc_start: 0.8254 (ptmm) cc_final: 0.8030 (ptmm) REVERT: C 215 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7806 (ttmm) REVERT: C 229 ASN cc_start: 0.7419 (t0) cc_final: 0.7145 (t0) REVERT: C 230 MET cc_start: 0.5688 (mtm) cc_final: 0.5055 (mtm) REVERT: E 6 ILE cc_start: 0.6820 (tp) cc_final: 0.6407 (tp) REVERT: E 36 THR cc_start: 0.7773 (p) cc_final: 0.7306 (p) REVERT: E 49 LEU cc_start: 0.7325 (mt) cc_final: 0.7120 (mt) REVERT: E 86 LYS cc_start: 0.7822 (tptm) cc_final: 0.7560 (mmmm) REVERT: E 101 LYS cc_start: 0.8652 (pttm) cc_final: 0.8062 (pttm) REVERT: E 117 GLU cc_start: 0.4969 (mp0) cc_final: 0.4642 (mp0) REVERT: E 126 SER cc_start: 0.8366 (t) cc_final: 0.7834 (p) REVERT: E 127 THR cc_start: 0.8153 (m) cc_final: 0.7905 (m) REVERT: E 135 THR cc_start: 0.8069 (m) cc_final: 0.7712 (p) REVERT: E 174 ILE cc_start: 0.7970 (mm) cc_final: 0.7644 (tp) REVERT: E 194 SER cc_start: 0.7915 (p) cc_final: 0.6797 (p) REVERT: E 197 ILE cc_start: 0.7953 (mm) cc_final: 0.7502 (tp) REVERT: E 203 LEU cc_start: 0.7767 (mt) cc_final: 0.7524 (mt) REVERT: E 239 GLU cc_start: 0.7305 (tp30) cc_final: 0.6769 (mp0) REVERT: E 248 LEU cc_start: 0.6711 (mp) cc_final: 0.6436 (mp) REVERT: E 265 ARG cc_start: 0.7511 (mtp180) cc_final: 0.7285 (mtm180) REVERT: E 274 LYS cc_start: 0.7108 (mppt) cc_final: 0.6863 (mppt) REVERT: E 281 ARG cc_start: 0.6499 (mtm180) cc_final: 0.6199 (mtm180) REVERT: E 285 ILE cc_start: 0.8663 (pt) cc_final: 0.8302 (mm) REVERT: E 290 PRO cc_start: 0.7968 (Cg_endo) cc_final: 0.7552 (Cg_exo) REVERT: E 325 GLN cc_start: 0.7280 (tp40) cc_final: 0.7053 (tp40) REVERT: E 326 GLU cc_start: 0.7727 (tp30) cc_final: 0.7519 (tp30) REVERT: E 397 LYS cc_start: 0.7852 (mmmt) cc_final: 0.7428 (mmtp) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.2852 time to fit residues: 131.8126 Evaluate side-chains 331 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.1980 chunk 61 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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: 0.3766 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= 0.191 Angle : 0.614 10.245 14963 Z= 0.329 Chirality : 0.044 0.155 1723 Planarity : 0.004 0.059 1683 Dihedral : 21.013 151.164 1931 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: -0.52 (0.31), residues: 305 sheet: 0.06 (0.31), residues: 322 loop : -3.04 (0.22), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 50 HIS 0.009 0.001 HIS B 157 PHE 0.022 0.002 PHE E 10 TYR 0.016 0.001 TYR C 59 ARG 0.007 0.000 ARG E 171 *********************** 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 352 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.082 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: A 24 ASP cc_start: 0.5829 (t70) cc_final: 0.5408 (t0) REVERT: A 57 LEU cc_start: 0.8164 (mt) cc_final: 0.7892 (mt) REVERT: A 65 PRO cc_start: 0.6617 (Cg_exo) cc_final: 0.6292 (Cg_endo) REVERT: A 69 LYS cc_start: 0.7618 (mptt) cc_final: 0.7161 (mmtm) REVERT: A 91 LEU cc_start: 0.7631 (tp) cc_final: 0.7297 (tt) REVERT: A 93 GLU cc_start: 0.8667 (pp20) cc_final: 0.8073 (pp20) REVERT: A 99 LYS cc_start: 0.7948 (tppp) cc_final: 0.7643 (tppp) REVERT: A 105 GLU cc_start: 0.6757 (tp30) cc_final: 0.6546 (tp30) REVERT: A 116 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7757 (tppt) REVERT: A 119 LYS cc_start: 0.7143 (mppt) cc_final: 0.6854 (mppt) REVERT: A 143 LEU cc_start: 0.7678 (mm) cc_final: 0.7339 (mt) REVERT: A 213 ARG cc_start: 0.6948 (mtt90) cc_final: 0.6648 (mtt90) REVERT: A 227 LEU cc_start: 0.7467 (tp) cc_final: 0.7119 (tt) REVERT: B 21 ASP cc_start: 0.7454 (t0) cc_final: 0.6569 (t0) REVERT: B 22 PHE cc_start: 0.7547 (m-10) cc_final: 0.7191 (m-10) REVERT: B 67 GLU cc_start: 0.6394 (mt-10) cc_final: 0.6183 (mp0) REVERT: B 132 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7585 (ttmm) REVERT: B 155 ASN cc_start: 0.7365 (t0) cc_final: 0.6923 (t0) REVERT: B 159 LYS cc_start: 0.7919 (ttmm) cc_final: 0.7665 (ttmm) REVERT: C 3 VAL cc_start: 0.8529 (t) cc_final: 0.8037 (p) REVERT: C 7 ASP cc_start: 0.7763 (t70) cc_final: 0.7422 (t0) REVERT: C 28 LYS cc_start: 0.8239 (mttm) cc_final: 0.7578 (mttm) REVERT: C 35 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6237 (tm-30) REVERT: C 55 MET cc_start: 0.7019 (ttm) cc_final: 0.6777 (ttm) REVERT: C 75 MET cc_start: 0.7633 (tpp) cc_final: 0.7369 (tpp) REVERT: C 85 GLU cc_start: 0.7430 (mp0) cc_final: 0.7173 (mp0) REVERT: C 99 ILE cc_start: 0.7554 (mt) cc_final: 0.7297 (mt) REVERT: C 108 GLU cc_start: 0.7943 (pt0) cc_final: 0.7553 (tm-30) REVERT: C 109 PHE cc_start: 0.8514 (m-80) cc_final: 0.7836 (m-80) REVERT: C 154 VAL cc_start: 0.7875 (t) cc_final: 0.7631 (p) REVERT: C 165 LYS cc_start: 0.7976 (pttp) cc_final: 0.7256 (ptpt) REVERT: C 171 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7174 (mm-30) REVERT: C 189 SER cc_start: 0.8147 (t) cc_final: 0.7739 (p) REVERT: C 195 SER cc_start: 0.8503 (m) cc_final: 0.8199 (p) REVERT: C 205 LEU cc_start: 0.8256 (mt) cc_final: 0.7910 (tp) REVERT: C 209 LYS cc_start: 0.8164 (ptmm) cc_final: 0.7956 (ptmm) REVERT: C 215 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7696 (ttmm) REVERT: C 229 ASN cc_start: 0.7403 (t0) cc_final: 0.7149 (t0) REVERT: C 230 MET cc_start: 0.5674 (mtm) cc_final: 0.5011 (mtm) REVERT: E 1 MET cc_start: 0.7339 (mtm) cc_final: 0.7013 (mtm) REVERT: E 6 ILE cc_start: 0.6737 (tp) cc_final: 0.6449 (tp) REVERT: E 19 ARG cc_start: 0.6538 (mtm-85) cc_final: 0.6276 (mtm-85) REVERT: E 36 THR cc_start: 0.7744 (p) cc_final: 0.7270 (p) REVERT: E 46 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7598 (tm-30) REVERT: E 49 LEU cc_start: 0.7305 (mt) cc_final: 0.7103 (mt) REVERT: E 86 LYS cc_start: 0.7804 (tptm) cc_final: 0.7548 (mmmm) REVERT: E 126 SER cc_start: 0.8336 (t) cc_final: 0.7796 (p) REVERT: E 135 THR cc_start: 0.8384 (m) cc_final: 0.8102 (p) REVERT: E 171 ARG cc_start: 0.8227 (mtm-85) cc_final: 0.7903 (mtm-85) REVERT: E 174 ILE cc_start: 0.7970 (mm) cc_final: 0.7631 (tp) REVERT: E 194 SER cc_start: 0.7595 (p) cc_final: 0.6565 (p) REVERT: E 198 GLU cc_start: 0.6409 (pm20) cc_final: 0.6058 (pm20) REVERT: E 203 LEU cc_start: 0.7782 (mt) cc_final: 0.7534 (mt) REVERT: E 236 MET cc_start: 0.7451 (ptp) cc_final: 0.7225 (ptp) REVERT: E 239 GLU cc_start: 0.7101 (tp30) cc_final: 0.6602 (mp0) REVERT: E 274 LYS cc_start: 0.7126 (mppt) cc_final: 0.6616 (mppt) REVERT: E 285 ILE cc_start: 0.8689 (pt) cc_final: 0.8278 (mm) REVERT: E 290 PRO cc_start: 0.8017 (Cg_endo) cc_final: 0.7570 (Cg_exo) REVERT: E 325 GLN cc_start: 0.7284 (tp40) cc_final: 0.7032 (tp40) REVERT: E 326 GLU cc_start: 0.7696 (tp30) cc_final: 0.7493 (tp30) REVERT: E 394 GLU cc_start: 0.7357 (pm20) cc_final: 0.7009 (tp30) REVERT: E 397 LYS cc_start: 0.7733 (mmmt) cc_final: 0.7386 (mmtp) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.2851 time to fit residues: 131.0592 Evaluate side-chains 327 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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: 6.