Starting phenix.real_space_refine on Thu Sep 26 10:15:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osg_13050/09_2024/7osg_13050.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osg_13050/09_2024/7osg_13050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osg_13050/09_2024/7osg_13050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osg_13050/09_2024/7osg_13050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osg_13050/09_2024/7osg_13050.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osg_13050/09_2024/7osg_13050.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 Cu 1 5.60 5 Mg 1 5.21 5 S 45 5.16 5 C 8203 2.51 5 N 2250 2.21 5 O 2330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12831 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3077 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2375 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain: "C" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2015 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain breaks: 1 Chain: "E" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1896 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 2 Chain: "H" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1097 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 138} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11844 SG CYS H 45 45.534 43.242 48.186 1.00110.24 S ATOM 11867 SG CYS H 48 43.342 44.334 45.851 1.00107.87 S ATOM 12048 SG CYS H 72 46.293 45.139 44.175 1.00111.38 S Time building chain proxies: 8.03, per 1000 atoms: 0.63 Number of scatterers: 12831 At special positions: 0 Unit cell: (80.352, 92.016, 190.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 S 45 16.00 Mg 1 11.99 O 2330 8.00 N 2250 7.00 C 8203 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 - 3.00 Amino acid : True - 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: 3.29 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 45 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 48 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 72 " 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2998 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 13 sheets defined 46.6% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 344 through 348 removed outlier: 4.287A pdb=" N GLY A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.649A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.530A pdb=" N MET A 390 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.623A pdb=" N TRP A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.602A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.649A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 4.184A pdb=" N VAL B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 192' Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 232 through 243 removed outlier: 4.200A pdb=" N GLN B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ARG B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP B 240 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 removed outlier: 3.532A pdb=" N LEU B 267 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.517A pdb=" N MET C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 50 " --> pdb=" O MET C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 106 through 111 removed outlier: 4.432A pdb=" N ASP C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 106 through 111' 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: 3.713A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 192 removed outlier: 4.070A pdb=" N VAL C 191 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 192' Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 240 through 244 removed outlier: 3.735A pdb=" N ALA C 243 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 removed outlier: 3.680A pdb=" N LEU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.010A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.534A pdb=" N PHE D 28 " --> pdb=" O ILE D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.620A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Proline residue: D 67 - end of helix Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.679A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.179A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 167 removed outlier: 3.532A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.667A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.570A