Starting phenix.real_space_refine on Fri Mar 15 15:29:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o17_12692/03_2024/7o17_12692_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o17_12692/03_2024/7o17_12692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o17_12692/03_2024/7o17_12692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o17_12692/03_2024/7o17_12692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o17_12692/03_2024/7o17_12692_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o17_12692/03_2024/7o17_12692_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 341 atoms to isotropic. 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 P 6 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 7456 2.51 5 N 2054 2.21 5 O 2127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "E GLU 83": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11679 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3057 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 16, 'TRANS': 386} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "C" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "D" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2030 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 264} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1938 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.46, per 1000 atoms: 0.55 Number of scatterers: 11679 At special positions: 0 Unit cell: (84.24, 81.648, 195.696, 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) S 34 16.00 P 6 15.00 Mg 2 11.99 O 2127 8.00 N 2054 7.00 C 7456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.15 Conformation dependent library (CDL) restraints added in 2.4 seconds 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2746 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 16 sheets defined 36.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 376 through 382 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.546A pdb=" N ARG A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 removed outlier: 3.663A pdb=" N VAL A 397 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 428 Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.591A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 115 removed outlier: 3.632A pdb=" N GLU B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 131 through 142 removed outlier: 3.616A pdb=" N GLN B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 172 removed outlier: 4.015A pdb=" N GLN B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 193 No H-bonds generated for 'chain 'B' and resid 191 through 193' Processing helix chain 'B' and resid 212 through 218 removed outlier: 3.570A pdb=" N ALA B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 240 removed outlier: 3.748A pdb=" N TRP B 240 " --> pdb=" O TRP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 274 removed outlier: 3.838A pdb=" N GLY B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 removed outlier: 3.674A pdb=" N TYR B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.997A pdb=" N MET C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.626A pdb=" N LEU C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 101 " --> pdb=" O HIS C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 116 removed outlier: 3.924A pdb=" N ASP C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 131 through 142 removed outlier: 3.804A pdb=" N LEU C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 142 " --> pdb=" O GLY C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 175 removed outlier: 3.749A pdb=" N GLN C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 212 through 218 removed outlier: 3.755A pdb=" N ALA C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'C' and resid 267 through 271 Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'D' and resid 5 through 17 removed outlier: 3.864A pdb=" N SER D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D 15 " --> pdb=" O GLU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 35 removed outlier: 3.543A pdb=" N LEU D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA D 32 " --> pdb=" O PHE D 28 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 61 removed outlier: 3.611A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 59 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 74 removed outlier: 3.849A pdb=" N ALA D 70 " --> pdb=" O MET D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 82 No H-bonds generated for 'chain 'D' and resid 79 through 82' Processing helix chain 'D' and resid 87 through 90 No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 99 through 119 removed outlier: 3.740A pdb=" N GLY D 103 " --> pdb=" O GLN D 99 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 112 " --> pdb=" O HIS D 108 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 129 removed outlier: 3.528A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 167 removed outlier: 4.565A pdb=" N ILE D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 159 " --> pdb=" O TRP D 155 