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 117 optimal weight: 0.0010 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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: 0.6957 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10899 Z= 0.180 Angle : 0.610 9.283 14963 Z= 0.326 Chirality : 0.044 0.169 1723 Planarity : 0.004 0.058 1683 Dihedral : 21.005 149.644 1931 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.24), residues: 1171 helix: -0.38 (0.31), residues: 302 sheet: 0.16 (0.31), residues: 316 loop : -3.01 (0.22), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 50 HIS 0.003 0.001 HIS A 39 PHE 0.022 0.001 PHE A 30 TYR 0.019 0.001 TYR B 218 ARG 0.006 0.000 ARG E 171 *********************** 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 349 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 1.162 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: A 24 ASP cc_start: 0.5978 (t70) cc_final: 0.5615 (t0) REVERT: A 57 LEU cc_start: 0.8148 (mt) cc_final: 0.7879 (mt) REVERT: A 59 GLU cc_start: 0.8168 (tp30) cc_final: 0.7904 (tm-30) REVERT: A 69 LYS cc_start: 0.7671 (mptt) cc_final: 0.7223 (mmtm) REVERT: A 91 LEU cc_start: 0.7522 (tp) cc_final: 0.7308 (tt) REVERT: A 93 GLU cc_start: 0.8700 (pp20) cc_final: 0.8099 (pp20) REVERT: A 112 THR cc_start: 0.5762 (p) cc_final: 0.4999 (p) REVERT: A 116 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7764 (tppt) REVERT: A 119 LYS cc_start: 0.7117 (mppt) cc_final: 0.6881 (mppt) REVERT: A 143 LEU cc_start: 0.7644 (mm) cc_final: 0.7310 (mt) REVERT: A 164 ASP cc_start: 0.6566 (t0) cc_final: 0.6346 (t0) REVERT: A 206 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7679 (ttmm) REVERT: A 213 ARG cc_start: 0.6985 (mtt90) cc_final: 0.6627 (mtt90) REVERT: A 227 LEU cc_start: 0.7380 (tp) cc_final: 0.7129 (tt) REVERT: B 21 ASP cc_start: 0.7353 (t0) cc_final: 0.6453 (t0) REVERT: B 22 PHE cc_start: 0.7618 (m-10) cc_final: 0.7245 (m-10) REVERT: B 132 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7589 (ttmm) REVERT: B 159 LYS cc_start: 0.7847 (ttmm) cc_final: 0.7562 (ttmm) REVERT: B 162 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7380 (mmmt) REVERT: B 207 LYS cc_start: 0.8976 (ptpp) cc_final: 0.8731 (ptpp) REVERT: C 2 LYS cc_start: 0.7589 (tppt) cc_final: 0.7129 (tppt) REVERT: C 3 VAL cc_start: 0.8334 (t) cc_final: 0.7803 (p) REVERT: C 7 ASP cc_start: 0.7783 (t70) cc_final: 0.7410 (t0) REVERT: C 28 LYS cc_start: 0.8214 (mttm) cc_final: 0.7726 (mttm) REVERT: C 35 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6354 (tm-30) REVERT: C 55 MET cc_start: 0.7112 (ttm) cc_final: 0.6675 (ttm) REVERT: C 75 MET cc_start: 0.7522 (tpp) cc_final: 0.7316 (tpp) REVERT: C 77 ILE cc_start: 0.8252 (pt) cc_final: 0.7970 (tt) REVERT: C 85 GLU cc_start: 0.7389 (mp0) cc_final: 0.7128 (mp0) REVERT: C 165 LYS cc_start: 0.7968 (pttp) cc_final: 0.7353 (ptpt) REVERT: C 167 GLU cc_start: 0.7425 (pp20) cc_final: 0.7165 (pp20) REVERT: C 173 GLU cc_start: 0.6184 (tm-30) cc_final: 0.5911 (tm-30) REVERT: C 189 SER cc_start: 0.8174 (t) cc_final: 0.7741 (p) REVERT: C 195 SER cc_start: 0.8500 (m) cc_final: 0.8174 (p) REVERT: C 205 LEU cc_start: 0.8270 (mt) cc_final: 0.7912 (tp) REVERT: C 