pdb=" N SER D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 216 through 226 Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.701A pdb=" N LEU D 239 " --> pdb=" O MET D 236 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER D 240 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 273 removed outlier: 3.621A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 7 through 16 removed outlier: 3.688A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.562A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.528A pdb=" N ALA E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 85 through 92 removed outlier: 3.608A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR E 92 " --> pdb=" O MET E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.636A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 4.174A 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: 3.808A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.575A pdb=" N VAL E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.565A pdb=" N ALA E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.658A pdb=" N LEU E 196 " --> pdb=" O VAL E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 212 removed outlier: 4.047A pdb=" N TRP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.511A pdb=" N ILE E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 272 removed outlier: 4.105A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 55 removed outlier: 3.773A pdb=" N ASP H 54 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 82 Processing helix chain 'H' and resid 113 through 117 removed outlier: 3.523A pdb=" N SER H 116 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA H 117 " --> pdb=" O ALA H 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 113 through 117' Processing helix chain 'H' and resid 139 through 150 removed outlier: 3.683A pdb=" N GLY H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 172 removed outlier: 3.689A pdb=" N GLN H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47 removed outlier: 6.193A pdb=" N TRP A 45 " --> pdb=" O ARG A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.759A pdb=" N GLN A 73 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.274A 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: 6.360A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.368A pdb=" N PHE A 56 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY A 131 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 333 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N HIS A 311 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.646A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.265A 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: 7.725A pdb=" N SER A 322 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 298 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 25 removed outlier: 5.853A pdb=" N VAL B 9 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN B 23 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN B 7 " --> pdb=" O ASN B 23 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN B 25 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU B 5 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 removed outlier: 7.528A pdb=" N GLY B 77 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ASP B 153 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 31 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA B 199 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B 201 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE B 35 " --> pdb=" O LEU B 201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 246 through 248 removed outlier: 4.020A pdb=" N GLU B 256 " --> pdb=" O ARG B 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.312A pdb=" N GLY C 77 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASP C 153 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 79 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE C 35 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA C 202 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 249 removed outlier: 4.083A pdb=" N ARG C 248 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA C 227 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 228 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 279 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AB4, first strand: chain 'H' and resid 119 through 120 525 hydrogen bonds defined for protein. 