Starting phenix.real_space_refine on Sun Apr 7 22:02:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o11_12686/04_2024/7o11_12686.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o11_12686/04_2024/7o11_12686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o11_12686/04_2024/7o11_12686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o11_12686/04_2024/7o11_12686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o11_12686/04_2024/7o11_12686.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o11_12686/04_2024/7o11_12686.pdb" } resolution = 3.7 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 37 5.16 5 C 7466 2.51 5 N 2038 2.21 5 O 2109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 42": "OE1" <-> "OE2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A ASP 377": "OD1" <-> "OD2" 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 "B ASP 110": "OD1" <-> "OD2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "C ASP 21": "OD1" <-> "OD2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ASP 69": "OD1" <-> "OD2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "E ASP 190": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11651 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3140 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 16, 'TRANS': 385} Chain: "B" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2303 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} 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: 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: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 6.30, per 1000 atoms: 0.54 Number of scatterers: 11651 At special positions: 0 Unit cell: (87.21, 163.134, 137.484, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 Mg 1 11.99 O 2109 8.00 N 2038 7.00 C 7466 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: 4.50 Conformation dependent library (CDL) restraints added in 2.2 seconds 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2722 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 45.4% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.735A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.625A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 removed outlier: 4.041A pdb=" N SER B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 50 " --> pdb=" O MET B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 removed outlier: 3.679A pdb=" N ARG B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.607A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 removed outlier: 4.465A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.540A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.584A pdb=" N GLU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 243 removed outlier: 3.634A pdb=" N THR B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 275 removed outlier: 3.569A pdb=" N GLY B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.560A pdb=" N LEU B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 50 removed outlier: 4.052A pdb=" N SER C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 50 " --> pdb=" O MET C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 107 through 113 removed outlier: 3.960A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (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: 3.530A pdb=" N LEU C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C 177 " --> pdb=" O ARG C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.664A pdb=" N ALA C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 235 through 240 Processing helix chain 'C' and resid 265 through 272 removed outlier: 3.726A pdb=" N ARG C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.651A pdb=" N LEU C 290 " --> pdb=" O SER C 286 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 298 " --> pdb=" O TYR C 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.083A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.622A pdb=" N ILE D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.569A pdb=" N ILE D 55 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Proline residue: D 67 - end of helix removed outlier: 3.507A pdb=" N TYR D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.876A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.072A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 