Starting phenix.real_space_refine on Thu Feb 15 16:52:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osf_13049/02_2024/7osf_13049.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osf_13049/02_2024/7osf_13049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osf_13049/02_2024/7osf_13049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osf_13049/02_2024/7osf_13049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osf_13049/02_2024/7osf_13049.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osf_13049/02_2024/7osf_13049.pdb" } resolution = 3.8 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 Cu 1 5.60 5 Mg 1 5.21 5 S 45 5.16 5 C 8200 2.51 5 N 2249 2.21 5 O 2329 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 59": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" 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 ARG 242": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H ARG 152": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12826 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3077 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2375 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain: "C" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2015 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain breaks: 1 Chain: "E" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1896 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 2 Chain: "H" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1092 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11839 SG CYS H 45 45.459 41.805 48.159 1.00122.68 S ATOM 11862 SG CYS H 48 43.354 42.911 45.783 1.00122.45 S ATOM 12043 SG CYS H 72 46.189 43.837 44.237 1.00129.62 S Time building chain proxies: 6.92, per 1000 atoms: 0.54 Number of scatterers: 12826 At special positions: 0 Unit cell: (80.352, 90.72, 194.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 S 45 16.00 Mg 1 11.99 O 2329 8.00 N 2249 7.00 C 8200 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: 4.53 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 72 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 48 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 45 " 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 13 sheets defined 43.7% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.662A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.511A pdb=" N MET A 390 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.656A pdb=" N TRP A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 69 through 74 removed outlier: 3.512A pdb=" N ARG B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.657A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 4.247A pdb=" N ASP B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 162 through 178 removed outlier: 3.844A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.570A pdb=" N ARG B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 297 removed outlier: 3.529A pdb=" N TYR B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.868A pdb=" N MET C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.600A pdb=" N ARG C 74 " --> pdb=" O PRO C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 108 through 113 removed outlier: 3.546A pdb=" N LEU C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 160 through 177 removed outlier: 3.851A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 233 through 241 removed outlier: 3.564A pdb=" N GLN C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 273 removed outlier: 3.531A pdb=" N LEU C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.504A pdb=" N GLY C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.166A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.536A pdb=" N PHE D 28 " --> pdb=" O ILE D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.661A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Proline residue: D 67 - end of helix Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.778A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.159A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 167 removed outlier: 3.531A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.788A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.513A pdb=" N LEU D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 216 through 226 Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.844A pdb=" N LEU D 241 