1473 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: 3.68 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4177 1.34 - 1.46: 2805 1.46 - 1.58: 6011 1.58 - 1.70: 2 1.70 - 1.83: 77 Bond restraints: 13072 Sorted by residual: bond pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 1.525 1.583 -0.058 2.10e-02 2.27e+03 7.75e+00 bond pdb=" CB VAL A 336 " pdb=" CG1 VAL A 336 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.89e+00 bond pdb=" CB GLN A 232 " pdb=" CG GLN A 232 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.17e+00 bond pdb=" CG1 ILE B 195 " pdb=" CD1 ILE B 195 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.84e+00 bond pdb=" C LEU E 209 " pdb=" N PRO E 210 " ideal model delta sigma weight residual 1.335 1.362 -0.026 1.36e-02 5.41e+03 3.72e+00 ... (remaining 13067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 17364 3.19 - 6.37: 317 6.37 - 9.56: 44 9.56 - 12.74: 6 12.74 - 15.93: 2 Bond angle restraints: 17733 Sorted by residual: angle pdb=" CA HIS C 37 " pdb=" C HIS C 37 " pdb=" N ASN C 38 " ideal model delta sigma weight residual 119.46 116.46 3.00 6.10e-01 2.69e+00 2.43e+01 angle pdb=" CB MET B 295 " pdb=" CG MET B 295 " pdb=" SD MET B 295 " ideal model delta sigma weight residual 112.70 126.72 -14.02 3.00e+00 1.11e-01 2.18e+01 angle pdb=" C GLU H 64 " pdb=" N LYS H 65 " pdb=" CA LYS H 65 " ideal model delta sigma weight residual 125.02 133.17 -8.15 1.76e+00 3.23e-01 2.15e+01 angle pdb=" N GLY B 299 " pdb=" CA GLY B 299 " pdb=" C GLY B 299 " ideal model delta sigma weight residual 113.48 120.15 -6.67 1.46e+00 4.69e-01 2.09e+01 angle pdb=" CA LEU A 35 " pdb=" CB LEU A 35 " pdb=" CG LEU A 35 " ideal model delta sigma weight residual 116.30 132.23 -15.93 3.50e+00 8.16e-02 2.07e+01 ... (remaining 17728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 6883 17.72 - 35.45: 695 35.45 - 53.17: 132 53.17 - 70.90: 25 70.90 - 88.62: 4 Dihedral angle restraints: 7739 sinusoidal: 3041 harmonic: 4698 Sorted by residual: dihedral pdb=" CA GLU B 305 " pdb=" C GLU B 305 " pdb=" N GLY B 306 " pdb=" CA GLY B 306 " ideal model delta harmonic sigma weight residual 180.00 148.24 31.76 0 5.00e+00 4.00e-02 4.04e+01 dihedral pdb=" CA ASP H 108 " pdb=" C ASP H 108 " pdb=" N GLY H 109 " pdb=" CA GLY H 109 " ideal model delta harmonic sigma weight residual 180.00 148.74 31.26 0 5.00e+00 4.00e-02 3.91e+01 dihedral pdb=" CA ARG C 307 " pdb=" C ARG C 307 " pdb=" N LEU C 308 " pdb=" CA LEU C 308 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 7736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1723 0.081 - 0.162: 266 0.162 - 0.244: 36 0.244 - 0.325: 5 0.325 - 0.406: 1 Chirality restraints: 2031 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 -2.22 -0.41 2.00e-01 2.50e+01 4.12e+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 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU E 199 " pdb=" CB LEU E 199 " pdb=" CD1 LEU E 199 " pdb=" CD2 LEU E 199 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 2028 not shown) Planarity restraints: 2277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 209 " -0.068 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO E 210 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 43 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C THR C 43 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 43 " -0.020 2.00e-02 2.50e+03 pdb=" N THR C 44 " -0.018 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 7.47e-02 8.92e+00 pdb=" N PRO D 67 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.042 5.00e-02 4.00e+02 ... (remaining 2274 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 100 2.55 - 3.14: 9104 3.14 - 3.72: 20067 3.72 - 4.31: 28451 4.31 - 4.90: 47202 Nonbonded interactions: 104924 Sorted by model distance: nonbonded pdb=" OE1 GLU H 76 " pdb="ZN ZN H 201 " model vdw 1.962 2.230 nonbonded pdb=" NE2 HIS A 207 " pdb="CU CU A 502 " model vdw 2.069 2.320 nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 2.086 2.170 nonbonded pdb=" OD1 ASP A 359 " pdb="MG MG A 501 " model vdw 2.091 2.170 nonbonded pdb=" OD1 ASP A 367 " pdb="MG MG A 501 " model vdw 2.129 2.170 ... (remaining 104919 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 2 through 308) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or resid 245 through \ 274)) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.190 