209 LYS cc_start: 0.8188 (ptmm) cc_final: 0.7982 (ptmm) REVERT: C 229 ASN cc_start: 0.7396 (t0) cc_final: 0.7125 (t0) REVERT: C 230 MET cc_start: 0.5591 (mtm) cc_final: 0.4967 (mtm) REVERT: E 1 MET cc_start: 0.7336 (mtm) cc_final: 0.7086 (mtm) REVERT: E 6 ILE cc_start: 0.6697 (tp) cc_final: 0.6424 (tp) REVERT: E 14 GLU cc_start: 0.7062 (tp30) cc_final: 0.6797 (tp30) REVERT: E 15 LYS cc_start: 0.8302 (mtmm) cc_final: 0.7872 (mmtm) REVERT: E 19 ARG cc_start: 0.6500 (mtm-85) cc_final: 0.6285 (mtm-85) REVERT: E 36 THR cc_start: 0.7853 (p) cc_final: 0.7402 (p) REVERT: E 86 LYS cc_start: 0.7812 (tptm) cc_final: 0.7543 (mmmm) REVERT: E 101 LYS cc_start: 0.8689 (pttm) cc_final: 0.8307 (pttm) REVERT: E 126 SER cc_start: 0.8306 (t) cc_final: 0.7770 (p) REVERT: E 127 THR cc_start: 0.8048 (m) cc_final: 0.7809 (m) REVERT: E 135 THR cc_start: 0.8089 (m) cc_final: 0.7724 (p) REVERT: E 171 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7886 (mtm-85) REVERT: E 174 ILE cc_start: 0.7929 (mm) cc_final: 0.7657 (tp) REVERT: E 194 SER cc_start: 0.7449 (p) cc_final: 0.6462 (p) REVERT: E 198 GLU cc_start: 0.6369 (pm20) cc_final: 0.5960 (pm20) REVERT: E 224 THR cc_start: 0.7102 (p) cc_final: 0.6898 (p) REVERT: E 239 GLU cc_start: 0.7128 (tp30) cc_final: 0.6339 (mp0) REVERT: E 274 LYS cc_start: 0.7128 (mppt) cc_final: 0.6694 (mppt) REVERT: E 281 ARG cc_start: 0.6646 (mtm180) cc_final: 0.6276 (mtm110) REVERT: E 285 ILE cc_start: 0.8761 (pt) cc_final: 0.8271 (mm) REVERT: E 290 PRO cc_start: 0.8061 (Cg_endo) cc_final: 0.7553 (Cg_exo) REVERT: E 291 ASP cc_start: 0.7768 (p0) cc_final: 0.7346 (p0) REVERT: E 326 GLU cc_start: 0.7677 (tp30) cc_final: 0.7460 (tp30) REVERT: E 397 LYS cc_start: 0.7699 (mmmt) cc_final: 0.7347 (mmtp) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2862 time to fit residues: 130.3940 Evaluate side-chains 325 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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: 0.5980 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN B 155 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: 0.6970 moved from start: 0.4027 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= 0.193 Angle : 0.618 8.853 14963 Z= 0.331 Chirality : 0.044 0.171 1723 Planarity : 0.004 0.058 1683 Dihedral : 21.034 150.145 1931 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -2.03 (0.24), residues: 1171 helix: -0.35 (0.31), residues: 304 sheet: 0.18 (0.31), residues: 313 loop : -2.96 (0.23), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 50 HIS 0.003 0.001 HIS A 39 PHE 0.028 0.002 PHE A 30 TYR 0.016 0.001 TYR C 59 ARG 0.008 0.001 ARG B 209 *********************** 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 335 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 1.077 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: A 2 PHE cc_start: 0.6244 (t80) cc_final: 0.5417 (t80) REVERT: A 24 ASP cc_start: 0.6021 (t70) cc_final: 0.5611 (t0) REVERT: A 57 LEU cc_start: 0.8152 (mt) cc_final: 0.7887 (mt) REVERT: A 69 LYS cc_start: 0.7685 (mptt) cc_final: 0.7200 (mmtm) REVERT: A 112 THR cc_start: 0.5714 (p) cc_final: 0.5023 (p) REVERT: A 116 LYS cc_start: 0.8060 (mtmm) cc_final: 0.7752 (tppt) REVERT: A 119 LYS cc_start: 0.7122 (mppt) cc_final: 0.6901 (mppt) REVERT: A 165 LYS cc_start: 0.7586 (mptt) cc_final: 0.7178 (mptt) REVERT: A 210 LYS cc_start: 0.8514 (mttt) cc_final: 0.8260 (mtmm) REVERT: A 213 ARG cc_start: 0.6984 (mtt90) cc_final: 0.6543 (mtt90) REVERT: B 21 ASP cc_start: 0.7194 (t0) cc_final: 0.6349 (t0) REVERT: B 22 PHE cc_start: 0.7618 (m-10) cc_final: 0.7253 (m-10) REVERT: B 107 THR cc_start: 0.8028 (p) cc_final: 0.7602 (t) REVERT: B 132 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7676 (ttmm) REVERT: B 162 LYS cc_start: 0.7812 (mmmt) cc_final: 0.7416 (mmmt) REVERT: B 200 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7162 (tm-30) REVERT: C 3 VAL cc_start: 0.8411 (t) cc_final: 0.7895 (p) REVERT: C 7 ASP cc_start: 0.7789 (t70) cc_final: 0.7408 (t0) REVERT: C 28 LYS cc_start: 0.8231 (mttm) cc_final: 0.7814 (mttm) REVERT: C 35 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6381 (tm-30) REVERT: C 55 MET cc_start: 0.7074 (ttm) cc_final: 0.6613 (ttm) REVERT: C 77 ILE cc_start: 0.8377 (pt) cc_final: 0.8092 (tt) REVERT: C 85 GLU cc_start: 0.7401 (mp0) cc_final: 0.7125 (mp0) REVERT: C 109 PHE cc_start: 0.8470 (m-80) cc_final: 0.7644 (m-80) REVERT: C 165 LYS cc_start: 0.7947 (pttp) cc_final: 0.7496 (ptpt) REVERT: C 167 GLU cc_start: 0.7448 (pp20) cc_final: 0.7208 (pp20) REVERT: C 173 GLU cc_start: 0.6193 (tm-30) cc_final: 0.5944 (tm-30) REVERT: C 189 SER cc_start: 0.8176 (t) cc_final: 0.7740 (p) REVERT: C 195 SER cc_start: 0.8505 (m) cc_final: 0.8144 (p) REVERT: C 205 LEU cc_start: 0.8376 (mt) cc_final: 0.7962 (tp) REVERT: C 220 ASN cc_start: 0.6481 (t0) cc_final: 0.6278 (t0) REVERT: C 229 ASN cc_start: 0.7409 (t0) cc_final: 0.7145 (t0) REVERT: C 230 MET cc_start: 0.5680 (mtm) cc_final: 0.5069 (mtm) REVERT: E 1 MET cc_start: 0.7339 (mtm) cc_final: 0.7082 (mtm) REVERT: E 6 ILE cc_start: 0.6666 (tp) cc_final: 0.6364 (tp) REVERT: E 15 LYS cc_start: 0.8327 (mtmm) cc_final: 0.7941 (mmtm) REVERT: E 36 THR cc_start: 0.7861 (p) cc_final: 0.7488 (p) REVERT: E 86 LYS cc_start: 0.7822 (tptm) cc_final: 0.7557 (mmmm) REVERT: E 101 LYS cc_start: 0.8582 (pttm) cc_final: 0.8250 (pttm) REVERT: E 126 SER cc_start: 0.8289 (t) cc_final: 0.7754 (p) REVERT: E 127 THR cc_start: 0.8047 (m) cc_final: 0.7812 (m) REVERT: E 135 THR cc_start: 0.8408 (m) cc_final: 0.8113 (p) REVERT: E 171 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.7944 (mtm-85) REVERT: E 174 ILE cc_start: 0.7933 (mm) cc_final: 0.7670 (tp) REVERT: E 198 GLU cc_start: 0.6387 (pm20) cc_final: 0.6154 (pm20) REVERT: E 224 THR cc_start: 0.7117 (p) cc_final: 0.6917 (p) REVERT: E 239 GLU cc_start: 0.7125 (tp30) cc_final: 0.6245 (mp0) REVERT: E 274 LYS cc_start: 0.7167 (mppt) cc_final: 0.6730 (mppt) REVERT: E 285 ILE cc_start: 0.8666 (pt) cc_final: 0.8379 (tt) REVERT: E 290 PRO cc_start: 0.8092 (Cg_endo) cc_final: 0.7670 (Cg_exo) REVERT: E 325 GLN cc_start: 0.7310 (tp40) cc_final: 0.7062 (tp40) REVERT: E 326 GLU cc_start: 0.7654 (tp30) cc_final: 0.7359 (tp30) REVERT: E 397 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7424 (mmtp) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.2921 time to fit residues: 127.3732 Evaluate side-chains 324 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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: 2.9990 chunk 102 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 47 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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** B 116 GLN B 155 ASN B 157 HIS ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10899 Z= 0.169 Angle : 0.602 