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 273 removed outlier: 3.613A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 7 through 16 removed outlier: 3.755A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.630A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.572A pdb=" N ALA E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Proline residue: E 67 - end of helix removed outlier: 3.506A pdb=" N TYR E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 85 through 91 removed outlier: 3.605A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.508A pdb=" N ILE E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 135 through 143 removed outlier: 3.788A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.512A pdb=" N PHE E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.553A pdb=" N ALA E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 removed outlier: 3.593A pdb=" N LEU E 196 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU E 197 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 213 removed outlier: 4.515A pdb=" N TRP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.513A pdb=" N ILE E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 272 removed outlier: 4.158A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 55 removed outlier: 3.800A pdb=" N ASP H 54 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 82 Processing helix chain 'H' and resid 139 through 150 Processing helix chain 'H' and resid 160 through 172 removed outlier: 3.683A pdb=" N GLN H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.602A pdb=" N GLY A 131 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLN A 332 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.226A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.586A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 142 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217 removed outlier: 6.317A pdb=" N LEU A 216 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER A 322 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE A 298 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 23 removed outlier: 5.933A pdb=" N VAL B 9 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN B 23 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLN B 7 " --> pdb=" O ASN B 23 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 removed outlier: 7.650A pdb=" N GLY B 77 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ASP B 153 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL B 31 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ALA B 199 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 228 Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 26 removed outlier: 5.583A pdb=" N LEU C 22 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.752A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N PHE C 35 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA C 202 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 249 through 251 removed outlier: 6.890A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AB4, first strand: chain 'H' and resid 119 through 121 removed outlier: 3.552A pdb=" N VAL H 121 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG H 152 " --> pdb=" O VAL H 121 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1425 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: 3.60 Time building geometry restraints manager: 4.97 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: 4117 1.34 - 1.46: 2180 1.46 - 1.57: 6691 1.57 - 1.69: 2 1.69 - 1.81: 77 Bond restraints: 13067 Sorted by residual: bond pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 1.525 1.587 -0.062 2.10e-02 2.27e+03 8.70e+00 bond pdb=" CA ILE E 51 " pdb=" CB ILE E 51 " ideal model delta sigma weight residual 1.540 1.597 -0.057 2.70e-02 1.37e+03 4.39e+00 bond pdb=" C LEU E 209 " pdb=" N PRO E 210 " ideal model delta sigma weight residual 1.335 1.363 -0.027 1.36e-02 5.41e+03 4.05e+00 bond pdb=" CB GLN A 232 " pdb=" CG GLN A 232 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 4.04e+00 bond pdb=" CB VAL A 407 " pdb=" CG2 VAL A 407 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.67e+00 ... (remaining 13062 not shown) Histogram of bond angle deviations from ideal: 97.31 - 104.76: 199 104.76 - 112.20: 6192 112.20 - 119.65: 5093 119.65 - 127.10: 6055 127.10 - 134.54: 187 Bond angle restraints: 