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.008 0.080 13072 Z= 0.531 Angle : 1.075 15.927 17733 Z= 0.570 Chirality : 0.062 0.406 2031 Planarity : 0.007 0.101 2277 Dihedral : 14.454 88.625 4741 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.97 % Allowed : 9.23 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.46 (0.15), residues: 1646 helix: -4.31 (0.09), residues: 699 sheet: -3.23 (0.29), residues: 210 loop : -2.86 (0.19), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 240 HIS 0.024 0.002 HIS C 37 PHE 0.034 0.002 PHE B 35 TYR 0.028 0.002 TYR C 291 ARG 0.006 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.9331 (mmtt) cc_final: 0.9101 (tppp) REVERT: B 57 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: B 61 LYS cc_start: 0.8461 (mttp) cc_final: 0.8110 (mmmm) REVERT: B 84 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8668 (p) REVERT: B 283 HIS cc_start: 0.9114 (m90) cc_final: 0.8774 (m90) REVERT: D 66 MET cc_start: 0.8869 (mmm) cc_final: 0.8660 (mmt) REVERT: D 82 ASP cc_start: 0.8786 (t70) cc_final: 0.8450 (t0) REVERT: D 190 ASP cc_start: 0.8584 (m-30) cc_final: 0.8272 (m-30) REVERT: E 82 ASP cc_start: 0.9040 (t0) cc_final: 0.8635 (t0) REVERT: H 40 HIS cc_start: 0.8650 (m-70) cc_final: 0.8198 (m-70) REVERT: H 43 ASP cc_start: 0.7819 (m-30) cc_final: 0.7336 (m-30) REVERT: H 65 LYS cc_start: 0.8710 (pttm) cc_final: 0.8473 (pttm) REVERT: H 92 LYS cc_start: 0.8949 (tttp) cc_final: 0.8731 (mtpp) REVERT: H 104 GLU cc_start: 0.8820 (mp0) cc_final: 0.8541 (mp0) REVERT: H 141 ASP cc_start: 0.8496 (p0) cc_final: 0.8100 (p0) REVERT: H 143 LYS cc_start: 0.9312 (mmtt) cc_final: 0.8955 (mmtm) REVERT: H 157 GLU cc_start: 0.8375 (pp20) cc_final: 0.8048 (pp20) REVERT: H 158 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7772 (mt-10) REVERT: H 165 GLN cc_start: 0.8443 (mt0) cc_final: 0.8161 (mt0) REVERT: H 166 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8162 (tp30) REVERT: H 170 MET cc_start: 0.8460 (mmp) cc_final: 0.7604 (mmm) outliers start: 13 outliers final: 4 residues processed: 158 average time/residue: 0.3548 time to fit residues: 75.4897 Evaluate side-chains 99 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 250 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.0000 chunk 66 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 0.0370 chunk 95 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 overall best weight: 1.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 77 GLN A 123 ASN A 141 GLN A 145 ASN A 160 ASN A 174 HIS A 175 ASN A 179 ASN A 190 ASN A 212 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 324 ASN B 11 GLN B 20 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 270 GLN C 25 ASN C 115 GLN C 194 HIS D 225 ASN E 108 HIS E 225 ASN H 149 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13072 Z= 0.187 Angle : 0.600 7.728 17733 Z= 0.313 Chirality : 0.042 0.202 2031 Planarity : 0.005 0.059 2277 Dihedral : 5.577 50.376 1813 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.49 % Allowed : 13.10 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.18), residues: 1646 helix: -1.82 (0.16), residues: 714 sheet: -2.82 (0.30), residues: 232 loop : -2.38 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 211 HIS 0.004 0.001 HIS B 20 PHE 0.011 0.001 PHE D 157 TYR 0.019 0.001 TYR C 13 ARG 0.004 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.9256 (mmtt) cc_final: 0.8990 (ttmm) REVERT: A 305 LYS cc_start: 0.9036 (mtmm) cc_final: 0.8773 (mtmt) REVERT: B 57 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6891 (tm-30) REVERT: B 61 LYS cc_start: 0.8331 (mttp) cc_final: 0.8097 (mmmm) REVERT: B 283 HIS cc_start: 0.9119 (m90) cc_final: 0.8807 (m90) REVERT: D 82 ASP cc_start: 0.8690 (t70) cc_final: 0.8401 (t0) REVERT: D 88 MET cc_start: 0.8413 (tpp) cc_final: 0.8205 (tpp) REVERT: D 135 GLU cc_start: 0.7954 (tp30) cc_final: 0.7725 (pm20) REVERT: D 190 ASP cc_start: 0.8525 (m-30) cc_final: 0.8271 (m-30) REVERT: D 219 ASP cc_start: 0.8469 (m-30) cc_final: 0.8258 (m-30) REVERT: D 230 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7417 (tm-30) REVERT: E 11 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8150 (mm-30) REVERT: E 82 ASP cc_start: 0.9017 (t0) cc_final: 0.8564 (t0) REVERT: E 190 ASP cc_start: 0.8471 (m-30) cc_final: 0.8223 (m-30) REVERT: H 40 HIS cc_start: 0.8656 (m-70) cc_final: 0.8279 (m-70) REVERT: H 43 