146 through 167 removed outlier: 3.633A pdb=" N THR D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 4.076A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.620A pdb=" N SER D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 215 removed outlier: 3.504A pdb=" N LEU D 212 " --> pdb=" O LEU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.525A pdb=" N ASN D 225 " --> pdb=" O TYR D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 245 removed outlier: 3.769A pdb=" N LEU D 241 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 272 removed outlier: 3.629A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 removed outlier: 3.511A pdb=" N ILE E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3 through 7' Processing helix chain 'E' and resid 7 through 16 removed outlier: 3.668A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.664A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.913A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Proline residue: E 67 - end of helix removed outlier: 3.514A 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: 3.617A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.680A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 4.162A 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: 3.689A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.507A pdb=" N SER E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.631A pdb=" N ALA E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.528A pdb=" N LEU E 197 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 213 removed outlier: 3.633A pdb=" N LEU E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.653A pdb=" N ILE E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 272 removed outlier: 3.972A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 8.120A pdb=" N ARG A 44 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TRP A 45 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.542A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.822A 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: 6.207A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.517A 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: 6.417A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.479A 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: 7.542A pdb=" N SER A 322 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE A 298 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.607A pdb=" N VAL B 4 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 11 removed outlier: 7.401A pdb=" N GLN B 11 " --> pdb=" O HIS B 20 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N HIS B 20 " --> pdb=" O GLN B 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 153 removed outlier: 3.669A pdb=" N LEU B 150 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL B 31 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA B 199 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 246 through 248 removed outlier: 4.120A pdb=" N SER B 246 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 256 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 226 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.558A pdb=" N GLN C 59 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 11 removed outlier: 5.714A pdb=" N VAL C 9 " --> pdb=" O ASP C 21 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.994A pdb=" N LEU C 150 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N CYS C 184 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU C 152 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA C 198 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL C 209 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE C 200 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 254 through 259 removed outlier: 3.507A pdb=" N SER C 228 " --> pdb=" O ASP C 279 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1332 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: 3.73 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3104 1.33 - 1.45: 2076 1.45 - 1.57: 6625 1.57 - 1.69: 2 1.69 - 1.81: 64 Bond restraints: 11871 Sorted by residual: bond pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 1.525 1.593 -0.068 2.10e-02 