10.412 14963 Z= 0.322 Chirality : 0.043 0.163 1723 Planarity : 0.004 0.057 1683 Dihedral : 20.999 150.052 1931 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: -1.93 (0.24), residues: 1171 helix: -0.31 (0.31), residues: 309 sheet: 0.18 (0.31), residues: 324 loop : -2.90 (0.24), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 50 HIS 0.008 0.001 HIS B 157 PHE 0.025 0.002 PHE C 65 TYR 0.015 0.001 TYR B 218 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 333 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.5981 (t70) cc_final: 0.5564 (t0) REVERT: A 57 LEU cc_start: 0.8114 (mt) cc_final: 0.7838 (mt) REVERT: A 69 LYS cc_start: 0.7735 (mptt) cc_final: 0.7219 (mmtm) REVERT: A 112 THR cc_start: 0.5673 (p) cc_final: 0.5005 (p) REVERT: A 116 LYS cc_start: 0.8043 (mtmm) cc_final: 0.7774 (tptt) REVERT: A 165 LYS cc_start: 0.7449 (mptt) cc_final: 0.7015 (mptt) REVERT: A 213 ARG cc_start: 0.6993 (mtt90) cc_final: 0.6521 (mtt90) REVERT: B 21 ASP cc_start: 0.7271 (t0) cc_final: 0.6367 (t0) REVERT: B 22 PHE cc_start: 0.7594 (m-10) cc_final: 0.7221 (m-10) REVERT: B 107 THR cc_start: 0.8028 (p) cc_final: 0.7603 (t) REVERT: B 132 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7617 (ttmm) REVERT: B 159 LYS cc_start: 0.7803 (ttmm) cc_final: 0.7573 (ttmm) REVERT: B 162 LYS cc_start: 0.7754 (mmmt) cc_final: 0.7343 (mmmt) REVERT: B 207 LYS cc_start: 0.9044 (ptpt) cc_final: 0.8785 (ptpp) REVERT: C 3 VAL cc_start: 0.8370 (t) cc_final: 0.7859 (p) REVERT: C 7 ASP cc_start: 0.7785 (t70) cc_final: 0.7397 (t0) REVERT: C 28 LYS cc_start: 0.8270 (mttm) cc_final: 0.8061 (mttm) REVERT: C 55 MET cc_start: 0.7172 (ttm) cc_final: 0.6682 (ttm) REVERT: C 75 MET cc_start: 0.7908 (tpp) cc_final: 0.7505 (tpp) REVERT: C 77 ILE cc_start: 0.8380 (pt) cc_final: 0.8149 (tt) REVERT: C 85 GLU cc_start: 0.7600 (mp0) cc_final: 0.7194 (mp0) REVERT: C 112 ARG cc_start: 0.8089 (tpp80) cc_final: 0.7644 (tpp80) REVERT: C 165 LYS cc_start: 0.7964 (pttp) cc_final: 0.7453 (ptpt) REVERT: C 167 GLU cc_start: 0.7389 (pp20) cc_final: 0.7164 (pp20) REVERT: C 173 GLU cc_start: 0.6181 (tm-30) cc_final: 0.5906 (tm-30) REVERT: C 189 SER cc_start: 0.8185 (t) cc_final: 0.7763 (p) REVERT: C 195 SER cc_start: 0.8458 (m) cc_final: 0.8123 (p) REVERT: C 205 LEU cc_start: 0.8309 (mt) cc_final: 0.7894 (tp) REVERT: C 220 ASN cc_start: 0.6508 (t0) cc_final: 0.6286 (t0) REVERT: C 229 ASN cc_start: 0.7377 (t0) cc_final: 0.7083 (t0) REVERT: C 230 MET cc_start: 0.5759 (mtm) cc_final: 0.5189 (mtm) REVERT: E 1 MET cc_start: 0.7356 (mtm) cc_final: 0.7104 (mtm) REVERT: E 6 ILE cc_start: 0.6660 (tp) cc_final: 0.6344 (tp) REVERT: E 15 LYS cc_start: 0.8355 (mtmm) cc_final: 0.7935 (mmtm) REVERT: E 36 THR cc_start: 0.7816 (p) cc_final: 0.7474 (p) REVERT: E 86 LYS cc_start: 0.7795 (tptm) cc_final: 0.7579 (mmmm) REVERT: E 101 LYS cc_start: 0.8655 (pttm) cc_final: 0.8362 (pttm) REVERT: E 126 SER cc_start: 0.8270 (t) cc_final: 0.7781 (p) REVERT: E 127 THR cc_start: 0.8081 (m) cc_final: 0.7534 (t) REVERT: E 135 THR cc_start: 0.8061 (m) cc_final: 0.7765 (p) REVERT: E 171 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7972 (mtm-85) REVERT: E 174 ILE cc_start: 0.7947 (mm) cc_final: 0.7606 (tt) REVERT: E 198 GLU cc_start: 0.6348 (pm20) cc_final: 0.6088 (pm20) REVERT: E 239 GLU cc_start: 0.7151 (tp30) cc_final: 0.6278 (mp0) REVERT: E 274 LYS cc_start: 0.7177 (mppt) cc_final: 0.6795 (mppt) REVERT: E 285 ILE cc_start: 0.8644 (pt) cc_final: 0.8354 (tt) REVERT: E 290 PRO cc_start: 0.8108 (Cg_endo) cc_final: 0.7722 (Cg_exo) REVERT: E 325 GLN cc_start: 0.7272 (tp40) cc_final: 0.7021 (tp40) REVERT: E 326 GLU cc_start: 0.7615 (tp30) cc_final: 0.7332 (tp30) REVERT: E 397 LYS cc_start: 0.7784 (mmmt) cc_final: 0.7322 (mmtp) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.2951 time to fit residues: 128.1397 Evaluate side-chains 307 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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: 0.0470 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- 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** B 27 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: 0.6992 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10899 Z= 0.255 Angle : 0.674 11.612 14963 Z= 0.359 Chirality : 0.045 0.198 1723 Planarity : 0.004 0.059 1683 Dihedral : 21.157 152.555 1931 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 0.10 % Allowed : 0.19 % 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: -2.13 (0.24), residues: 1171 helix: -0.55 (0.30), residues: 304 sheet: 0.06 (0.30), residues: 326 loop : -2.98 (0.23), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 50 HIS 0.004 0.001 HIS A 39 PHE 0.028 0.002 PHE E 10 TYR 0.020 0.002 TYR C 59 ARG 0.006 0.001 ARG E 171 ********************** 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 340 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 339 time to evaluate : 1.193 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: A 2 PHE cc_start: 0.6321 (t80) cc_final: 0.5693 (t80) REVERT: A 24 ASP cc_start: 0.6028 (t70) cc_final: 0.5653 (t0) REVERT: A 65 PRO cc_start: 0.6733 (Cg_exo) cc_final: 0.6489 (Cg_endo) REVERT: A 69 LYS cc_start: 0.7706 (mptt) cc_final: 0.7139 (mmtm) REVERT: A 105 GLU cc_start: 0.6880 (tp30) cc_final: 0.6638 (tp30) REVERT: A 112 THR cc_start: 0.5830 (p) cc_final: 0.5154 (p) REVERT: A 116 LYS cc_start: 0.8086 (mtmm) cc_final: 0.7756 (tppt) REVERT: A 165 LYS cc_start: 0.7445 (mptt) cc_final: 0.7022 (mptt) REVERT: A 213 ARG cc_start: 0.6993 (mtt90) cc_final: 0.6526 (mtt90) REVERT: A 229 MET cc_start: 0.6167 (ttt) cc_final: 0.5964 (ttt) REVERT: B 21 ASP cc_start: 0.7333 (t0) cc_final: 0.6314 (t0) REVERT: B 22 PHE cc_start: 0.7661 (m-10) cc_final: 0.7262 (m-10) REVERT: B 107 THR cc_start: 0.8028 (p) cc_final: 0.7623 (t) REVERT: B 132 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7662 (ttmm) REVERT: B 159 LYS cc_start: 0.7892 (ttmm) cc_final: 0.7646 (ttmm) REVERT: B 162 LYS cc_start: 0.7805 (mmmt) cc_final: 0.7364 (mmmt) REVERT: B 207 LYS cc_start: 0.9043 (ptpt) cc_final: 0.8779 (ptpp) REVERT: C 3 VAL cc_start: 0.8496 (t) cc_final: 0.8106 (p) REVERT: C 7 ASP cc_start: 0.7785 (t70) cc_final: 0.7432 (t0) REVERT: C 24 GLU cc_start: 0.8305 (pt0) cc_final: 0.7287 (pt0) REVERT: C 30 LYS cc_start: 0.7524 (mmmm) cc_final: 0.7313 (mmmm) REVERT: C 35 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6601 (mm-30) REVERT: C 55 MET cc_start: 0.7122 (ttm) cc_final: 0.6580 (ttm) REVERT: C 75 MET cc_start: 0.7975 (tpp) cc_final: 0.7445 (tpp) REVERT: C 77 ILE cc_start: 0.8395 (pt) cc_final: 0.8173 (tt) REVERT: C 85 GLU cc_start: 0.7411 (mp0) cc_final: 0.7159 (mp0) REVERT: C 112 ARG cc_start: 0.8163 (tpp80) cc_final: 0.7694 (tpp80) REVERT: C 115 GLU cc_start: 0.8283 (tp30) cc_final: 0.8082 (tp30) REVERT: C 140 