ASP cc_start: 0.7958 (m-30) cc_final: 0.7502 (m-30) REVERT: H 143 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8728 (mmtm) outliers start: 20 outliers final: 10 residues processed: 130 average time/residue: 0.2777 time to fit residues: 51.1429 Evaluate side-chains 102 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 54 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 37 HIS B 261 ASN C 238 GLN C 283 HIS E 225 ASN H 172 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13072 Z= 0.374 Angle : 0.661 7.943 17733 Z= 0.333 Chirality : 0.044 0.174 2031 Planarity : 0.004 0.044 2277 Dihedral : 5.284 46.061 1811 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.46 % Allowed : 15.04 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.20), residues: 1646 helix: -0.09 (0.19), residues: 715 sheet: -2.57 (0.32), residues: 221 loop : -2.10 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 20 HIS 0.005 0.001 HIS A 174 PHE 0.021 0.002 PHE D 157 TYR 0.019 0.002 TYR C 13 ARG 0.006 0.001 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 88 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9672 (OUTLIER) cc_final: 0.9461 (mp) REVERT: A 235 LYS cc_start: 0.9288 (mmtt) cc_final: 0.9024 (ttmm) REVERT: A 305 LYS cc_start: 0.9113 (mtmm) cc_final: 0.8784 (mtmt) REVERT: B 61 LYS cc_start: 0.8319 (mttp) cc_final: 0.8088 (mmmm) REVERT: B 133 MET cc_start: 0.8987 (mtp) cc_final: 0.8611 (mtm) REVERT: B 292 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8205 (ttt90) REVERT: C 292 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.9044 (ttm-80) REVERT: C 295 MET cc_start: 0.9046 (mmm) cc_final: 0.8763 (mmm) REVERT: D 82 ASP cc_start: 0.8823 (t70) cc_final: 0.8469 (t0) REVERT: D 88 MET cc_start: 0.8274 (tpp) cc_final: 0.7929 (tpp) REVERT: D 230 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7433 (tm-30) REVERT: E 64 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8783 (t80) REVERT: E 81 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8108 (mm-30) REVERT: E 82 ASP cc_start: 0.9046 (t0) cc_final: 0.8644 (t0) REVERT: E 138 MET cc_start: 0.8438 (tmm) cc_final: 0.8092 (tmm) REVERT: E 190 ASP cc_start: 0.8538 (m-30) cc_final: 0.8319 (m-30) REVERT: H 40 HIS cc_start: 0.8463 (m-70) cc_final: 0.8143 (m-70) REVERT: H 65 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8221 (ptpp) REVERT: H 143 LYS cc_start: 0.9032 (mmtt) cc_final: 0.8759 (mmtm) outliers start: 33 outliers final: 17 residues processed: 117 average time/residue: 0.2906 time to fit residues: 48.4965 Evaluate side-chains 100 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 0.0270 chunk 148 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS E 225 ASN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13072 Z= 0.147 Angle : 0.535 9.521 17733 Z= 0.270 Chirality : 0.041 0.151 2031 Planarity : 0.003 0.042 2277 Dihedral : 4.671 30.212 1808 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.94 % Allowed : 16.60 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.21), residues: 1646 helix: 0.67 (0.20), residues: 716 sheet: -2.54 (0.30), residues: 260 loop : -1.95 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 98 HIS 0.003 0.001 HIS B 20 PHE 0.010 0.001 PHE D 157 TYR 0.010 0.001 TYR B 86 ARG 0.007 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.9161 (mmtt) cc_final: 0.8950 (ttmm) REVERT: A 305 LYS cc_start: 0.9233 (mtmm) cc_final: 0.9004 (mtmt) REVERT: B 57 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6732 (tm-30) REVERT: B 61 LYS cc_start: 0.8227 (mttp) cc_final: 0.8017 (mmmm) REVERT: B 292 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8032 (ttt90) REVERT: C 295 MET cc_start: 0.8899 (mmm) cc_final: 0.8689 (mmm) REVERT: D 82 ASP cc_start: 0.8760 (t70) cc_final: 0.8428 (t0) REVERT: D 88 MET cc_start: 0.8307 (tpp) cc_final: 0.7948 (tpp) REVERT: D 230 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7324 (tm-30) REVERT: E 64 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8836 (t80) REVERT: E 66 MET cc_start: 0.8719 (mmp) cc_final: 0.8455 (tpp) REVERT: E 81 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7923 (mm-30) REVERT: E 82 ASP cc_start: 0.8999 (t0) cc_final: 0.8578 (t0) REVERT: E 138 MET cc_start: 0.8312 (tmm) cc_final: 0.7923 (tmm) REVERT: H 40 HIS cc_start: 0.8380 (m-70) cc_final: 0.8110 (m-70) REVERT: H 65 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8082 (ptpp) REVERT: H 143 