2.27e+03 1.04e+01 bond pdb=" CA ILE E 51 " pdb=" CB ILE E 51 " ideal model delta sigma weight residual 1.540 1.608 -0.068 2.70e-02 1.37e+03 6.32e+00 bond pdb=" CA ILE D 51 " pdb=" C ILE D 51 " ideal model delta sigma weight residual 1.523 1.543 -0.020 9.20e-03 1.18e+04 4.74e+00 bond pdb=" C LEU B 188 " pdb=" N PRO B 189 " ideal model delta sigma weight residual 1.333 1.356 -0.023 1.17e-02 7.31e+03 3.92e+00 bond pdb=" C ILE D 51 " pdb=" N PRO D 52 " ideal model delta sigma weight residual 1.337 1.358 -0.021 1.11e-02 8.12e+03 3.74e+00 ... (remaining 11866 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.73: 348 106.73 - 113.84: 6553 113.84 - 120.95: 5560 120.95 - 128.06: 3528 128.06 - 135.18: 127 Bond angle restraints: 16116 Sorted by residual: angle pdb=" CA LEU A 356 " pdb=" CB LEU A 356 " pdb=" CG LEU A 356 " ideal model delta sigma weight residual 116.30 135.18 -18.88 3.50e+00 8.16e-02 2.91e+01 angle pdb=" C GLU B 81 " pdb=" N ASN B 82 " pdb=" CA ASN B 82 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" CA LEU A 35 " pdb=" CB LEU A 35 " pdb=" CG LEU A 35 " ideal model delta sigma weight residual 116.30 133.89 -17.59 3.50e+00 8.16e-02 2.53e+01 angle pdb=" C GLN A 247 " pdb=" N ASN A 248 " pdb=" CA ASN A 248 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.32e+01 angle pdb=" CA GLU D 201 " pdb=" CB GLU D 201 " pdb=" CG GLU D 201 " ideal model delta sigma weight residual 114.10 123.57 -9.47 2.00e+00 2.50e-01 2.24e+01 ... (remaining 16111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 6215 17.22 - 34.44: 643 34.44 - 51.65: 132 51.65 - 68.87: 23 68.87 - 86.09: 8 Dihedral angle restraints: 7021 sinusoidal: 2752 harmonic: 4269 Sorted by residual: dihedral pdb=" CA GLU B 276 " pdb=" C GLU B 276 " pdb=" N PRO B 277 " pdb=" CA PRO B 277 " ideal model delta harmonic sigma weight residual -180.00 -123.38 -56.62 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA ILE B 230 " pdb=" C ILE B 230 " pdb=" N SER B 231 " pdb=" CA SER B 231 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA LEU D 73 " pdb=" C LEU D 73 " pdb=" N ALA D 74 " pdb=" CA ALA D 74 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 7018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1672 0.100 - 0.200: 169 0.200 - 0.300: 17 0.300 - 0.400: 2 0.400 - 0.500: 1 Chirality restraints: 1861 Sorted by residual: 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 -2.13 -0.50 2.00e-01 2.50e+01 6.25e+00 chirality pdb=" CB VAL C 187 " pdb=" CA VAL C 187 " pdb=" CG1 VAL C 187 " pdb=" CG2 VAL C 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ASP A 182 " pdb=" N ASP A 182 " pdb=" C ASP A 182 " pdb=" CB ASP A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1858 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 276 " -0.064 5.00e-02 4.00e+02 9.62e-02 1.48e+01 pdb=" N PRO B 277 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO B 277 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 277 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 30 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C VAL D 30 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL D 30 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU D 31 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " 0.050 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO D 67 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.042 5.00e-02 4.00e+02 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 116 2.55 - 3.14: 7928 3.14 - 3.72: 18612 3.72 - 4.31: 26243 4.31 - 4.90: 42841 Nonbonded interactions: 95740 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 1.960 2.170 nonbonded pdb=" OD1 ASP A 363 " pdb="MG MG A 501 " model vdw 2.156 2.170 nonbonded pdb=" OD1 ASN A 361 " pdb="MG MG A 501 " model vdw 2.321 2.170 nonbonded pdb=" OG SER C 286 " pdb=" OE1 GLU C 288 " model vdw 2.324 2.440 nonbonded pdb=" O SER B 90 " pdb=" OG1 THR B 94 " model vdw 2.340 2.440 ... (remaining 95735 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 299) 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: 1.450 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: 6.250 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 33.100 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.006 0.075 11871 Z= 0.387 Angle : 1.107 18.875 16116 