Starting phenix.real_space_refine on Thu Feb 15 17:07:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osj_13053/02_2024/7osj_13053.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osj_13053/02_2024/7osj_13053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osj_13053/02_2024/7osj_13053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osj_13053/02_2024/7osj_13053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osj_13053/02_2024/7osj_13053.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osj_13053/02_2024/7osj_13053.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 Cu 1 5.60 5 Mg 1 5.21 5 S 45 5.16 5 C 8217 2.51 5 N 2252 2.21 5 O 2336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C ARG 292": "NH1" <-> "NH2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H GLU 138": "OE1" <-> "OE2" Residue "H ARG 152": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12853 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: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1119 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 145} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 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 11876 SG CYS H 45 45.635 42.945 48.071 1.00134.07 S ATOM 11899 SG CYS H 48 43.473 44.057 45.660 1.00133.90 S ATOM 12070 SG CYS H 72 46.294 44.996 44.126 1.00133.41 S Time building chain proxies: 7.45, per 1000 atoms: 0.58 Number of scatterers: 12853 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 2336 8.00 N 2252 7.00 C 8217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.16 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 72 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 48 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 45 " 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3010 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 13 sheets defined 45.7% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.713A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.291A 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: 3.696A pdb=" N TRP A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.793A 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 103 removed outlier: 3.565A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.534A 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: 3.982A pdb=" N GLN B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 3.939A pdb=" N VAL B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 232 through 238 removed outlier: 4.140A pdb=" N GLN B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 4.019A pdb=" N ASP B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 238 through 243' Processing helix chain 'B' and resid 263 through 275 removed outlier: 3.716A pdb=" N LEU B 267 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.501A pdb=" N ALA B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.607A pdb=" N MET C 46 " --> pdb=" O LYS C 42 " (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 105 through 109 removed outlier: 3.622A pdb=" N VAL C 109 " --> pdb=" O LEU C 106 " (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: 3.768A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 218 removed outlier: 3.504A pdb=" N ALA C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 240 through 244 removed outlier: 3.727A pdb=" N ALA C 243 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 removed outlier: 3.909A pdb=" N LEU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.536A pdb=" N TYR C 293 " --> pdb=" O ASP C 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 removed outlier: 3.578A pdb=" N ILE D 7 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.552A pdb=" N ILE D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D 28 " --> pdb=" O ILE D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.532A pdb=" N ILE D 55 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) Proline residue: D 67 - end of helix removed outlier: 3.543A 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: 3.737A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.066A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 112 " --> pdb=" O HIS D 108 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 168 removed outlier: 3.580A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.696A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.571A 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: 3.538A pdb=" N LEU D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 3.575A 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 removed outlier: 3.538A pdb=" N ASN D 225 " --> pdb=" O TYR D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.522A pdb=" N SER D 240 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 241 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 273 removed outlier: 3.576A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.803A 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: 3.722A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 38 removed outlier: 3.537A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.507A pdb=" N ALA E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Proline residue: E 67 - end of helix removed outlier: 3.573A 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: 3.588A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.706A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 129 removed outlier: 3.567A pdb=" N ALA E 126 " --> pdb=" O CYS E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 