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8701 (mmtm) outliers start: 26 outliers final: 16 residues processed: 119 average time/residue: 0.2730 time to fit residues: 46.4849 Evaluate side-chains 104 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 0.4980 chunk 89 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 0.0060 chunk 134 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.0770 chunk 141 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS C 97 HIS H 165 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13072 Z= 0.133 Angle : 0.510 9.404 17733 Z= 0.255 Chirality : 0.040 0.141 2031 Planarity : 0.003 0.038 2277 Dihedral : 4.346 29.880 1808 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.53 % Allowed : 16.23 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1646 helix: 1.18 (0.21), residues: 716 sheet: -2.35 (0.31), residues: 259 loop : -1.77 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 98 HIS 0.003 0.001 HIS H 149 PHE 0.010 0.001 PHE D 157 TYR 0.013 0.001 TYR B 86 ARG 0.008 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 94 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9246 (mtmm) cc_final: 0.9016 (mtmt) REVERT: B 57 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6664 (tm-30) REVERT: B 183 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8304 (mm) REVERT: B 292 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8080 (ttt90) REVERT: C 295 MET cc_start: 0.8896 (mmm) cc_final: 0.8632 (mmm) REVERT: D 82 ASP cc_start: 0.8739 (t70) cc_final: 0.8432 (t0) REVERT: D 88 MET cc_start: 0.8400 (tpp) cc_final: 0.8083 (tpp) REVERT: D 135 GLU cc_start: 0.7988 (tp30) cc_final: 0.7773 (tp30) REVERT: D 190 ASP cc_start: 0.8423 (m-30) cc_final: 0.8156 (m-30) REVERT: D 230 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7298 (tm-30) REVERT: E 10 LYS cc_start: 0.8980 (tmtt) cc_final: 0.8582 (tmtt) REVERT: E 11 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8222 (mm-30) REVERT: E 64 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8857 (t80) REVERT: E 76 ASP cc_start: 0.9117 (p0) cc_final: 0.8653 (p0) REVERT: E 81 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7962 (mm-30) REVERT: E 82 ASP cc_start: 0.8972 (t0) cc_final: 0.8578 (t0) REVERT: E 138 MET cc_start: 0.8340 (tmm) cc_final: 0.8003 (tmm) REVERT: H 65 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8225 (ptpp) REVERT: H 143 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8679 (mmtm) REVERT: H 155 ARG cc_start: 0.8698 (mmm-85) cc_final: 0.8296 (tpp80) outliers start: 34 outliers final: 16 residues processed: 125 average time/residue: 0.2770 time to fit residues: 49.3174 Evaluate side-chains 109 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13072 Z= 0.182 Angle : 0.521 9.608 17733 Z= 0.260 Chirality : 0.041 0.144 2031 Planarity : 0.003 0.035 2277 Dihedral : 4.309 30.696 1807 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.79 % Allowed : 16.90 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.22), residues: 1646 helix: 1.44 (0.21), residues: 716 sheet: -2.30 (0.31), residues: 255 loop : -1.68 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 98 HIS 0.003 0.001 HIS B 37 PHE 0.012 0.001 PHE D 157 TYR 0.012 0.001 TYR B 86 ARG 0.007 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9245 (mtmm) cc_final: 0.9023 (mtmt) REVERT: B 57 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: B 183 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8362 (mm) REVERT: B 292 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8038 (ttt90) REVERT: D 82 ASP cc_start: 0.8760 (t70) cc_final: 0.8466 (t0) REVERT: D 88 MET cc_start: 0.8395 (tpp) cc_final: 0.8108 (tpp) REVERT: D 190 ASP cc_start: 0.8396 (m-30) cc_final: 0.8133 (m-30) REVERT: D 230 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7366 (tm-30) REVERT: E 64 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8847 (t80) REVERT: E 81 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7913 (mm-30) REVERT: E 82 ASP cc_start: 0.8971 (t0) cc_final: 0.8594 (t0) REVERT: E 138 MET cc_start: 0.8344 (tmm) cc_final: 0.7962 (tmm) REVERT: H 65 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8079 (ptpp) REVERT: H 143 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8684 (mmtm) outliers start: 24 outliers final: 16 residues processed: 107 average time/residue: 0.2601 time to fit residues: 40.8604 Evaluate side-chains 101 