Z= 0.570 Chirality : 0.063 0.500 1861 Planarity : 0.007 0.096 2063 Dihedral : 14.722 86.089 4299 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.74 % Allowed : 9.40 % Favored : 89.87 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -5.78 (0.15), residues: 1498 helix: -4.54 (0.07), residues: 654 sheet: -3.49 (0.28), residues: 199 loop : -2.94 (0.20), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 45 HIS 0.010 0.002 HIS A 163 PHE 0.020 0.002 PHE E 64 TYR 0.019 0.002 TYR A 204 ARG 0.004 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8011 (pt) cc_final: 0.7765 (pp) REVERT: A 106 ASP cc_start: 0.7100 (m-30) cc_final: 0.6653 (m-30) REVERT: A 125 MET cc_start: 0.9202 (mpp) cc_final: 0.8972 (mpp) REVERT: A 235 LYS cc_start: 0.9546 (mmmt) cc_final: 0.9298 (tppp) REVERT: A 305 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8647 (mtmt) REVERT: B 2 ASN cc_start: 0.8674 (m110) cc_final: 0.7991 (m-40) REVERT: B 46 MET cc_start: 0.9111 (ttp) cc_final: 0.8536 (ttp) REVERT: B 86 TYR cc_start: 0.9025 (m-80) cc_final: 0.8815 (m-10) REVERT: B 131 LYS cc_start: 0.9598 (tptt) cc_final: 0.9309 (tppt) REVERT: B 263 HIS cc_start: 0.8689 (m90) cc_final: 0.8440 (m90) REVERT: B 281 GLU cc_start: 0.8886 (pt0) cc_final: 0.8433 (pm20) REVERT: C 133 MET cc_start: 0.9103 (mtm) cc_final: 0.8635 (mtm) REVERT: D 9 ARG cc_start: 0.8679 (ttm170) cc_final: 0.8331 (mtm180) REVERT: D 11 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7709 (mm-30) REVERT: D 66 MET cc_start: 0.9056 (mmm) cc_final: 0.8800 (mmp) REVERT: D 201 GLU cc_start: 0.8077 (pm20) cc_final: 0.7869 (pm20) REVERT: D 203 LYS cc_start: 0.9039 (mttt) cc_final: 0.8516 (pptt) REVERT: D 216 ASN cc_start: 0.8789 (t0) cc_final: 0.8188 (t0) REVERT: E 3 GLN cc_start: 0.8360 (mt0) cc_final: 0.8053 (mt0) REVERT: E 20 TRP cc_start: 0.8844 (m100) cc_final: 0.8348 (m-10) REVERT: E 81 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7660 (mt-10) REVERT: E 138 MET cc_start: 0.7566 (tpt) cc_final: 0.7179 (tmm) outliers start: 9 outliers final: 2 residues processed: 162 average time/residue: 0.2565 time to fit residues: 59.7229 Evaluate side-chains 103 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 63 GLN A 75 GLN A 77 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** 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 190 ASN A 212 ASN ** 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 341 GLN A 417 HIS B 20 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 214 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 97 HIS C 214 GLN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN E 6 ASN E 108 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11871 Z= 0.322 Angle : 0.677 10.609 16116 Z= 0.344 Chirality : 0.044 0.166 1861 Planarity : 0.005 0.098 2063 Dihedral : 5.472 47.588 1644 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.80 % Allowed : 14.95 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -3.51 (0.19), residues: 1498 helix: -1.91 (0.16), residues: 654 sheet: -2.95 (0.29), residues: 219 loop : -2.39 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 236 HIS 0.004 0.001 HIS B 37 PHE 0.014 0.001 PHE E 157 TYR 0.020 0.002 TYR C 13 ARG 0.003 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9139 (mpp) cc_final: 0.8848 (mpp) REVERT: A 235 LYS cc_start: 0.9567 (mmmt) cc_final: 0.9361 (tppp) REVERT: A 305 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8736 (mtmt) REVERT: B 2 ASN cc_start: 0.8573 (m110) cc_final: 0.8166 (m-40) REVERT: B 281 GLU cc_start: 0.8852 (pt0) cc_final: 0.8083 (pm20) REVERT: C 61 LYS cc_start: 0.8680 (mttm) cc_final: 0.8253 (mmmt) REVERT: C 133 MET cc_start: 0.9129 (mtm) cc_final: 0.8695 (mtm) REVERT: D 83 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8637 (mm-30) REVERT: D 201 GLU cc_start: 0.8463 (pm20) cc_final: 0.8040 (pm20) REVERT: D 203 LYS cc_start: 0.9136 (mttt) cc_final: 0.8659 (pptt) REVERT: D 216 ASN cc_start: 0.8544 (t0) cc_final: 0.7888 (t0) REVERT: E 20 TRP cc_start: 0.8830 (m100) cc_final: 0.8564 (m-10) REVERT: E 138 MET cc_start: 0.7400 (tpt) cc_final: 0.7192 (tmm) REVERT: E 187 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8785 (pp) outliers start: 22 outliers final: 10 residues processed: 129 average time/residue: 0.2474 time to fit residues: 