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 164 " --> pdb=" O PHE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 184 removed outlier: 3.984A pdb=" N GLY D 180 " --> pdb=" O GLY D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 196 removed outlier: 3.895A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU D 193 " --> pdb=" O PHE D 189 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 removed outlier: 3.674A pdb=" N LEU D 215 " --> pdb=" O LEU D 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 215' Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 239 through 244 removed outlier: 3.758A pdb=" N ASP D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 272 removed outlier: 3.602A pdb=" N TRP D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 14 removed outlier: 4.059A pdb=" N ILE E 7 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU E 12 " --> pdb=" O ARG E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 22 No H-bonds generated for 'chain 'E' and resid 19 through 22' Processing helix chain 'E' and resid 24 through 35 removed outlier: 3.787A pdb=" N ALA E 32 " --> pdb=" O PHE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 71 removed outlier: 4.003A pdb=" N THR E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 65 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Proline residue: E 67 - end of helix removed outlier: 3.665A pdb=" N ALA E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 84 Processing helix chain 'E' and resid 86 through 92 Processing helix chain 'E' and resid 97 through 127 removed outlier: 3.803A pdb=" N GLY E 103 " --> pdb=" O GLN E 99 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY E 121 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS E 122 " --> pdb=" O ILE E 118 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA E 123 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 141 removed outlier: 3.610A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 165 removed outlier: 4.591A pdb=" N SER E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU E 164 " --> pdb=" O PHE E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 187 removed outlier: 4.345A pdb=" N ALA E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 199 removed outlier: 3.502A pdb=" N LEU E 193 " --> pdb=" O PHE E 189 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 194 " --> pdb=" O ASP E 190 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 271 removed outlier: 3.547A pdb=" N LEU E 254 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU E 257 " --> pdb=" O TRP E 253 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP E 259 " --> pdb=" O CYS E 255 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU E 266 " --> pdb=" O VAL E 262 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 44 through 46 removed outlier: 5.798A pdb=" N GLN A 63 " --> pdb=" O TRP A 45 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 89 " --> pdb=" O LEU A 64 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 50 through 53 Processing sheet with id= C, first strand: chain 'A' and resid 56 through 58 Processing sheet with id= D, first strand: chain 'A' and resid 119 through 121 removed outlier: 5.973A pdb=" N GLN A 141 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG A 171 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N SER A 215 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A 237 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 322 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 146 through 148 removed outlier: 6.668A pdb=" N HIS A 176 " --> pdb=" O ILE A 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 184 through 187 Processing sheet with id= G, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.892A pdb=" N VAL A 220 " --> pdb=" O ILE A 199 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 242 through 244 removed outlier: 6.807A pdb=" N PHE A 265 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N HIS A 302 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA A 325 " --> pdb=" O PHE A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 4 through 6 Processing sheet with id= J, first strand: chain 'B' and resid 197 through 200 removed outlier: 3.913A pdb=" N PHE B 35 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE B 181 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N LEU B 34 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B 183 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.887A pdb=" N GLU B 281 " --> pdb=" O ARG B 226 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.507A pdb=" N GLN B 11 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR B 13 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 4 through 6 Processing sheet with id= N, first strand: chain 'C' and resid 197 through 200 removed outlier: 6.875A pdb=" N ILE C 181 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU C 34 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU C 183 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 150 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS C 184 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 224 through 228 removed outlier: 3.667A pdb=" N ASP C 279 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 246 through 250 removed outlier: 3.595A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 5.