143 removed outlier: 3.814A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.562A pdb=" N SER E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.550A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.578A pdb=" N ILE E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 272 removed outlier: 4.058A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 34 removed outlier: 3.787A pdb=" N GLN H 32 " --> pdb=" O GLU H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 55 removed outlier: 3.749A pdb=" N ASP H 54 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 82 Processing helix chain 'H' and resid 139 through 150 removed outlier: 3.503A pdb=" N GLY H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 172 removed outlier: 3.678A pdb=" N GLN H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.277A pdb=" N PHE A 56 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY A 131 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 333 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N HIS A 311 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 73 removed outlier: 5.944A pdb=" N MET A 125 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.471A 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: 6.590A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A 142 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217 removed outlier: 6.335A pdb=" N LEU A 216 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N SER A 322 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.136A 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: 5.893A pdb=" N VAL B 9 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN B 23 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN B 7 " --> pdb=" O ASN B 23 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN B 25 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU B 5 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 4.125A 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: 7.545A pdb=" N GLY B 77 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ASP B 153 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 246 through 248 removed outlier: 3.579A pdb=" N ARG B 248 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 4.714A 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: 6.245A pdb=" N GLY C 77 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP C 153 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 79 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE C 35 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA C 202 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 5.082A 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: 3.807A pdb=" N SER C 246 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 258 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG C 248 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA C 227 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER C 228 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 4.332A 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 120 500 hydrogen bonds defined for protein. 1407 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: 3.43 Time building geometry restraints manager: 5.46 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: 4065 1.34 - 1.46: 2313 1.46 - 1.58: 6637 1.58 - 1.69: 2 1.69 - 1.81: 77 Bond restraints: 13094 Sorted by residual: bond pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 1.525 1.587 -0.062 2.10e-02 2.27e+03 8.68e+00 bond pdb=" CA ILE E 51 " pdb=" CB ILE E 51 " ideal model delta sigma weight residual 1.540 1.595 -0.055 2.70e-02 1.37e+03 4.21e+00 bond pdb=" CB VAL A 336 " pdb=" CG1 VAL A 336 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.56e+00 bond pdb=" CB VAL A 202 " pdb=" CG1 VAL A 202 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.28e+00 bond pdb=" CG1 ILE B 181 " pdb=" CD1 ILE B 181 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.27e+00 ... (remaining 13089 not shown) Histogram of bond angle deviations from ideal: 93.63 - 101.86: 31 101.86 - 110.09: 2691 110.09 - 118.32: 7343 118.32 - 126.54: 7469 126.54 - 134.77: 233 Bond angle restraints: 17767 Sorted by residual: angle pdb=" C GLU B 81 " pdb=" N ASN B 82 " pdb=" CA ASN B 82 " ideal model delta sigma weight residual 122.08 129.88 -7.80 1.47e+00 4.63e-01 2.82e+01 angle pdb=" C GLU H 138 " pdb=" N GLU H 139 " pdb=" CA GLU H 139 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.35e+01 angle pdb=" CA LEU A 35 " pdb=" CB LEU A 35 " pdb=" CG LEU A 35 " ideal model delta sigma weight residual 116.30 133.22 -16.92 3.50e+00 8.16e-02 2.34e+01 angle pdb=" C GLN A 247 " pdb=" N ASN A 248 " pdb=" CA ASN A 248 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.07e+01 angle pdb=" N LEU C 188 " pdb=" CA LEU C 188 " pdb=" C LEU C 188 " ideal model delta sigma weight residual 109.81 119.58 -9.77 2.21e+00 2.05e-01 1.95e+01 ... (remaining 17762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6876 17.70 - 35.40: 695 35.40 - 53.10: 144 53.10 - 70.79: 29 70.79 - 88.49: 3 Dihedral angle restraints: 7747 sinusoidal: 3030 harmonic: 4717 Sorted by residual: dihedral pdb=" CA GLY B 299 " pdb=" C GLY B 299 " pdb=" N ASP B 300 " pdb=" CA ASP B 300 " ideal model delta harmonic sigma weight residual 180.00 146.95 33.05 0 5.00e+00 4.00e-02 4.37e+01 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 180.00 148.51 31.49 0 5.00e+00 4.00e-02 3.97e+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 -156.90 -23.10 