45.8895 Evaluate side-chains 98 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 218 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 0.0570 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 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 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 324 ASN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11871 Z= 0.157 Angle : 0.581 9.963 16116 Z= 0.284 Chirality : 0.042 0.169 1861 Planarity : 0.004 0.097 2063 Dihedral : 5.004 44.373 1643 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.04 % Allowed : 16.26 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -2.31 (0.21), residues: 1498 helix: -0.45 (0.20), residues: 663 sheet: -2.62 (0.30), residues: 221 loop : -2.23 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 400 HIS 0.004 0.001 HIS B 37 PHE 0.011 0.001 PHE D 64 TYR 0.020 0.001 TYR C 13 ARG 0.004 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: A 73 GLN cc_start: 0.9177 (tt0) cc_final: 0.8935 (tm-30) REVERT: A 125 MET cc_start: 0.9109 (mpp) cc_final: 0.8789 (mpp) REVERT: A 305 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8697 (mtmt) REVERT: B 2 ASN cc_start: 0.8446 (m110) cc_final: 0.8034 (m-40) REVERT: B 86 TYR cc_start: 0.9074 (m-80) cc_final: 0.8689 (m-80) REVERT: C 61 LYS cc_start: 0.8693 (mttm) cc_final: 0.8270 (mmmt) REVERT: D 83 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8570 (mm-30) REVERT: D 201 GLU cc_start: 0.8459 (pm20) cc_final: 0.8041 (pm20) REVERT: D 203 LYS cc_start: 0.9143 (mttt) cc_final: 0.8619 (pptt) REVERT: D 216 ASN cc_start: 0.8407 (t0) cc_final: 0.7817 (t0) REVERT: E 20 TRP cc_start: 0.8729 (m100) cc_final: 0.8515 (m-10) REVERT: E 27 LEU cc_start: 0.9106 (tt) cc_final: 0.8410 (mm) REVERT: E 138 MET cc_start: 0.7397 (tpt) cc_final: 0.7175 (tmm) REVERT: E 187 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8809 (pp) REVERT: E 211 TRP cc_start: 0.7805 (m-10) cc_final: 0.6741 (t60) outliers start: 25 outliers final: 11 residues processed: 130 average time/residue: 0.2240 time to fit residues: 43.4710 Evaluate side-chains 106 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 187 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 0.0970 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 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 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11871 Z= 0.316 Angle : 0.642 9.262 16116 Z= 0.316 Chirality : 0.043 0.239 1861 Planarity : 0.004 0.098 2063 Dihedral : 4.992 43.743 1643 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.02 % Allowed : 18.22 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -1.66 (0.22), residues: 1498 helix: 0.32 (0.21), residues: 667 sheet: -2.52 (0.31), residues: 227 loop : -2.11 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 236 HIS 0.003 0.001 HIS E 108 PHE 0.014 0.001 PHE D 157 TYR 0.021 0.002 TYR C 13 ARG 0.003 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 98 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: A 73 GLN cc_start: 0.9168 (tt0) cc_final: 0.8911 (tm-30) REVERT: A 125 MET cc_start: 0.9132 (mpp) cc_final: 0.8814 (mpp) REVERT: A 305 LYS cc_start: 0.9210 (mmtt) cc_final: 0.8703 (mtmt) REVERT: B 2 ASN cc_start: 0.8506 (m110) cc_final: 0.8161 (m-40) REVERT: B 50 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9134 (mt) REVERT: B 86 TYR cc_start: 0.9185 (m-80) cc_final: 0.8786 (m-80) REVERT: C 61 LYS cc_start: 0.8754 (mttm) cc_final: 0.8286 (mmmt) REVERT: D 82 ASP cc_start: 0.8902 (t0) cc_final: 0.8541 (t0) REVERT: D 83 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8597 (mm-30) REVERT: D 201 GLU cc_start: 0.8757 (pm20) cc_final: 0.8527 (pm20) REVERT: D 203 LYS cc_start: 0.9160 (mttt) cc_final: 0.8651 (pptt) REVERT: D 216 ASN cc_start: 0.8462 (t0) cc_final: 0.7816 (t0) REVERT: E 20 TRP cc_start: 0.8880 (m100) cc_final: 0.8622 (m-10) REVERT: E 138 MET cc_start: 0.7384 (tpt) cc_final: 0.7143 (tmm) REVERT: E 187 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8809 (pp) outliers start: 37 outliers final: 21 residues processed: 126 average time/residue: 0.2081 time to fit residues: 39.8167 Evaluate side-chains 114 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 255 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 