LYS cc_start: 0.7906 (ttpt) cc_final: 0.7422 (tptp) REVERT: C 165 LYS cc_start: 0.7968 (pttp) cc_final: 0.7504 (ptpt) REVERT: C 167 GLU cc_start: 0.7435 (pp20) cc_final: 0.7174 (pp20) REVERT: C 173 GLU cc_start: 0.6239 (tm-30) cc_final: 0.5946 (tm-30) REVERT: C 189 SER cc_start: 0.8168 (t) cc_final: 0.7711 (p) REVERT: C 195 SER cc_start: 0.8495 (m) cc_final: 0.8160 (p) REVERT: C 205 LEU cc_start: 0.8379 (mt) cc_final: 0.8094 (tp) REVERT: C 220 ASN cc_start: 0.6538 (t0) cc_final: 0.6281 (t0) REVERT: C 229 ASN cc_start: 0.7454 (t0) cc_final: 0.7154 (t0) REVERT: C 230 MET cc_start: 0.5770 (mtm) cc_final: 0.5146 (mtm) REVERT: E 1 MET cc_start: 0.7302 (mtm) cc_final: 0.7052 (mtm) REVERT: E 6 ILE cc_start: 0.6667 (tp) cc_final: 0.6379 (tp) REVERT: E 49 LEU cc_start: 0.7294 (mt) cc_final: 0.6948 (mt) REVERT: E 93 GLU cc_start: 0.7941 (tp30) cc_final: 0.7617 (tp30) REVERT: E 101 LYS cc_start: 0.8693 (pttm) cc_final: 0.8259 (pttm) REVERT: E 126 SER cc_start: 0.8336 (t) cc_final: 0.7779 (p) REVERT: E 127 THR cc_start: 0.8081 (m) cc_final: 0.7839 (m) REVERT: E 171 ARG cc_start: 0.8283 (mtm-85) cc_final: 0.7985 (mtm-85) REVERT: E 174 ILE cc_start: 0.7961 (mm) cc_final: 0.7608 (tp) REVERT: E 198 GLU cc_start: 0.6415 (pm20) cc_final: 0.6114 (pm20) REVERT: E 203 LEU cc_start: 0.7770 (mt) cc_final: 0.7529 (mt) REVERT: E 239 GLU cc_start: 0.7106 (tp30) cc_final: 0.6600 (mp0) REVERT: E 274 LYS cc_start: 0.7173 (mppt) cc_final: 0.6739 (mppt) REVERT: E 285 ILE cc_start: 0.8770 (pt) cc_final: 0.8386 (tt) REVERT: E 290 PRO cc_start: 0.8030 (Cg_endo) cc_final: 0.7605 (Cg_exo) REVERT: E 325 GLN cc_start: 0.7406 (tp40) cc_final: 0.7157 (tp40) REVERT: E 326 GLU cc_start: 0.7696 (tp30) cc_final: 0.7406 (tp30) REVERT: E 394 GLU cc_start: 0.7388 (pm20) cc_final: 0.7028 (tp30) REVERT: E 397 LYS cc_start: 0.7807 (mmmt) cc_final: 0.7375 (mmtp) outliers start: 1 outliers final: 0 residues processed: 339 average time/residue: 0.2957 time to fit residues: 130.0790 Evaluate side-chains 313 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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: 0.0000 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.0770 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 0.0270 overall best weight: 0.2400 ------------------------------------------------------------------------------- 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 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118630 restraints weight = 19066.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121506 restraints weight = 12053.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123476 restraints weight = 8558.562| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.4347 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= 0.164 Angle : 0.623 10.725 14963 Z= 0.330 Chirality : 0.044 0.175 1723 Planarity : 0.004 0.056 1683 Dihedral : 21.014 150.695 1931 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % 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: -1.93 (0.24), residues: 1171 helix: -0.37 (0.30), residues: 308 sheet: 0.23 (0.31), residues: 320 loop : -2.87 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 50 HIS 0.008 0.001 HIS B 157 PHE 0.024 0.002 PHE E 324 TYR 0.015 0.001 TYR E 354 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: 3004.32 seconds wall clock time: 53 minutes 34.19 seconds (3214.19 seconds total)