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3789 1.34 - 1.46: 2430 1.46 - 1.58: 5613 1.58 - 1.70: 11 1.70 - 1.82: 58 Bond restraints: 11901 Sorted by residual: bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.74e+01 bond pdb=" C4 ATP B 401 " pdb=" C5 ATP B 401 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" C5 ATP C 401 " pdb=" C6 ATP C 401 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.94e+01 bond pdb=" C5 ATP B 401 " pdb=" C6 ATP B 401 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.90e+01 bond pdb=" C4 ATP B 401 " pdb=" N9 ATP B 401 " ideal model delta sigma weight residual 1.374 1.320 0.054 1.00e-02 1.00e+04 2.92e+01 ... (remaining 11896 not shown) Histogram of bond angle deviations from ideal: 96.60 - 104.57: 183 104.57 - 112.54: 6058 112.54 - 120.52: 5617 120.52 - 128.49: 4219 128.49 - 136.46: 113 Bond angle restraints: 16190 Sorted by residual: angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 120.83 19.04 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PA ATP B 401 " pdb=" O3A ATP B 401 " pdb=" PB ATP B 401 " ideal model delta sigma weight residual 136.83 118.04 18.79 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 123.32 16.55 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PA ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sigma weight residual 136.83 126.48 10.35 1.00e+00 1.00e+00 1.07e+02 angle pdb=" C5 ATP C 401 " pdb=" C4 ATP C 401 " pdb=" N3 ATP C 401 " ideal model delta sigma weight residual 126.80 119.16 7.64 1.00e+00 1.00e+00 5.84e+01 ... (remaining 16185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6099 17.91 - 35.82: 731 35.82 - 53.73: 174 53.73 - 71.65: 37 71.65 - 89.56: 10 Dihedral angle restraints: 7051 sinusoidal: 2740 harmonic: 4311 Sorted by residual: dihedral pdb=" CA GLY A 349 " pdb=" C GLY A 349 " pdb=" N ASN A 350 " pdb=" CA ASN A 350 " ideal model delta harmonic sigma weight residual 180.00 -139.80 -40.20 0 5.00e+00 4.00e-02 6.47e+01 dihedral pdb=" CA ARG A 225 " pdb=" C ARG A 225 " pdb=" N THR A 226 " pdb=" CA THR A 226 " ideal model delta harmonic sigma weight residual 180.00 144.04 35.96 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA VAL A 413 " pdb=" C VAL A 413 " pdb=" N GLN A 414 " pdb=" CA GLN A 414 " ideal model delta harmonic sigma weight residual 180.00 145.26 34.74 0 5.00e+00 4.00e-02 4.83e+01 ... (remaining 7048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1470 0.072 - 0.145: 343 0.145 - 0.217: 43 0.217 - 0.289: 14 0.289 - 0.361: 6 Chirality restraints: 1876 Sorted by residual: chirality pdb=" CB ILE A 298 " pdb=" CA ILE A 298 " pdb=" CG1 ILE A 298 " pdb=" CG2 ILE A 298 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA ASN A 248 " pdb=" N ASN A 248 " pdb=" C ASN A 248 " pdb=" CB ASN A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CB VAL D 168 " pdb=" CA VAL D 168 " pdb=" CG1 VAL D 168 " pdb=" CG2 VAL D 168 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1873 not shown) Planarity restraints: 2067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 112 " 0.052 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO A 113 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 66 " 0.051 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO E 67 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 28 " -0.050 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO A 29 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " -0.042 5.00e-02 4.00e+02 ... (remaining 2064 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 329 2.65 - 3.21: 10813 3.21 - 3.78: 21468 3.78 - 4.34: 27633 4.34 - 4.90: 41674 Nonbonded interactions: 101917 Sorted by model distance: nonbonded pdb=" OG1 THR C 43 " pdb="MG MG C 402 " model vdw 2.089 2.170 nonbonded pdb=" O2B ATP B 401 " pdb="MG MG B 402 " model vdw 2.100 2.170 nonbonded pdb=" O3G ATP C 401 " pdb="MG MG C 402 " model vdw 2.107 2.170 nonbonded pdb=" O3G ATP B 401 " pdb="MG MG B 402 " model vdw 2.114 2.170 nonbonded pdb=" O2B ATP C 401 " pdb="MG MG C 402 " model vdw 2.115 2.170 ... (remaining 101912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 200 or (resid 201 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 202 through 204 and \ (name N or name CA or name C or name O or name CB )) or resid 205 through 230 o \ r resid 245 through 274)) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 2.430 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.840 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.007 0.076 11901 Z= 0.453 Angle : 1.218 19.043 16190 Z= 0.689 Chirality : 0.066 0.361 1876 Planarity : 0.009 0.079 2067 Dihedral : 16.813 89.557 4305 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 1.09 % Allowed : 18.69 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -5.33 (0.16), residues: 1519 helix: -4.23 (0.11), residues: 546 sheet: -2.79 (0.31), residues: 214 loop : -3.18 (0.18), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 98 HIS 0.009 0.003 HIS B 120 PHE 0.022 0.003 PHE D 185 TYR 0.019 0.003 TYR C 13 ARG 0.027 0.003 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 1.466 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 62 MET cc_start: 0.8540 (tpp) cc_final: 0.8263 (tpt) REVERT: A 105 MET cc_start: 0.8162 (tpt) cc_final: 0.7433 (tpp) REVERT: A 209 MET cc_start: 0.9416 (mmm) cc_final: 0.9066 (mmm) REVERT: A 386 VAL cc_start: 0.9641 (p) cc_final: 0.9259 (p) REVERT: A 390 MET cc_start: 0.9771 (mmp) cc_final: 0.9506 (mmm) REVERT: B 34 LEU cc_start: 0.9720 (mp) cc_final: 0.9443 (tp) REVERT: B 102 LYS cc_start: 0.9268 (mmmm) cc_final: 0.9020 (mmmt) REVERT: B 133 MET cc_start: 0.9123 (mtp) cc_final: 0.8819 (mtp) REVERT: B 295 MET cc_start: 0.9136 (mmm) cc_final: 0.8874 (mmm) REVERT: C 46 MET cc_start: 0.9090 (mmt) cc_final: 0.8820 (mmm) REVERT: C 127 LYS cc_start: 0.9382 (pttm) cc_final: 0.9093 (pttm) REVERT: C 133 MET cc_start: 0.9447 (mtp) cc_final: 0.9043 (mtm) REVERT: D 81 GLU cc_start: 0.9326 (mp0) cc_final: 0.9075 (mp0) REVERT: D 185 PHE cc_start: 0.9211 (t80) cc_final: 0.8635 (t80) REVERT: D 189 PHE cc_start: 0.9247 (t80) cc_final: 0.8599 (t80) REVERT: E 20 TRP cc_start: 0.7417 (m-10) cc_final: 0.6842 (m-90) REVERT: E 66 MET cc_start: 0.9428 (tpp) cc_final: 0.8656 (tpp) REVERT: E 72 LEU cc_start: 0.9653 (mm) cc_final: 0.9268 (pp) REVERT: E 76 ASP cc_start: 0.8902 (p0) cc_final: 0.8588 (p0) REVERT: E 170 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8444 (tm-30) REVERT: E 221 TYR cc_start: 0.8948 (t80) cc_final: 0.8689 (t80) outliers start: 13 outliers final: 5 residues processed: 166 average time/residue: 0.2543 time to fit residues: 59.4511 Evaluate side-chains 105 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN A 212 ASN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN B 20 HIS B 23 ASN B 82 ASN C 20 HIS C 23 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN D 205 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11901 Z= 0.198 Angle : 0.690 9.332 16190 Z= 0.354 Chirality : 0.044 0.197 1876 Planarity : 0.005 0.060 2067 Dihedral : 8.955 89.034 1727 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.25 % Allowed : 6.71 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.02 (0.19), residues: 1519 helix: -2.52 (0.17), residues: 612 sheet: -2.39 (0.31), residues: 234 loop : -2.81 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 343 HIS 0.012 0.001 HIS C 97 PHE 0.015 0.002 PHE D 185 TYR 0.021 0.001 TYR C 168 ARG 0.004 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8627 (tpp) cc_final: 0.8339 (tpt) REVERT: A 208 TYR cc_start: 0.9065 (m-10) cc_final: 0.8722 (m-10) REVERT: A 209 MET cc_start: 0.9361 (mmm) cc_final: 0.8931 (mmm) REVERT: A 386 VAL cc_start: 0.9598 (p) cc_final: 0.9104 (p) REVERT: A 390 MET cc_start: 0.9737 (mmp) cc_final: 0.9453 (mmm) REVERT: A 402 GLN cc_start: 0.9701 (OUTLIER) cc_final: 0.9265 (mm110) REVERT: B 47 LYS cc_start: 0.9660 (mttm) cc_final: 0.9423 (mmtp) REVERT: B 102 LYS cc_start: 0.9283 (mmmm) cc_final: 0.9029 (mmmt) REVERT: B 133 MET cc_start: 0.9021 (mtp) cc_final: 0.8781 (mtp) REVERT: B 143 LEU cc_start: 0.9831 (mm) cc_final: 0.9594 (mt) REVERT: B 295 MET cc_start: 0.9045 (mmm) cc_final: 0.8818 (mmp) REVERT: C 47 LYS cc_start: 0.9411 (mtmm) cc_final: 0.9148 (mtmt) REVERT: C 133 MET cc_start: 0.9094 (mtp) cc_final: 0.8714 (mtp) REVERT: D 14 ASP cc_start: 0.8970 (p0) cc_final: 0.8556 (p0) REVERT: D 66 MET cc_start: 0.9587 (tpp) cc_final: 0.8932 (tpp) REVERT: D 81 GLU cc_start: 0.9291 (mp0) cc_final: 0.9083 (mp0) REVERT: D 101 LEU cc_start: 0.9423 (mt) cc_final: 0.9187 (mt) REVERT: D 158 LEU cc_start: 0.9691 (mt) cc_final: 0.9460 (mt) REVERT: D 189 PHE cc_start: 0.8963 (t80) cc_final: 0.8520 (t80) REVERT: D 221 TYR cc_start: 0.9002 (t80) cc_final: 0.8573 (t80) REVERT: E 20 TRP cc_start: 0.7162 (m-10) cc_final: 0.6686 (m-90) REVERT: E 66 MET cc_start: 0.9251 (tpp) cc_final: 0.8589 (tpp) REVERT: E 72 LEU cc_start: 0.9677 (mm) cc_final: 0.9222 (tt) REVERT: E 76 ASP cc_start: 0.8915 (p0) cc_final: 0.8189 (p0) REVERT: E 88 MET cc_start: 0.9526 (ptp) cc_final: 0.9228 (mpp) REVERT: E 104 LYS cc_start: 0.9685 (mmmt) cc_final: 0.9298 (tptp) REVERT: E 120 PHE cc_start: 0.8643 (t80) cc_final: 0.8394 (t80) REVERT: E 223 LEU cc_start: 0.9720 (mt) cc_final: 0.9422 (mt) outliers start: 3 outliers final: 1 residues processed: 145 average time/residue: 0.2244 time to fit residues: 47.2602 Evaluate side-chains 106 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 121 optimal weight: 30.0000 chunk 135 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11901 Z= 0.188 Angle : 0.644 8.515 16190 Z= 0.329 Chirality : 0.043 0.220 1876 Planarity : 0.004 0.053 2067 Dihedral : 8.115 89.997 1727 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.08 % Allowed : 7.21 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.15 (0.20), residues: 1519 helix: -1.56 (0.19), residues: 617 sheet: -2.24 (0.30), residues: 259 loop : -2.44 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 