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 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 261 ASN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11871 Z= 0.169 Angle : 0.578 11.795 16116 Z= 0.279 Chirality : 0.042 0.289 1861 Planarity : 0.004 0.096 2063 Dihedral : 4.763 42.955 1643 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.78 % Allowed : 19.12 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -1.30 (0.22), residues: 1498 helix: 0.70 (0.21), residues: 669 sheet: -2.38 (0.31), residues: 227 loop : -2.01 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 400 HIS 0.003 0.001 HIS B 37 PHE 0.010 0.001 PHE E 157 TYR 0.022 0.001 TYR C 13 ARG 0.004 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 99 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: A 73 GLN cc_start: 0.9157 (tt0) cc_final: 0.8913 (tm-30) REVERT: A 125 MET cc_start: 0.9138 (mpp) cc_final: 0.8924 (mpp) REVERT: A 305 LYS cc_start: 0.9168 (mmtt) cc_final: 0.8663 (mtmt) REVERT: B 2 ASN cc_start: 0.8425 (m110) cc_final: 0.8112 (m-40) REVERT: B 46 MET cc_start: 0.8842 (ttp) cc_final: 0.8613 (tpp) REVERT: B 133 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8480 (mpp) REVERT: C 61 LYS cc_start: 0.8793 (mttm) cc_final: 0.8306 (mmmt) REVERT: D 75 TYR cc_start: 0.9154 (p90) cc_final: 0.8929 (p90) REVERT: D 83 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8506 (mm-30) REVERT: D 201 GLU cc_start: 0.8687 (pm20) cc_final: 0.8229 (pm20) REVERT: D 203 LYS cc_start: 0.9167 (mttt) cc_final: 0.8666 (pptt) REVERT: D 216 ASN cc_start: 0.8411 (t0) cc_final: 0.7795 (t0) REVERT: E 20 TRP cc_start: 0.8838 (m100) cc_final: 0.8619 (m-10) REVERT: E 138 MET cc_start: 0.7363 (tpt) cc_final: 0.7119 (tmm) REVERT: E 187 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8807 (pp) REVERT: E 211 TRP cc_start: 0.7733 (m-10) cc_final: 0.6735 (t60) outliers start: 34 outliers final: 25 residues processed: 126 average time/residue: 0.2086 time to fit residues: 40.3715 Evaluate side-chains 118 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 257 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 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** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11871 Z= 0.200 Angle : 0.582 10.349 16116 Z= 0.281 Chirality : 0.042 0.167 1861 Planarity : 0.004 0.095 2063 Dihedral : 4.679 42.833 1643 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.86 % Allowed : 20.51 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -1.03 (0.23), residues: 1498 helix: 1.01 (0.21), residues: 668 sheet: -2.20 (0.31), residues: 234 loop : -1.99 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 236 HIS 0.012 0.001 HIS B 283 PHE 0.011 0.001 PHE E 157 TYR 0.024 0.001 TYR C 13 ARG 0.003 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 94 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: A 73 GLN cc_start: 0.9132 (tt0) cc_final: 0.8887 (tm-30) REVERT: A 125 MET cc_start: 0.9142 (mpp) cc_final: 0.8820 (mpp) REVERT: A 305 LYS cc_start: 0.9182 (mmtt) cc_final: 0.8675 (mtmt) REVERT: B 133 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8571 (mpp) REVERT: C 61 LYS cc_start: 0.8808 (mttm) cc_final: 0.8275 (mmmt) REVERT: D 75 TYR cc_start: 0.9124 (p90) cc_final: 0.8913 (p90) REVERT: D 83 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8505 (mm-30) REVERT: D 201 GLU cc_start: 0.8695 (pm20) cc_final: 0.8240 (pm20) REVERT: D 203 LYS cc_start: 0.9179 (mttt) cc_final: 0.8677 (pptt) REVERT: D 216 ASN cc_start: 0.8465 (t0) cc_final: 0.7840 (t0) REVERT: E 20 TRP cc_start: 0.8840 (m100) cc_final: 0.8614 (m-10) REVERT: E 138 MET cc_start: 0.7336 (tpt) cc_final: 0.7081 (tmm) REVERT: E 187 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8818 (pp) REVERT: E 211 TRP cc_start: 0.7761 (m-10) cc_final: 0.6748 (t60) outliers start: 35 outliers final: 24 residues processed: 120 average time/residue: 0.2207 time to fit residues: 40.0421 Evaluate side-chains 116 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 255 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 86 optimal weight: 0.2980 chunk 65 optimal weight: 0.0970 chunk 88 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 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 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** 