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13072 Z= 0.234 Angle : 0.557 9.272 17733 Z= 0.277 Chirality : 0.042 0.227 2031 Planarity : 0.003 0.043 2277 Dihedral : 4.378 31.363 1807 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.31 % Allowed : 17.20 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1646 helix: 1.53 (0.21), residues: 718 sheet: -2.26 (0.31), residues: 254 loop : -1.62 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 20 HIS 0.004 0.001 HIS B 37 PHE 0.014 0.001 PHE D 157 TYR 0.013 0.001 TYR B 86 ARG 0.008 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 86 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9249 (mtmm) cc_final: 0.9037 (mtmt) REVERT: A 336 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8725 (m) REVERT: B 57 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: C 295 MET cc_start: 0.9083 (mmm) cc_final: 0.8739 (mmm) REVERT: D 82 ASP cc_start: 0.8791 (t70) cc_final: 0.8475 (t0) REVERT: D 88 MET cc_start: 0.8392 (tpp) cc_final: 0.8057 (tpp) REVERT: D 190 ASP cc_start: 0.8394 (m-30) cc_final: 0.8135 (m-30) REVERT: D 230 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7365 (tm-30) REVERT: E 10 LYS cc_start: 0.9001 (tmtt) cc_final: 0.8387 (tmtt) REVERT: E 11 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8254 (mm-30) REVERT: E 64 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8829 (t80) REVERT: E 66 MET cc_start: 0.8576 (mmp) cc_final: 0.8276 (tpp) REVERT: E 81 GLU cc_start: 0.8242 (mm-30) cc_final: 0.8033 (mm-30) REVERT: E 82 ASP cc_start: 0.8982 (t0) cc_final: 0.8608 (t0) REVERT: E 138 MET cc_start: 0.8344 (tmm) cc_final: 0.8043 (tmm) REVERT: H 143 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8700 (mmtm) outliers start: 31 outliers final: 20 residues processed: 113 average time/residue: 0.2606 time to fit residues: 42.7476 Evaluate side-chains 103 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR 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 417 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 20.0000 chunk 93 optimal weight: 40.0000 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13072 Z= 0.273 Angle : 0.578 9.635 17733 Z= 0.286 Chirality : 0.043 0.215 2031 Planarity : 0.003 0.037 2277 Dihedral : 4.476 32.435 1807 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.71 % Allowed : 18.17 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.22), residues: 1646 helix: 1.55 (0.21), residues: 718 sheet: -2.26 (0.30), residues: 259 loop : -1.56 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 211 HIS 0.004 0.001 HIS H 110 PHE 0.015 0.001 PHE D 157 TYR 0.012 0.001 TYR B 86 ARG 0.008 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9253 (mtmm) cc_final: 0.9038 (mtmt) REVERT: A 336 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8820 (m) REVERT: B 57 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6414 (tm-30) REVERT: C 295 MET cc_start: 0.9100 (mmm) cc_final: 0.8865 (mmm) REVERT: D 82 ASP cc_start: 0.8793 (t70) cc_final: 0.8472 (t0) REVERT: D 88 MET cc_start: 0.8404 (tpp) cc_final: 0.8070 (tpp) REVERT: D 230 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7370 (tm-30) REVERT: E 10 LYS cc_start: 0.9041 (tmtt) cc_final: 0.8430 (tmtt) REVERT: E 11 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8250 (mm-30) REVERT: E 64 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8857 (t80) REVERT: E 66 MET cc_start: 0.8692 (mmp) cc_final: 0.8322 (tpp) REVERT: E 82 ASP cc_start: 0.8967 (t0) cc_final: 0.8640 (t0) REVERT: E 138 MET cc_start: 0.8426 (tmm) cc_final: 0.8211 (tmm) REVERT: H 65 LYS cc_start: 0.8420 (ptpp) cc_final: 0.8099 (ptpp) REVERT: H 143 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8751 (mmtm) outliers start: 23 outliers final: 17 residues processed: 104 average time/residue: 0.2610 time to fit residues: 40.7199 Evaluate side-chains 99 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR 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 417 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 0.0070 chunk 132 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS C 59 GLN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13072 Z= 0.290 Angle : 0.584 10.172 17733 Z= 0.290 Chirality : 0.043 0.216 2031 Planarity : 0.003 0.038 2277 Dihedral : 4.498 32.415 1806 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.94 % Allowed : 17.87 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.22), residues: 