343 HIS 0.007 0.001 HIS C 97 PHE 0.026 0.002 PHE E 143 TYR 0.017 0.001 TYR C 168 ARG 0.004 0.000 ARG C 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.527 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 62 MET cc_start: 0.8627 (tpp) cc_final: 0.8360 (tpt) REVERT: A 208 TYR cc_start: 0.9186 (m-10) cc_final: 0.8869 (m-10) REVERT: A 209 MET cc_start: 0.9356 (mmm) cc_final: 0.8931 (mmm) REVERT: A 386 VAL cc_start: 0.9629 (p) cc_final: 0.9186 (p) REVERT: A 390 MET cc_start: 0.9745 (mmp) cc_final: 0.9479 (mmm) REVERT: B 25 ASN cc_start: 0.9203 (p0) cc_final: 0.8934 (p0) REVERT: B 47 LYS cc_start: 0.9651 (mttm) cc_final: 0.9427 (mmtp) REVERT: B 82 ASN cc_start: 0.8897 (p0) cc_final: 0.8664 (p0) REVERT: B 102 LYS cc_start: 0.9333 (mmmm) cc_final: 0.9058 (mmmt) REVERT: B 133 MET cc_start: 0.9031 (mtp) cc_final: 0.8802 (mtp) REVERT: B 143 LEU cc_start: 0.9848 (mm) cc_final: 0.9609 (mt) REVERT: B 295 MET cc_start: 0.9126 (mmm) cc_final: 0.8866 (mmm) REVERT: C 24 LEU cc_start: 0.9525 (tt) cc_final: 0.9195 (mp) REVERT: C 25 ASN cc_start: 0.9445 (m-40) cc_final: 0.9193 (t0) REVERT: C 47 LYS cc_start: 0.9422 (mtmm) cc_final: 0.9201 (mmtp) REVERT: D 66 MET cc_start: 0.9550 (tpp) cc_final: 0.9016 (tpp) REVERT: D 72 LEU cc_start: 0.9266 (pp) cc_final: 0.9050 (pp) REVERT: D 101 LEU cc_start: 0.9343 (mt) cc_final: 0.9095 (mt) REVERT: D 158 LEU cc_start: 0.9689 (mt) cc_final: 0.9429 (mt) REVERT: D 189 PHE cc_start: 0.9006 (t80) cc_final: 0.8592 (t80) REVERT: D 221 TYR cc_start: 0.9017 (t80) cc_final: 0.8491 (t80) REVERT: E 66 MET cc_start: 0.9234 (tpp) cc_final: 0.8689 (tpp) REVERT: E 72 LEU cc_start: 0.9691 (mm) cc_final: 0.9269 (tt) REVERT: E 76 ASP cc_start: 0.8845 (p0) cc_final: 0.8494 (p0) REVERT: E 104 LYS cc_start: 0.9652 (mmmt) cc_final: 0.9260 (tptp) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.2364 time to fit residues: 49.7073 Evaluate side-chains 107 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 30.0000 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11901 Z= 0.263 Angle : 0.681 8.527 16190 Z= 0.350 Chirality : 0.044 0.202 1876 Planarity : 0.004 0.049 2067 Dihedral : 7.877 86.788 1727 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.64 (0.21), residues: 1519 helix: -0.98 (0.20), residues: 614 sheet: -2.13 (0.31), residues: 259 loop : -2.25 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 236 HIS 0.006 0.002 HIS B 120 PHE 0.019 0.002 PHE E 143 TYR 0.014 0.002 TYR E 221 ARG 0.003 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.405 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 62 MET cc_start: 0.8656 (tpp) cc_final: 0.8415 (tpt) REVERT: A 208 TYR cc_start: 0.9126 (m-10) cc_final: 0.8833 (m-10) REVERT: A 209 MET cc_start: 0.9368 (mmm) cc_final: 0.8948 (mmm) REVERT: A 386 VAL cc_start: 0.9614 (p) cc_final: 0.9096 (p) REVERT: A 390 MET cc_start: 0.9707 (mmp) cc_final: 0.9437 (mmm) REVERT: B 25 ASN cc_start: 0.9142 (p0) cc_final: 0.8809 (p0) REVERT: B 102 LYS cc_start: 0.9345 (mmmm) cc_final: 0.9073 (mmmt) REVERT: B 295 MET cc_start: 0.9142 (mmm) cc_final: 0.8873 (mmm) REVERT: C 24 LEU cc_start: 0.9527 (tt) cc_final: 0.9178 (mp) REVERT: C 47 LYS cc_start: 0.9428 (mtmm) cc_final: 0.9190 (mmtp) REVERT: C 133 MET cc_start: 0.9055 (mtp) cc_final: 0.8624 (mtp) REVERT: C 168 TYR cc_start: 0.9586 (m-80) cc_final: 0.9013 (m-80) REVERT: C 295 MET cc_start: 0.9445 (tmm) cc_final: 0.9244 (tmm) REVERT: D 65 LEU cc_start: 0.9778 (pt) cc_final: 0.9391 (tp) REVERT: D 66 MET cc_start: 0.9548 (tpp) cc_final: 0.9074 (tpp) REVERT: D 72 LEU cc_start: 0.9266 (pp) cc_final: 0.9052 (pp) REVERT: D 101 LEU cc_start: 0.9366 (mt) cc_final: 0.9110 (mt) REVERT: D 158 LEU cc_start: 0.9672 (mt) cc_final: 0.9339 (mt) REVERT: D 221 TYR cc_start: 0.9072 (t80) cc_final: 0.8571 (t80) REVERT: D 222 ARG cc_start: 0.9604 (mtm-85) cc_final: 0.9129 (mtm-85) REVERT: E 66 MET cc_start: 0.9235 (tpp) cc_final: 0.8616 (tpp) REVERT: E 76 ASP cc_start: 0.8830 (p0) cc_final: 0.8560 (p0) REVERT: E 104 LYS cc_start: 0.9654 (mmmt) cc_final: 0.9292 (tptp) REVERT: E 143 PHE cc_start: 0.9118 (m-80) cc_final: 0.8904 (m-80) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.2338 time to fit residues: 45.9101 Evaluate side-chains 102 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS A 179 ASN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11901 Z= 0.270 Angle : 0.690 8.924 16190 Z= 0.353 Chirality : 0.044 0.241 1876 Planarity : 0.004 0.048 2067 Dihedral : 7.713 84.462 1727 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.35 (0.21), residues: 1519 helix: -0.71 (0.21), residues: 593 sheet: -1.98 (0.31), residues: 254 loop : -2.09 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 236 HIS 0.007 0.002 HIS B 120 PHE 0.033 0.002 PHE E 183 TYR 0.018 0.002 TYR B 86 ARG 0.003 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.282 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 62 MET cc_start: 0.8699 (tpp) cc_final: 0.8480 (tpt) REVERT: A 209 MET cc_start: 0.9413 (mmm) cc_final: 0.8995 (mmm) REVERT: A 386 VAL cc_start: 0.9650 (p) cc_final: 0.9240 (p) REVERT: B 25 ASN cc_start: 