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 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11871 Z= 0.156 Angle : 0.565 10.465 16116 Z= 0.271 Chirality : 0.041 0.180 1861 Planarity : 0.003 0.094 2063 Dihedral : 4.540 42.240 1643 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.45 % Allowed : 21.41 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1498 helix: 1.29 (0.22), residues: 662 sheet: -2.07 (0.32), residues: 235 loop : -1.93 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 400 HIS 0.002 0.001 HIS B 37 PHE 0.010 0.001 PHE E 157 TYR 0.027 0.001 TYR C 13 ARG 0.004 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 99 time to evaluate : 2.120 Fit side-chains revert: symmetry clash REVERT: A 73 GLN cc_start: 0.9134 (tt0) cc_final: 0.8873 (tm-30) REVERT: A 125 MET cc_start: 0.9123 (mpp) cc_final: 0.8905 (mpp) REVERT: A 305 LYS cc_start: 0.9166 (mmtt) cc_final: 0.8663 (mtmt) REVERT: B 46 MET cc_start: 0.8795 (ttp) cc_final: 0.8574 (tpp) REVERT: B 133 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8494 (mpp) REVERT: C 61 LYS cc_start: 0.8808 (mttm) cc_final: 0.8312 (mmmt) REVERT: D 81 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8043 (mt-10) REVERT: D 83 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8475 (mm-30) REVERT: D 201 GLU cc_start: 0.8647 (pm20) cc_final: 0.8209 (pm20) REVERT: D 203 LYS cc_start: 0.9181 (mttt) cc_final: 0.8683 (pptt) REVERT: D 216 ASN cc_start: 0.8434 (t0) cc_final: 0.7723 (t0) REVERT: E 211 TRP cc_start: 0.7767 (m-10) cc_final: 0.6812 (t60) outliers start: 30 outliers final: 23 residues processed: 121 average time/residue: 0.2597 time to fit residues: 47.3081 Evaluate side-chains 115 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 255 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 90 optimal weight: 0.0570 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 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 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** 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 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11871 Z= 0.245 Angle : 0.596 11.920 16116 Z= 0.289 Chirality : 0.043 0.234 1861 Planarity : 0.004 0.094 2063 Dihedral : 4.564 42.338 1643 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.37 % Allowed : 22.14 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.23), residues: 1498 helix: 1.40 (0.22), residues: 668 sheet: -2.08 (0.32), residues: 235 loop : -1.88 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 37 HIS 0.004 0.001 HIS B 283 PHE 0.012 0.001 PHE D 157 TYR 0.029 0.001 TYR C 13 ARG 0.003 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 73 GLN cc_start: 0.9118 (tt0) cc_final: 0.8873 (tm-30) REVERT: A 125 MET cc_start: 0.9141 (mpp) cc_final: 0.8810 (mpp) REVERT: A 305 LYS cc_start: 0.9182 (mmtt) cc_final: 0.8692 (mtmt) REVERT: B 133 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8483 (mpp) REVERT: C 61 LYS cc_start: 0.8841 (mttm) cc_final: 0.8336 (mmmt) REVERT: D 83 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8763 (mm-30) REVERT: D 201 GLU cc_start: 0.8735 (pm20) cc_final: 0.8313 (pm20) REVERT: D 203 LYS cc_start: 0.9270 (mttt) cc_final: 0.8711 (pptt) REVERT: D 216 ASN cc_start: 0.8461 (t0) cc_final: 0.7738 (t0) REVERT: E 187 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8823 (pp) REVERT: E 211 TRP cc_start: 0.7682 (m-10) cc_final: 0.6776 (t60) outliers start: 29 outliers final: 24 residues processed: 114 average time/residue: 0.2321 time to fit residues: 39.5418 Evaluate side-chains 116 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 255 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.2980 chunk 124 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 87 optimal weight: 0.2980 chunk 140 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** 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 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11871 Z= 0.145 Angle : 0.569 12.057 16116 Z= 0.272 Chirality : 0.042 0.232 1861 Planarity : 0.003 0.094 2063 Dihedral : 4.484 41.843 1643 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.12 % Allowed : 22.39 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.23), residues: 1498 helix: 1.49 (0.22), residues: 666 