17726 Sorted by residual: angle pdb=" C VAL C 260 " pdb=" N ASN C 261 " pdb=" CA ASN C 261 " ideal model delta sigma weight residual 121.54 133.17 -11.63 1.91e+00 2.74e-01 3.71e+01 angle pdb=" C GLU H 64 " pdb=" N LYS H 65 " pdb=" CA LYS H 65 " ideal model delta sigma weight residual 125.02 133.56 -8.54 1.76e+00 3.23e-01 2.35e+01 angle pdb=" C GLU H 138 " pdb=" N GLU H 139 " pdb=" CA GLU H 139 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 angle pdb=" CA LEU A 35 " pdb=" CB LEU A 35 " pdb=" CG LEU A 35 " ideal model delta sigma weight residual 116.30 132.92 -16.62 3.50e+00 8.16e-02 2.26e+01 angle pdb=" C GLN A 247 " pdb=" N ASN A 248 " pdb=" CA ASN A 248 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.23e+01 ... (remaining 17721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 6649 14.86 - 29.72: 818 29.72 - 44.57: 221 44.57 - 59.43: 32 59.43 - 74.29: 16 Dihedral angle restraints: 7736 sinusoidal: 3041 harmonic: 4695 Sorted by residual: dihedral pdb=" CA VAL B 266 " pdb=" C VAL B 266 " pdb=" N LEU B 267 " pdb=" CA LEU B 267 " ideal model delta harmonic sigma weight residual -180.00 -121.50 -58.50 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA HIS B 263 " pdb=" C HIS B 263 " pdb=" N LYS B 264 " pdb=" CA LYS B 264 " ideal model delta harmonic sigma weight residual -180.00 -131.64 -48.36 0 5.00e+00 4.00e-02 9.35e+01 dihedral pdb=" CA ASP H 108 " pdb=" C ASP H 108 " pdb=" N GLY H 109 " pdb=" CA GLY H 109 " ideal model delta harmonic sigma weight residual 180.00 149.17 30.83 0 5.00e+00 4.00e-02 3.80e+01 ... (remaining 7733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1787 0.092 - 0.184: 209 0.184 - 0.276: 27 0.276 - 0.368: 5 0.368 - 0.460: 2 Chirality restraints: 2030 Sorted by residual: chirality pdb=" CG LEU B 265 " pdb=" CB LEU B 265 " pdb=" CD1 LEU B 265 " pdb=" CD2 LEU B 265 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CB VAL A 413 " pdb=" CA VAL A 413 " pdb=" CG1 VAL A 413 " pdb=" CG2 VAL A 413 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CB THR A 297 " pdb=" CA THR A 297 " pdb=" OG1 THR A 297 " pdb=" CG2 THR A 297 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2027 not shown) Planarity restraints: 2276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 209 " -0.063 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO E 210 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 192 " 0.016 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" C VAL E 192 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL E 192 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU E 193 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " 0.051 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO D 67 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.043 5.00e-02 4.00e+02 ... (remaining 2273 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 107 2.56 - 3.15: 9202 3.15 - 3.73: 19932 3.73 - 4.32: 28121 4.32 - 4.90: 46425 Nonbonded interactions: 103787 Sorted by model distance: nonbonded pdb=" OE1 GLU H 76 " pdb="ZN ZN H 201 " model vdw 1.976 2.230 nonbonded pdb=" NE2 HIS A 207 " pdb="CU CU A 502 " model vdw 2.000 2.320 nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 2.111 2.170 nonbonded pdb=" SD MET H 50 " pdb="CU CU A 502 " model vdw 2.130 2.600 nonbonded pdb=" OD1 ASN A 361 " pdb="MG MG A 501 " model vdw 2.163 2.170 ... (remaining 103782 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' and resid 2 through 308) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.410 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.800 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 0.073 13067 Z= 0.477 Angle : 1.113 16.623 17726 Z= 0.588 Chirality : 0.066 0.460 2030 Planarity : 0.007 0.094 2276 Dihedral : 14.292 74.290 4740 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.93 % Favored : 93.01 % Rotamer: Outliers : 0.52 % Allowed : 9.16 % Favored : 90.32 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -5.56 (0.14), residues: 1645 helix: -4.44 (0.08), residues: 696 sheet: -2.91 (0.28), residues: 250 loop : -2.94 (0.19), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 211 HIS 0.015 0.003 HIS C 37 PHE 0.025 0.002 PHE E 204 TYR 0.012 0.002 TYR A 249 ARG 0.005 0.001 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8955 (tp) cc_final: 0.8648 (tp) REVERT: B 86 TYR cc_start: 0.8972 (m-80) cc_final: 0.8537 (m-10) REVERT: B 196 