0.9187 (p0) cc_final: 0.8837 (p0) REVERT: B 85 PHE cc_start: 0.9411 (m-80) cc_final: 0.9065 (m-80) REVERT: B 102 LYS cc_start: 0.9332 (mmmm) cc_final: 0.9082 (mmmt) REVERT: B 295 MET cc_start: 0.9204 (mmm) cc_final: 0.8898 (mmp) REVERT: C 24 LEU cc_start: 0.9561 (tt) cc_final: 0.9200 (mp) REVERT: C 46 MET cc_start: 0.9358 (mmp) cc_final: 0.9084 (mmm) REVERT: C 47 LYS cc_start: 0.9420 (mtmm) cc_final: 0.9189 (mmtp) REVERT: C 93 GLU cc_start: 0.9550 (mt-10) cc_final: 0.9235 (mm-30) REVERT: C 133 MET cc_start: 0.9041 (mtp) cc_final: 0.8630 (mtp) REVERT: C 168 TYR cc_start: 0.9575 (m-80) cc_final: 0.9217 (m-10) REVERT: C 295 MET cc_start: 0.9471 (tmm) cc_final: 0.9263 (tmm) REVERT: D 66 MET cc_start: 0.9547 (tpp) cc_final: 0.9174 (tpp) REVERT: D 101 LEU cc_start: 0.9348 (mt) cc_final: 0.9100 (mt) REVERT: D 158 LEU cc_start: 0.9668 (mt) cc_final: 0.9419 (mt) REVERT: D 189 PHE cc_start: 0.9099 (t80) cc_final: 0.8789 (t80) REVERT: D 221 TYR cc_start: 0.9170 (t80) cc_final: 0.8846 (t80) REVERT: E 66 MET cc_start: 0.9257 (tpp) cc_final: 0.8643 (tpp) REVERT: E 104 LYS cc_start: 0.9648 (mmmt) cc_final: 0.9166 (mtmt) REVERT: E 171 LYS cc_start: 0.8942 (tptp) cc_final: 0.8721 (tptp) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.2261 time to fit residues: 43.2712 Evaluate side-chains 102 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 30.0000 chunk 12 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11901 Z= 0.173 Angle : 0.649 9.777 16190 Z= 0.320 Chirality : 0.044 0.241 1876 Planarity : 0.004 0.074 2067 Dihedral : 7.426 83.909 1727 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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 (0.22), residues: 1519 helix: -0.48 (0.21), residues: 608 sheet: -1.99 (0.31), residues: 259 loop : -2.04 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 236 HIS 0.004 0.001 HIS C 194 PHE 0.029 0.002 PHE E 183 TYR 0.017 0.001 TYR B 86 ARG 0.003 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.377 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 62 MET cc_start: 0.8618 (tpp) cc_final: 0.8397 (tpt) REVERT: A 209 MET cc_start: 0.9243 (mmm) cc_final: 0.8815 (mmm) REVERT: A 386 VAL cc_start: 0.9673 (p) cc_final: 0.9301 (p) REVERT: B 25 ASN cc_start: 0.9187 (p0) cc_final: 0.8842 (p0) REVERT: B 85 PHE cc_start: 0.9389 (m-80) cc_final: 0.9131 (m-80) REVERT: B 102 LYS cc_start: 0.9349 (mmmm) cc_final: 0.9087 (mmmt) REVERT: B 127 LYS cc_start: 0.9574 (tmtt) cc_final: 0.9346 (tptt) REVERT: B 133 MET cc_start: 0.9320 (mtp) cc_final: 0.9108 (mtp) REVERT: B 143 LEU cc_start: 0.9844 (mm) cc_final: 0.9634 (mt) REVERT: B 295 MET cc_start: 0.9132 (mmm) cc_final: 0.8877 (mmm) REVERT: C 24 LEU cc_start: 0.9547 (tt) cc_final: 0.9182 (mp) REVERT: C 35 PHE cc_start: 0.8879 (m-80) cc_final: 0.8666 (m-80) REVERT: C 46 MET cc_start: 0.9327 (mmp) cc_final: 0.8999 (mmm) REVERT: C 47 LYS cc_start: 0.9421 (mtmm) cc_final: 0.9136 (mtmt) REVERT: C 133 MET cc_start: 0.9154 (mtp) cc_final: 0.8708 (mtp) REVERT: C 295 MET cc_start: 0.9490 (tmm) cc_final: 0.9290 (tmm) REVERT: D 66 MET cc_start: 0.9520 (tpp) cc_final: 0.9162 (tpp) REVERT: D 76 ASP cc_start: 0.9404 (p0) cc_final: 0.9063 (p0) REVERT: D 101 LEU cc_start: 0.9340 (mt) cc_final: 0.9051 (mt) REVERT: D 158 LEU cc_start: 0.9647 (mt) cc_final: 0.9402 (mt) REVERT: D 189 PHE cc_start: 0.9070 (t80) cc_final: 0.8813 (t80) REVERT: D 221 TYR cc_start: 0.9123 (t80) cc_final: 0.8891 (t80) REVERT: E 66 MET cc_start: 0.9263 (tpp) cc_final: 0.8773 (tpp) REVERT: E 83 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8175 (mp0) REVERT: E 104 LYS cc_start: 0.9644 (mmmt) cc_final: 0.9184 (mtmt) REVERT: E 171 LYS cc_start: 0.8937 (tptp) cc_final: 0.8651 (tptp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2457 time to fit residues: 48.6805 Evaluate side-chains 103 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 66 optimal weight: 30.0000 chunk 89 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11901 Z= 0.175 Angle : 0.644 9.115 16190 Z= 0.319 Chirality : 0.044 0.237 1876 Planarity : 0.004 0.057 2067 Dihedral : 7.284 83.573 1727 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: -2.08 (0.22), residues: 1519 helix: -0.39 (0.21), residues: 609 sheet: -1.98 (0.31), residues: 259 loop : -2.00 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 182 HIS 0.006 0.001 HIS B 97 PHE 0.028 0.002 PHE E 183 TYR 0.017 0.001 TYR B 86 ARG 0.003 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.413 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 62 MET cc_start: 0.8606 (tpp) cc_final: 0.8391 (tpt) REVERT: A 209 MET cc_start: 0.9254 (mmm) cc_final: 0.8858 (mmm) REVERT: A 386 VAL cc_start: 0.9646 (p) cc_final: 0.9178 (p) REVERT: A 390 MET cc_start: 0.9596 (mmp) cc_final: 0.9229 (mmm) REVERT: A 396 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8508 (mm-30) REVERT: B 25 ASN cc_start: 0.9208 (p0) cc_final: 0.8863 (p0) REVERT: B 85 PHE cc_start: 0.9389 (m-80) cc_final: 0.9139 (m-80) REVERT: B 102 LYS cc_start: 0.9341 (mmmm) cc_final: 0.9060 (mmmt) REVERT: B 127 LYS cc_start: 0.9611 (tmtt) cc_final: 0.9368 (tptt) REVERT: B 133 MET cc_start: 0.9325 (mtp) cc_final: 0.9115 (mtp) REVERT: B 143 LEU cc_start: 0.9841 (mm) cc_final: 0.9630 (mt) REVERT: B 295 MET cc_start: 0.9134 (mmm) cc_final: 0.8880 (mmm) REVERT: C 24 LEU cc_start: 0.9549 (tt) cc_final: 0.9182 (mp) REVERT: C 35 PHE cc_start: 0.8859 (m-80) cc_final: 0.8647 (m-80) REVERT: C 46 MET cc_start: 0.9322 (mmp) cc_final: 0.8974 (mmm) REVERT: C 47 LYS cc_start: 0.9413 (mtmm) cc_final: 0.9142 (mmtp) REVERT: C 133 MET cc_start: 0.9155 (mtp) cc_final: 0.8702 (mtp) REVERT: C 168 TYR cc_start: 0.9580 (m-80) cc_final: 0.9352 (m-10) REVERT: C 295 MET cc_start: 0.9494 (tmm) cc_final: 0.9290 (tmm) REVERT: D 66 MET cc_start: 0.9545 (tpp) cc_final: 0.9201 (tpp) REVERT: D 76 ASP cc_start: 0.9464 (p0) cc_final: 0.9145 (p0) REVERT: D 101 LEU cc_start: 0.9335 (mt) cc_final: 0.9050 (mt) REVERT: D 158 LEU cc_start: 0.9662 (mt) cc_final: 0.9399 (mt) REVERT: D 179 LEU cc_start: 0.9306 (pp) cc_final: 0.9081 (pp) REVERT: D 189 PHE cc_start: 0.9085 (t80) cc_final: 0.8825 (t80) REVERT: E 66 MET cc_start: 0.9244 (tpp) cc_final: 0.8756 (tpp) REVERT: E 72 LEU cc_start: 0.9668 (mm) cc_final: 0.9294 (tt) REVERT: E 76 ASP cc_start: 0.8885 (p0) cc_final: 0.8355 (p0) REVERT: E 83 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8103 (mp0) REVERT: E 104 LYS cc_start: 0.9641 (mmmt) cc_final: 0.9181 (mtmt) REVERT: E 118 ILE cc_start: 0.8756 (tp) cc_final: 0.8417 (tp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2486 time to fit residues: 49.2839 Evaluate side-chains 106 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 113 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 126 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11901 Z= 0.180 Angle : 0.646 8.196 16190 Z= 0.319 Chirality : 0.044 0.233 1876 Planarity : 0.004 0.048 2067 Dihedral : 7.149 82.900 1727 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.22), residues: 1519 helix: -0.31 (0.21), residues: 616 sheet: -1.98 (0.31), residues: 259 loop : -2.01 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 182 HIS 0.005 0.001 HIS B 194 PHE 0.026 0.002 PHE E 183 TYR 0.016 0.001 TYR B 86 ARG 0.003 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8595 (tpp) cc_final: 0.8384 (tpt) REVERT: A 209 MET cc_start: 0.9264 (mmm) cc_final: 0.8893 (mmm) REVERT: A 386 VAL cc_start: 0.9642 (p) cc_final: 0.9162 (p) REVERT: A 390 MET cc_start: 0.9638 (mmp) cc_final: 0.9257 (mmm) REVERT: A 396 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8455 (mm-30) REVERT: B 25 ASN cc_start: 0.9181 (p0) cc_final: 0.8821 (p0) REVERT: B 85 PHE cc_start: 0.9390 (m-80) cc_final: 0.9124 (m-80) REVERT: B 102 LYS cc_start: 0.9356 (mmmm) cc_final: 0.9061 (mmmt) REVERT: B 127 LYS cc_start: 0.9625 (tmtt) cc_final: 0.9385 (tptt) REVERT: B 143 LEU cc_start: 0.9842 (mm) cc_final: 0.9630 (mt) REVERT: B 295 MET cc_start: 0.9134 (mmm) cc_final: 0.8878 (mmm) REVERT: C 24 LEU cc_start: 0.9549 (tt) cc_final: 0.9182 (mp) REVERT: C 46 MET cc_start: 0.9336 (mmp) cc_final: 0.9002 (mmm) REVERT: C 47 LYS cc_start: 0.9399 (mtmm) cc_final: 0.9169 (mmtp) REVERT: C 133 MET cc_start: 0.9159 (mtp) cc_final: 0.8705 (mtp) REVERT: D 66 MET cc_start: 0.9561 (tpp) cc_final: 0.9233 (tpp) REVERT: D 76 ASP cc_start: 0.9511 (p0) cc_final: 0.9162 (p0) REVERT: D 101 LEU cc_start: 0.9390 (mt) cc_final: 0.9104 (mt) REVERT: D 158 LEU cc_start: 0.9634 (mt) cc_final: 0.9369 (mt) REVERT: D 189 PHE cc_start: 0.9109 (t80) cc_final: 0.8850 (t80) REVERT: D 221 TYR cc_start: 0.9045 (t80) cc_final: 0.8607 (t80) REVERT: D 222 ARG cc_start: 0.9566 (mtm-85) cc_final: 0.8880 (mtm-85) REVERT: E 66 MET cc_start: 0.9247 (tpp) cc_final: 0.8745 (tpp) REVERT: E 76 ASP cc_start: 0.8908 (p0) cc_final: 0.8663 (p0) REVERT: E 83 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8183 (mp0) REVERT: E 97 ARG cc_start: 0.8941 (mtt180) cc_final: 0.8479 (mmm-85) REVERT: E 118 ILE cc_start: 0.8747 (tp) cc_final: 0.8447 (tp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2456 time to fit residues: 47.4342 Evaluate side-chains 104 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 8.9990 chunk 138 optimal weight: 0.0050 chunk 81 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 0.0020 chunk 121 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 overall best weight: 2.1806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11901 Z= 0.182 Angle : 0.643 8.553 16190 Z= 0.317 Chirality : 0.043 0.231 1876 Planarity : 0.004 0.048 2067 Dihedral : 7.091 82.679 1727 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -1.94 (0.22), residues: 1519 helix: -0.22 (0.21), residues: 620 sheet: -1.96 (0.32), residues: 259 loop : -1.99 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 182 HIS 0.008 0.001 HIS B 194 PHE 0.025 0.002 PHE E 183 TYR 0.015 0.001 TYR B 86 ARG 0.004 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.488 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 62 MET cc_start: 0.8583 (tpp) cc_final: 0.8375 (tpt) REVERT: A 209 MET cc_start: 0.9274 (mmm) cc_final: 0.8996 (mmm) REVERT: A 386 VAL cc_start: 0.9668 (p) cc_final: 0.9179 (p) REVERT: A 390 MET cc_start: 0.9653 (mmp) cc_final: 