sheet: -1.92 (0.32), residues: 235 loop : -1.84 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 400 HIS 0.007 0.001 HIS B 283 PHE 0.010 0.001 PHE E 157 TYR 0.031 0.001 TYR C 13 ARG 0.003 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.9117 (tt0) cc_final: 0.8836 (tm-30) REVERT: A 125 MET cc_start: 0.9150 (mpp) cc_final: 0.8900 (mpp) REVERT: A 305 LYS cc_start: 0.9128 (mmtt) cc_final: 0.8662 (mtmt) REVERT: B 133 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8458 (mpp) REVERT: D 81 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8003 (mt-10) REVERT: D 83 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8762 (mm-30) REVERT: D 201 GLU cc_start: 0.8655 (pm20) cc_final: 0.8262 (pm20) REVERT: D 203 LYS cc_start: 0.9178 (mttt) cc_final: 0.8679 (pptt) REVERT: D 216 ASN cc_start: 0.8290 (t0) cc_final: 0.7659 (t0) REVERT: D 236 MET cc_start: 0.7481 (mpp) cc_final: 0.7228 (mpp) REVERT: E 187 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8799 (pp) REVERT: E 211 TRP cc_start: 0.7750 (m-10) cc_final: 0.6829 (t60) outliers start: 26 outliers final: 22 residues processed: 117 average time/residue: 0.2344 time to fit residues: 40.6101 Evaluate side-chains 116 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 37 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11871 Z= 0.245 Angle : 0.610 13.004 16116 Z= 0.294 Chirality : 0.043 0.223 1861 Planarity : 0.004 0.093 2063 Dihedral : 4.524 41.943 1643 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.21 % Allowed : 22.55 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1498 helix: 1.57 (0.22), residues: 666 sheet: -1.86 (0.32), residues: 235 loop : -1.79 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 37 HIS 0.005 0.001 HIS B 194 PHE 0.011 0.001 PHE E 157 TYR 0.031 0.001 TYR C 13 ARG 0.004 0.000 ARG C 224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: A 73 GLN cc_start: 0.9141 (tt0) cc_final: 0.8843 (tm-30) REVERT: A 125 MET cc_start: 0.9144 (mpp) cc_final: 0.8911 (mpp) REVERT: A 305 LYS cc_start: 0.9185 (mmtt) cc_final: 0.8702 (mtmt) REVERT: B 46 MET cc_start: 0.9014 (tpp) cc_final: 0.8792 (tpp) REVERT: B 133 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8488 (mpp) REVERT: C 61 LYS cc_start: 0.8840 (mttm) cc_final: 0.8325 (mmmt) REVERT: D 81 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8069 (mt-10) REVERT: D 83 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8824 (mm-30) REVERT: D 201 GLU cc_start: 0.8749 (pm20) cc_final: 0.8418 (pm20) REVERT: D 203 LYS cc_start: 0.9265 (mttt) cc_final: 0.8780 (pttp) REVERT: D 216 ASN cc_start: 0.8436 (t0) cc_final: 0.7765 (t0) REVERT: D 236 MET cc_start: 0.7451 (mpp) cc_final: 0.7211 (mpp) REVERT: E 187 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8847 (pp) REVERT: E 211 TRP cc_start: 0.7645 (m-10) cc_final: 0.6857 (t60) outliers start: 27 outliers final: 24 residues processed: 113 average time/residue: 0.2371 time to fit residues: 39.8435 Evaluate side-chains 119 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 255 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 120 optimal weight: 0.0060 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** 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 37 HIS C 261 ASN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.057858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.046610 restraints weight = 54354.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048085 restraints weight = 27044.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.049133 restraints weight = 17328.561| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11871 Z= 0.147 Angle : 0.578 13.288 16116 Z= 0.275 Chirality : 0.042 0.242 1861 Planarity : 0.003 0.092 2063 Dihedral : 4.458 41.631 1643 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.88 % Allowed : 22.79 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.23), residues: 1498 helix: 1.60 (0.22), residues: 668 sheet: -1.71 (0.33), residues: 235 loop : -1.78 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 400 HIS 0.005 0.001 HIS B 283 PHE 0.010 0.001 PHE E 157 TYR 0.031 0.001 TYR C 13 ARG 0.006 0.000 ARG C 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2155.59 seconds wall clock time: 43 minutes 48.66 seconds (2628.66 seconds total)