1646 helix: 1.59 (0.21), residues: 719 sheet: -2.30 (0.31), residues: 249 loop : -1.52 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 211 HIS 0.004 0.001 HIS B 194 PHE 0.016 0.001 PHE D 157 TYR 0.012 0.001 TYR B 86 ARG 0.009 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 80 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9701 (OUTLIER) cc_final: 0.9479 (mp) REVERT: A 305 LYS cc_start: 0.9258 (mtmm) cc_final: 0.9037 (mtmt) REVERT: A 336 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8853 (m) REVERT: B 57 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6436 (tm-30) REVERT: C 241 THR cc_start: 0.4869 (OUTLIER) cc_final: 0.4391 (p) REVERT: C 295 MET cc_start: 0.9121 (mmm) cc_final: 0.8882 (mmm) REVERT: D 82 ASP cc_start: 0.8810 (t70) cc_final: 0.8483 (t0) REVERT: D 88 MET cc_start: 0.8426 (tpp) cc_final: 0.8086 (tpp) REVERT: E 10 LYS cc_start: 0.9020 (tmtt) cc_final: 0.8361 (tmtt) REVERT: E 82 ASP cc_start: 0.9000 (t0) cc_final: 0.8686 (t0) REVERT: E 138 MET cc_start: 0.8421 (tmm) cc_final: 0.8194 (tmm) REVERT: H 50 MET cc_start: 0.8347 (ptt) cc_final: 0.8141 (ptp) REVERT: H 65 LYS cc_start: 0.8389 (ptpp) cc_final: 0.7978 (ptpp) REVERT: H 143 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8752 (mmtm) outliers start: 26 outliers final: 20 residues processed: 105 average time/residue: 0.2462 time to fit residues: 38.2380 Evaluate side-chains 102 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 78 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR 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 397 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 129 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS C 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13072 Z= 0.153 Angle : 0.536 10.512 17733 Z= 0.267 Chirality : 0.041 0.170 2031 Planarity : 0.003 0.036 2277 Dihedral : 4.275 29.675 1806 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.41 % Allowed : 18.76 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1646 helix: 1.74 (0.21), residues: 718 sheet: -2.21 (0.31), residues: 249 loop : -1.44 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 98 HIS 0.003 0.001 HIS B 20 PHE 0.016 0.001 PHE D 229 TYR 0.010 0.001 TYR B 86 ARG 0.008 0.000 ARG H 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9243 (mtmm) cc_final: 0.9028 (mtmt) REVERT: A 336 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8614 (m) REVERT: A 374 ASP cc_start: 0.8051 (m-30) cc_final: 0.7611 (m-30) REVERT: B 57 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6725 (tm-30) REVERT: C 241 THR cc_start: 0.4792 (OUTLIER) cc_final: 0.4324 (p) REVERT: D 82 ASP cc_start: 0.8738 (t70) cc_final: 0.8439 (t0) REVERT: D 88 MET cc_start: 0.8408 (tpp) cc_final: 0.8133 (tpp) REVERT: D 190 ASP cc_start: 0.8392 (m-30) cc_final: 0.8098 (m-30) REVERT: E 10 LYS cc_start: 0.8859 (tmtt) cc_final: 0.8548 (tmtt) REVERT: E 82 ASP cc_start: 0.8973 (t0) cc_final: 0.8660 (t0) REVERT: E 138 MET cc_start: 0.8425 (tmm) cc_final: 0.8179 (tmm) REVERT: H 65 LYS cc_start: 0.8348 (ptpp) cc_final: 0.7957 (ptpp) REVERT: H 94 TYR cc_start: 0.8740 (m-10) cc_final: 0.8386 (m-10) REVERT: H 143 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8716 (mmtm) outliers start: 19 outliers final: 16 residues processed: 106 average time/residue: 0.2817 time to fit residues: 44.6465 Evaluate side-chains 99 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR 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 B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.068381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049851 restraints weight = 40120.756| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.51 r_work: 0.2741 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13072 Z= 0.307 Angle : 0.596 10.561 17733 Z= 0.296 Chirality : 0.043 0.207 2031 Planarity : 0.003 0.041 2277 Dihedral : 4.442 32.223 1806 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.79 % Allowed : 18.32 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1646 helix: 1.73 (0.21), residues: 717 sheet: -2.24 (0.31), residues: 249 loop : -1.45 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 211 HIS 0.005 0.001 HIS B 37 PHE 0.016 0.001 PHE D 157 TYR 0.019 0.001 TYR B 86 ARG 0.009 0.000 ARG D 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2364.13 seconds wall clock time: 43 minutes 16.67 seconds (2596.67 seconds total)