0.9264 (mmm) REVERT: A 396 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8430 (mm-30) REVERT: B 25 ASN cc_start: 0.9196 (p0) cc_final: 0.8839 (p0) REVERT: B 85 PHE cc_start: 0.9370 (m-80) cc_final: 0.9118 (m-80) REVERT: B 102 LYS cc_start: 0.9363 (mmmm) cc_final: 0.9065 (mmmt) REVERT: B 127 LYS cc_start: 0.9625 (tmtt) cc_final: 0.9380 (tptt) REVERT: B 133 MET cc_start: 0.9334 (mtp) cc_final: 0.9118 (mtp) REVERT: B 143 LEU cc_start: 0.9821 (mm) cc_final: 0.9612 (mt) REVERT: B 295 MET cc_start: 0.9139 (mmm) cc_final: 0.8878 (mmm) REVERT: C 24 LEU cc_start: 0.9551 (tt) cc_final: 0.9183 (mp) REVERT: C 46 MET cc_start: 0.9334 (mmp) cc_final: 0.9002 (mmm) REVERT: C 47 LYS cc_start: 0.9394 (mtmm) cc_final: 0.9161 (mmtp) REVERT: C 133 MET cc_start: 0.9164 (mtp) cc_final: 0.8709 (mtp) REVERT: D 66 MET cc_start: 0.9566 (tpp) cc_final: 0.9252 (tpp) REVERT: D 76 ASP cc_start: 0.9577 (p0) cc_final: 0.9266 (p0) REVERT: D 101 LEU cc_start: 0.9387 (mt) cc_final: 0.9103 (mt) REVERT: D 179 LEU cc_start: 0.9208 (pp) cc_final: 0.8985 (pp) REVERT: D 189 PHE cc_start: 0.9120 (t80) cc_final: 0.8867 (t80) REVERT: D 221 TYR cc_start: 0.9073 (t80) cc_final: 0.8586 (t80) REVERT: E 66 MET cc_start: 0.9247 (tpp) cc_final: 0.8742 (tpp) REVERT: E 72 LEU cc_start: 0.9650 (mm) cc_final: 0.9293 (tt) REVERT: E 76 ASP cc_start: 0.8908 (p0) cc_final: 0.8568 (p0) REVERT: E 83 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8209 (mp0) REVERT: E 97 ARG cc_start: 0.8945 (mtt180) cc_final: 0.8556 (mmm-85) REVERT: E 104 LYS cc_start: 0.9581 (mmmt) cc_final: 0.9166 (mtmt) REVERT: E 118 ILE cc_start: 0.8739 (tp) cc_final: 0.8441 (tp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2420 time to fit residues: 47.7476 Evaluate side-chains 107 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 149 optimal weight: 0.0570 chunk 137 optimal weight: 8.9990 chunk 118 optimal weight: 0.0000 chunk 12 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 94 optimal weight: 30.0000 chunk 126 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 overall best weight: 3.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11901 Z= 0.223 Angle : 0.675 10.387 16190 Z= 0.336 Chirality : 0.044 0.230 1876 Planarity : 0.004 0.048 2067 Dihedral : 7.172 83.781 1727 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -1.90 (0.22), residues: 1519 helix: -0.15 (0.21), residues: 610 sheet: -1.96 (0.32), residues: 259 loop : -1.98 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 182 HIS 0.010 0.001 HIS B 194 PHE 0.025 0.002 PHE E 183 TYR 0.014 0.001 TYR B 86 ARG 0.004 0.000 ARG A 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8616 (tpp) cc_final: 0.8396 (tpt) REVERT: A 209 MET cc_start: 0.9291 (mmm) cc_final: 0.8871 (mmm) REVERT: A 386 VAL cc_start: 0.9666 (p) cc_final: 0.9180 (p) REVERT: B 25 ASN cc_start: 0.9218 (p0) cc_final: 0.8862 (p0) REVERT: B 85 PHE cc_start: 0.9383 (m-80) cc_final: 0.9095 (m-80) REVERT: B 127 LYS cc_start: 0.9629 (tmtt) cc_final: 0.9408 (tptt) REVERT: B 143 LEU cc_start: 0.9842 (mm) cc_final: 0.9629 (mt) REVERT: B 295 MET cc_start: 0.9113 (mmm) cc_final: 0.8913 (mmm) REVERT: C 24 LEU cc_start: 0.9556 (tt) cc_final: 0.9187 (mp) REVERT: C 46 MET cc_start: 0.9317 (mmp) cc_final: 0.8957 (mmm) REVERT: C 133 MET cc_start: 0.9124 (mtp) cc_final: 0.8700 (mtp) REVERT: D 66 MET cc_start: 0.9554 (tpp) cc_final: 0.9228 (tpp) REVERT: D 76 ASP cc_start: 0.9577 (p0) cc_final: 0.9289 (p0) REVERT: D 101 LEU cc_start: 0.9373 (mt) cc_final: 0.9064 (mt) REVERT: D 221 TYR cc_start: 0.9126 (t80) cc_final: 0.8600 (t80) REVERT: E 66 MET cc_start: 0.9260 (tpp) cc_final: 0.8764 (tpp) REVERT: E 72 LEU cc_start: 0.9657 (mm) cc_final: 0.9291 (tt) REVERT: E 76 ASP cc_start: 0.8874 (p0) cc_final: 0.8634 (p0) REVERT: E 83 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8153 (mp0) REVERT: E 104 LYS cc_start: 0.9529 (mmmt) cc_final: 0.9125 (mtmt) REVERT: E 118 ILE cc_start: 0.8743 (tp) cc_final: 0.8438 (tp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2449 time to fit residues: 48.1090 Evaluate side-chains 105 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.0870 chunk 119 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.037517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.028218 restraints weight = 98159.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.029052 restraints weight = 63319.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.029661 restraints weight = 46353.319| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11901 Z= 0.149 Angle : 0.658 9.796 16190 Z= 0.316 Chirality : 0.044 0.238 1876 Planarity : 0.004 0.048 2067 Dihedral : 6.914 80.330 1727 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -1.87 (0.22), residues: 1519 helix: -0.18 (0.22), residues: 622 sheet: -1.84 (0.32), residues: 249 loop : -1.98 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 182 HIS 0.005 0.001 HIS B 194 PHE 0.021 0.001 PHE E 183 TYR 0.016 0.001 TYR C 86 ARG 0.005 0.000 ARG A 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2032.33 seconds wall clock time: 37 minutes 55.67 seconds (2275.67 seconds total)