ASN cc_start: 0.8851 (t0) cc_final: 0.8448 (m-40) REVERT: B 279 ASP cc_start: 0.8613 (m-30) cc_final: 0.8258 (t0) REVERT: B 283 HIS cc_start: 0.6550 (m-70) cc_final: 0.5737 (m-70) REVERT: D 66 MET cc_start: 0.8978 (mmm) cc_final: 0.8643 (mmm) REVERT: D 81 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8049 (mt-10) REVERT: D 83 GLU cc_start: 0.9103 (pt0) cc_final: 0.8890 (pt0) REVERT: D 135 GLU cc_start: 0.8932 (tp30) cc_final: 0.8588 (pm20) REVERT: D 171 LYS cc_start: 0.9433 (ttmt) cc_final: 0.8894 (ttmm) REVERT: D 190 ASP cc_start: 0.8229 (m-30) cc_final: 0.8013 (t0) REVERT: D 238 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8839 (t) REVERT: E 11 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8086 (mm-30) REVERT: E 66 MET cc_start: 0.9157 (mmm) cc_final: 0.8835 (mmp) REVERT: E 76 ASP cc_start: 0.9054 (p0) cc_final: 0.8745 (p0) REVERT: H 65 LYS cc_start: 0.8851 (pttm) cc_final: 0.8319 (tmtt) REVERT: H 94 TYR cc_start: 0.8941 (m-80) cc_final: 0.8197 (m-10) REVERT: H 143 LYS cc_start: 0.9415 (mmtt) cc_final: 0.9072 (mmtp) outliers start: 7 outliers final: 1 residues processed: 184 average time/residue: 0.3448 time to fit residues: 84.0076 Evaluate side-chains 105 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain D residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 30.0000 chunk 123 optimal weight: 0.0170 chunk 68 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 127 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 75 GLN A 77 GLN A 123 ASN A 141 GLN A 145 ASN A 174 HIS A 175 ASN A 179 ASN A 190 ASN A 212 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 324 ASN A 417 HIS B 20 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS B 176 GLN C 25 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN C 270 GLN D 205 ASN D 225 ASN E 225 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13067 Z= 0.147 Angle : 0.597 11.190 17726 Z= 0.305 Chirality : 0.042 0.200 2030 Planarity : 0.005 0.055 2276 Dihedral : 5.162 40.150 1805 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.96 % Favored : 93.98 % Rotamer: Outliers : 1.27 % Allowed : 14.67 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.48 (0.17), residues: 1645 helix: -2.02 (0.15), residues: 706 sheet: -2.60 (0.30), residues: 231 loop : -2.37 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 240 HIS 0.004 0.001 HIS H 149 PHE 0.010 0.001 PHE D 157 TYR 0.015 0.001 TYR C 13 ARG 0.006 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8960 (tp) cc_final: 0.8605 (tp) REVERT: A 125 MET cc_start: 0.8158 (mpp) cc_final: 0.7724 (mpp) REVERT: A 305 LYS cc_start: 0.9208 (mttt) cc_final: 0.8913 (mttp) REVERT: B 196 ASN cc_start: 0.8861 (t0) cc_final: 0.8584 (m-40) REVERT: C 261 ASN cc_start: 0.7195 (m-40) cc_final: 0.6928 (m-40) REVERT: D 66 MET cc_start: 0.9046 (mmm) cc_final: 0.8834 (mmp) REVERT: D 135 GLU cc_start: 0.8886 (tp30) cc_final: 0.8453 (pm20) REVERT: D 171 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8547 (ttmm) REVERT: D 190 ASP cc_start: 0.8584 (m-30) cc_final: 0.7820 (t0) REVERT: D 219 ASP cc_start: 0.8160 (m-30) cc_final: 0.7888 (m-30) REVERT: E 194 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8828 (tt) REVERT: E 221 TYR cc_start: 0.8918 (t80) cc_final: 0.8714 (t80) outliers start: 17 outliers final: 10 residues processed: 129 average time/residue: 0.2719 time to fit residues: 50.4289 Evaluate side-chains 102 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 260 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 123 optimal weight: 0.3980 chunk 100 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 20 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN E 108 HIS E 169 ASN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13067 Z= 0.277 Angle : 0.635 7.328 17726 Z= 0.322 Chirality : 0.043 0.171 2030 Planarity : 0.004 0.041 2276 Dihedral : 4.996 48.028 1804 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.94 % Allowed : 16.83 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.14 (0.20), residues: 1645 helix: -0.31 (0.19), residues: 708 sheet: -2.15 (0.29), residues: 277 loop : -2.24 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 20 HIS 0.008 0.001 HIS H 149 PHE 0.018 0.001 PHE H 55 TYR 0.015 0.001 TYR C 291 ARG 0.006 0.001 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.9040 (tp) cc_final: 0.8675 (tp) REVERT: A 125 MET cc_start: 0.8562 (mpp) cc_final: 0.7861 (mpp) REVERT: A 305 LYS cc_start: 0.9275 (mttt) cc_final: 0.8875 (mttt) REVERT: B 57 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: B 264 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7521 (pttp) REVERT: C 46 MET cc_start: 0.9025 (mmm) cc_final: 0.8661 (mtm) REVERT: D 81 GLU cc_start: 0.8504 (mt-10) cc_final: 0.7993 (mt-10) REVERT: D 88 MET cc_start: 0.8455 (tpp) cc_final: 0.8148 (tpp) REVERT: D 171 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8358 (ttmm) REVERT: D 203 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8959 (mmtt) REVERT: D 219 ASP cc_start: 0.7876 (m-30) cc_final: 0.7463 (m-30) REVERT: E 11 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8470 (tp30) REVERT: H 65 LYS cc_start: 0.8508 (tmtt) cc_final: 0.8051 (tptp) REVERT: H 138 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7616 (tm-30) outliers start: 26 outliers final: 15 residues processed: 114 average time/residue: 0.2765 time to fit residues: 45.5799 Evaluate side-chains 102 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 8.9990 chunk 111 optimal weight: 0.0470 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 99 optimal weight: 0.0030 chunk 148 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 overall best weight: 0.7290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 97 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 194 HIS H 96 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13067 Z= 0.136 Angle : 0.542 7.720 17726 Z= 0.271 Chirality : 0.040 0.156 2030 Planarity : 0.003 0.038 2276 Dihedral : 4.573 41.719 1804 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.27 % Allowed : 18.47 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.36 (0.21), residues: 1645 helix: 0.58 (0.20), residues: 704 sheet: -1.96 (0.30), residues: 272 loop : -2.02 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 240 HIS 0.006 0.001 HIS H 149 PHE 0.012 0.001 PHE D 157 TYR 0.016 0.001 TYR C 13 ARG 0.003 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.9053 (tp) cc_final: 0.8738 (tp) REVERT: A 125 MET cc_start: 0.8633 (mpp) cc_final: 0.7665 (mpp) REVERT: A 305 LYS cc_start: 0.9295 (mttt) cc_final: 0.8890 (mttt) REVERT: C 46 MET cc_start: 0.9143 (mmm) cc_final: 0.8930 (mtm) REVERT: D 81 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7873 (mt-10) REVERT: D 88 MET cc_start: 0.8402 (tpp) cc_final: 0.8034 (tpp) REVERT: D 135 GLU cc_start: 0.8802 (tp30) cc_final: 0.8263 (pm20) REVERT: D 138 MET cc_start: 0.7387 (tmm) cc_final: 0.7126 (tmm) REVERT: D 171 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8190 (ttmm) REVERT: D 219 ASP cc_start: 0.7882 (m-30) cc_final: 0.7429 (m-30) REVERT: E 11 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8036 (tp30) REVERT: H 65 LYS cc_start: 0.8478 (tmtt) cc_final: 0.7852 (tptp) REVERT: H 138 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7046 (tm-30) outliers start: 17 outliers final: 11 residues processed: 109 average time/residue: 0.2793 time to fit residues: 44.3701 Evaluate side-chains 94 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 85 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 75 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** B 37 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN E 205 ASN H 149 HIS H 172 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13067 Z= 0.402 Angle : 0.698 7.395 17726 Z= 0.346 Chirality : 0.045 0.193 2030 Planarity : 0.004 0.033 2276 Dihedral : 5.056 51.584 1804 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.46 % Allowed : 18.09 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.15 (0.21), residues: 1645 helix: 0.96 (0.21), residues: 699 sheet: -2.22 (0.29), residues: 275 loop : -1.96 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 20 HIS 0.008 0.001 HIS H 149 PHE 0.018 0.002 PHE H 71 TYR 0.015 0.002 TYR C 13 ARG 0.005 0.001 ARG B 302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.9119 (tp) cc_final: 0.8749 (tt) REVERT: A 125 MET cc_start: 0.8643 (mpp) cc_final: 0.7701 (mpp) REVERT: A 192 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8243 (p0) REVERT: A 294 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8922 (mm) REVERT: A 305 LYS cc_start: 0.9317 (mttt) cc_final: 0.8925 (mttt) REVERT: B 57 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: C 46 MET cc_start: 0.9113 (mmm) cc_final: 0.8884 (mtm) REVERT: D 81 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8036 (mt-10) REVERT: D 82 ASP cc_start: 0.8652 (t0) cc_final: 0.8268 (m-30) REVERT: D 88 MET cc_start: 0.8437 (tpp) cc_final: 0.7953 (tpp) REVERT: D 135 GLU cc_start: 0.8800 (tp30) cc_final: 0.8458 (pm20) REVERT: D 171 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8369 (ttmm) REVERT: D 219 ASP cc_start: 0.7701 (m-30) cc_final: 0.7432 (m-30) REVERT: E 11 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8007 (tp30) REVERT: H 65 LYS cc_start: 0.8575 (tmtt) cc_final: 0.7945 (tptp) REVERT: H 138 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7322 (tm-30) REVERT: H 161 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8569 (mm-40) outliers start: 33 outliers final: 19 residues processed: 120 average time/residue: 0.2702 time to fit residues: 47.7699 Evaluate side-chains 106 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 75 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** B 37 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 261 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13067 Z= 0.146 Angle : 0.554 7.938 17726 Z= 0.274 Chirality : 0.042 0.337 2030 Planarity : 0.003 0.039 2276 Dihedral : 4.605 42.036 1804 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.71 % Allowed : 19.88 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.22), residues: 1645 helix: 1.36 (0.21), residues: 699 sheet: -1.98 (0.30), residues: 269 loop : -1.82 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 240 HIS 0.003 0.001 HIS B 20 PHE 0.011 0.001 PHE D 157 TYR 0.018 0.001 TYR C 13 ARG 0.005 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.9063 (tp) cc_final: 0.8752 (tp) REVERT: A 125 MET cc_start: 0.8614 (mpp) cc_final: 0.7543 (mpp) REVERT: A 305 LYS cc_start: 0.9315 (mttt) cc_final: 0.9095 (mmmt) REVERT: C 61 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8172 (mmmm) REVERT: C 295 MET cc_start: 0.9075 (tpp) cc_final: 0.8616 (mpp) REVERT: D 81 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7858 (mt-10) REVERT: D 88 MET cc_start: 0.8361 (tpp) cc_final: 0.7932 (tpp) REVERT: D 135 GLU cc_start: 0.8743 (tp30) cc_final: 0.8513 (pm20) REVERT: D 171 LYS cc_start: 0.8330 (ttmt) cc_final: 0.8072 (ttmm) REVERT: D 219 ASP cc_start: 0.7807 (m-30) cc_final: 0.7397 (m-30) REVERT: E 11 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8020 (tp30) REVERT: E 81 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7347 (mt-10) REVERT: H 65 LYS cc_start: 0.8351 (tmtt) cc_final: 0.8049 (tptp) REVERT: H 90 ASP cc_start: 0.8678 (t0) cc_final: 0.8357 (t0) REVERT: H 100 ARG cc_start: 0.8955 (ttp-110) cc_final: 0.8524 (ttp-110) REVERT: H 129 MET cc_start: 0.8424 (tpp) cc_final: 0.8014 (tpp) REVERT: H 161 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8542 (mm-40) outliers start: 23 outliers final: 13 residues processed: 112 average time/residue: 0.2603 time to fit residues: 43.0715 Evaluate side-chains 96 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 85 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 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** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13067 Z= 0.235 Angle : 0.581 7.321 17726 Z= 0.288 Chirality : 0.042 0.281 2030 Planarity : 0.003 0.039 2276 Dihedral : 4.641 44.543 1804 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.01 % Allowed : 19.51 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1645 helix: 1.58 (0.21), residues: 694 sheet: -1.93 (0.29), residues: 275 loop : -1.81 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 211 HIS 0.002 0.001 HIS H 110 PHE 0.013 0.001 PHE D 157 TYR 0.016 0.001 TYR C 13 ARG 0.006 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 85 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LEU cc_start: 0.9181 (tp) cc_final: 0.8822 (tt) REVERT: A 125 MET cc_start: 0.8655 (mpp) cc_final: 0.7588 (mpp) REVERT: A 294 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8791 (mm) REVERT: B 264 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7295 (pttp) REVERT: C 295 MET cc_start: 0.9092 (tpp) cc_final: 0.8670 (mpp) REVERT: D 81 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7857 (mt-10) REVERT: D 88 MET cc_start: 0.8393 (tpp) cc_final: 0.8103 (tpp) REVERT: D 135 GLU cc_start: 0.8781 (tp30) cc_final: 0.8546 (pm20) REVERT: D 171 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8196 (ttmm) REVERT: D 219 ASP cc_start: 0.7794 (m-30) cc_final: 0.7425 (m-30) REVERT: E 11 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8052 (tp30) REVERT: H 65 LYS cc_start: 0.8534 (tmtt) cc_final: 0.8140 (tptp) REVERT: H 100 ARG cc_start: 0.8988 (ttp-110) cc_final: 0.8535 (ttp-110) REVERT: H 129 MET cc_start: 0.8582 (tpp) cc_final: 0.8176 (tpp) REVERT: H 161 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8582 (mm-40) outliers start: 27 outliers final: 15 residues processed: 109 average time/residue: 0.2624 time to fit residues: 41.9841 Evaluate side-chains 101 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 85 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 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** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13067 Z= 0.246 Angle : 0.593 8.298 17726 Z= 0.292 Chirality : 0.043 0.249 2030 Planarity : 0.003 0.037 2276 Dihedral : 4.667 45.738 1804 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.71 % Allowed : 19.88 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1645 helix: 1.73 (0.21), residues: 694 sheet: -1.97 (0.29), residues: 274 loop : -1.78 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 20 HIS 0.003 0.001 HIS H 110 PHE 0.014 0.001 PHE D 157 TYR 0.017 0.001 TYR C 13 ARG 0.005 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 1.581 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7737 (mmm) cc_final: 0.7095 (mpp) REVERT: A 89 LEU cc_start: 0.9089 (tp) cc_final: 0.8744 (tt) REVERT: A 125 MET cc_start: 0.8665 (mpp) cc_final: 0.7582 (mpp) REVERT: A 192 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.7968 (p0) REVERT: A 294 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8799 (mm) REVERT: A 305 LYS cc_start: 0.9261 (mmmt) cc_final: 0.8984 (mmmt) REVERT: B 7 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8176 (mm110) REVERT: B 264 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7341 (pttp) REVERT: C 61 LYS cc_start: 0.9234 (mmmm) cc_final: 0.8293 (mmmm) REVERT: C 295 MET cc_start: 0.9074 (tpp) cc_final: 0.8683 (mpp) REVERT: D 81 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7873 (mt-10) REVERT: D 88 MET cc_start: 0.8407 (tpp) cc_final: 0.8107 (tpp) REVERT: D 171 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8215 (ttmm) REVERT: D 219 ASP cc_start: 0.7781 (m-30) cc_final: 0.7406 (m-30) REVERT: E 11 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8089 (tp30) REVERT: E 81 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7315 (mt-10) REVERT: H 65 LYS cc_start: 0.8532 (tmtt) cc_final: 0.8110 (tptp) REVERT: H 129 MET cc_start: 0.8500 (tpp) cc_final: 0.8079 (tpp) REVERT: H 143 LYS cc_start: 0.9276 (mmtt) cc_final: 0.8816 (tppt) REVERT: H 161 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8572 (mm-40) outliers start: 23 outliers final: 16 residues processed: 109 average time/residue: 0.3106 time to fit residues: 48.3082 Evaluate side-chains 102 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 110 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 30.0000 chunk 146 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 63 optimal weight: 0.0570 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 145 optimal weight: 0.4980 chunk 96 optimal weight: 7.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** 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 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13067 Z= 0.147 Angle : 0.571 13.393 17726 Z= 0.275 Chirality : 0.041 0.239 2030 Planarity : 0.003 0.038 2276 Dihedral : 4.447 42.073 1804 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.64 % Allowed : 20.40 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1645 helix: 1.79 (0.21), residues: 708 sheet: -1.84 (0.30), residues: 274 loop : -1.69 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 98 HIS 0.003 0.001 HIS B 20 PHE 0.012 0.001 PHE D 157 TYR 0.015 0.001 TYR C 13 ARG 0.008 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 1.490 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7743 (mmm) cc_final: 0.7095 (mpp) REVERT: A 89 LEU cc_start: 0.9053 (tp) cc_final: 0.8705 (tt) REVERT: A 125 MET cc_start: 0.8638 (mpp) cc_final: 0.7974 (mpp) REVERT: A 305 LYS cc_start: 0.9269 (mmmt) cc_final: 0.8965 (mmmt) REVERT: B 7 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8187 (mm110) REVERT: B 264 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7120 (pttp) REVERT: C 61 LYS cc_start: 0.9208 (mmmm) cc_final: 0.8673 (mmmm) REVERT: C 295 MET cc_start: 0.8969 (tpp) cc_final: 0.8511 (mpp) REVERT: D 81 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7899 (mt-10) REVERT: D 88 MET cc_start: 0.8390 (tpp) cc_final: 0.8094 (tpp) REVERT: D 171 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8059 (ttmm) REVERT: D 219 ASP cc_start: 0.7847 (m-30) cc_final: 0.7439 (m-30) REVERT: D 254 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8198 (tt) REVERT: E 11 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8139 (tp30) REVERT: E 81 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7325 (mt-10) REVERT: H 129 MET cc_start: 0.8580 (tpp) cc_final: 0.8234 (tpp) REVERT: H 143 LYS cc_start: 0.9290 (mmtt) cc_final: 0.8828 (tppt) REVERT: H 148 MET cc_start: 0.8048 (ppp) cc_final: 0.7774 (ppp) REVERT: H 161 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8531 (mm-40) outliers start: 22 outliers final: 14 residues processed: 107 average time/residue: 0.2716 time to fit residues: 42.1759 Evaluate side-chains 107 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 68 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 129 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13067 Z= 0.151 Angle : 0.572 12.490 17726 Z= 0.278 Chirality : 0.041 0.237 2030 Planarity : 0.003 0.038 2276 Dihedral : 4.385 41.283 1804 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.27 % Allowed : 20.70 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.22), residues: 1645 helix: 1.90 (0.21), residues: 708 sheet: -1.75 (0.30), residues: 274 loop : -1.64 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 98 HIS 0.003 0.001 HIS B 20 PHE 0.012 0.001 PHE D 157 TYR 0.024 0.001 TYR C 13 ARG 0.007 0.000 ARG C 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7744 (mmm) cc_final: 0.7096 (mpp) REVERT: A 89 LEU cc_start: 0.9064 (tp) cc_final: 0.8705 (tt) REVERT: A 125 MET cc_start: 0.8645 (mpp) cc_final: 0.7975 (mpp) REVERT: A 305 LYS cc_start: 0.9236 (mmmt) cc_final: 0.8952 (mmmt) REVERT: B 7 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8248 (mm110) REVERT: B 264 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7052 (pttp) REVERT: C 61 LYS cc_start: 0.9167 (mmmm) cc_final: 0.8653 (mmmm) REVERT: C 295 MET cc_start: 0.8943 (tpp) cc_final: 0.8503 (mpp) REVERT: D 81 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7882 (mt-10) REVERT: D 88 MET cc_start: 0.8442 (tpp) cc_final: 0.8183 (tpp) REVERT: D 171 LYS cc_start: 0.8403 (ttmt) cc_final: 0.8107 (ttmm) REVERT: D 219 ASP cc_start: 0.7943 (m-30) cc_final: 0.7529 (m-30) REVERT: D 254 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8163 (tt) REVERT: E 11 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8141 (tp30) REVERT: E 81 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7297 (mt-10) REVERT: H 65 LYS cc_start: 0.8359 (tmtt) cc_final: 0.7975 (tptp) REVERT: H 129 MET cc_start: 0.8606 (tpp) cc_final: 0.8295 (tpp) REVERT: H 148 MET cc_start: 0.8011 (ppp) cc_final: 0.7766 (ppp) REVERT: H 161 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8518 (mm-40) outliers start: 17 outliers final: 13 residues processed: 105 average time/residue: 0.2574 time to fit residues: 39.6157 Evaluate side-chains 99 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 68 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.053532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.042247 restraints weight = 50911.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.043781 restraints weight = 27250.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.044812 restraints weight = 18020.927| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13067 Z= 0.210 Angle : 0.586 11.955 17726 Z= 0.286 Chirality : 0.042 0.232 2030 Planarity : 0.003 0.037 2276 Dihedral : 4.463 42.975 1804 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.34 % Allowed : 20.92 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.22), residues: 1645 helix: 1.92 (0.21), residues: 707 sheet: -1.77 (0.30), residues: 274 loop : -1.64 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 5 HIS 0.006 0.001 HIS B 263 PHE 0.013 0.001 PHE D 157 TYR 0.022 0.001 TYR C 13 ARG 0.005 0.000 ARG H 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2149.22 seconds wall clock time: 40 minutes 29.08 seconds (2429.08 seconds total)