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 7744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1785 0.089 - 0.177: 221 0.177 - 0.265: 26 0.265 - 0.354: 3 0.354 - 0.442: 3 Chirality restraints: 2038 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CB VAL A 413 " pdb=" CA VAL A 413 " pdb=" CG1 VAL A 413 " pdb=" CG2 VAL A 413 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.84e+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 -2.21 -0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 2035 not shown) Planarity restraints: 2282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 35 " 0.076 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO H 36 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO H 36 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO H 36 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " 0.051 5.00e-02 4.00e+02 7.68e-02 9.44e+00 pdb=" N PRO D 67 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 307 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" C ARG B 307 " 0.052 2.00e-02 2.50e+03 pdb=" O ARG B 307 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU B 308 " -0.018 2.00e-02 2.50e+03 ... (remaining 2279 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 115 2.56 - 3.14: 9116 3.14 - 3.73: 20070 3.73 - 4.31: 28227 4.31 - 4.90: 46395 Nonbonded interactions: 103923 Sorted by model distance: nonbonded pdb=" OE1 GLU H 76 " pdb="ZN ZN H 201 " model vdw 1.972 2.230 nonbonded pdb=" NE2 HIS A 207 " pdb="CU CU A 502 " model vdw 2.003 2.320 nonbonded pdb=" OD2 ASP A 367 " pdb="MG MG A 501 " model vdw 2.113 2.170 nonbonded pdb=" O TRP A 358 " pdb="MG MG A 501 " model vdw 2.118 2.170 nonbonded pdb=" SD MET A 231 " pdb="CU CU A 502 " model vdw 2.187 2.600 ... (remaining 103918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 2 through 308) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or resid 245 through \ 274)) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.230 Check model and map are aligned: 0.770 Set scattering table: 0.000 Process input model: 38.350 Find NCS groups from input model: 0.660 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: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 0.091 13094 Z= 0.423 Angle : 1.047 16.917 17767 Z= 0.556 Chirality : 0.063 0.442 2038 Planarity : 0.007 0.118 2282 Dihedral : 14.561 88.492 4737 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 0.89 % Allowed : 9.02 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -5.62 (0.14), residues: 1653 helix: -4.46 (0.08), residues: 708 sheet: -3.07 (0.30), residues: 208 loop : -2.98 (0.18), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 20 HIS 0.010 0.002 HIS A 207 PHE 0.018 0.002 PHE B 35 TYR 0.025 0.002 TYR C 291 ARG 0.008 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9581 (mt) cc_final: 0.9130 (pt) REVERT: A 235 LYS cc_start: 0.9320 (mmtt) cc_final: 0.9109 (mmmm) REVERT: A 305 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8594 (mmmt) REVERT: B 57 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: B 86 TYR cc_start: 0.8822 (m-80) cc_final: 0.8470 (m-10) REVERT: C 47 LYS cc_start: 0.9563 (mttt) cc_final: 0.9287 (mmtp) REVERT: C 102 LYS cc_start: 0.9372 (ttmt) cc_final: 0.9161 (ttmm) REVERT: C 203 LYS cc_start: 0.9078 (mmmt) cc_final: 0.8672 (mmmm) REVERT: D 14 ASP cc_start: 0.8999 (t0) cc_final: 0.8761 (t0) REVERT: D 66 MET cc_start: 0.9191 (mmm) cc_final: 0.8749 (mmm) REVERT: D 88 MET cc_start: 0.8512 (tpp) cc_final: 0.8181 (tpp) REVERT: E 76 ASP cc_start: 0.8621 (p0) cc_final: 0.8297 (p0) REVERT: E 81 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8325 (mt-10) REVERT: E 83 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8079 (mt-10) REVERT: E 135 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8492 (tm-30) REVERT: E 138 MET cc_start: 0.7043 (tpt) cc_final: 0.6726 (tmm) REVERT: E 171 LYS cc_start: 0.9281 (tttt) cc_final: 0.8809 (ttmm) REVERT: H 40 HIS cc_start: 0.8557 (m-70) cc_final: 0.8178 (m90) REVERT: H 161 GLN cc_start: 0.8615 (mt0) cc_final: 0.8409 (mt0) outliers start: 12 outliers final: 4 residues processed: 151 average time/residue: 0.3208 time to fit residues: 65.6721 Evaluate side-chains 95 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 84 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 75 GLN A 77 GLN A 122 ASN A 123 ASN A 141 GLN A 145 ASN A 174 HIS A 175 ASN A 179 ASN A 190 ASN A 212 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 324 ASN A 331 GLN B 11 GLN B 20 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 261 ASN B 270 GLN C 25 ASN C 97 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN D 205 ASN D 225 ASN E 225 ASN H 161 GLN H 172 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13094 Z= 0.229 Angle : 0.611 7.713 17767 Z= 0.314 Chirality : 0.042 0.152 2038 Planarity : 0.005 0.051 2282 Dihedral : 5.348 54.836 1817 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.64 % Allowed : 13.87 % Favored : 84.49 % 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: -3.62 (0.17), residues: 1653 helix: -2.08 (0.15), residues: 720 sheet: -2.39 (0.32), residues: 219 loop : -2.63 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 253 HIS 0.004 0.001 HIS B 20 PHE 0.014 0.001 PHE H 156 TYR 0.016 0.001 TYR E 93 ARG 0.003 0.000 ARG D 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9522 (mt) cc_final: 0.9164 (pt) REVERT: A 305 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8438 (mmmt) REVERT: B 295 MET cc_start: 0.9443 (mmp) cc_final: 0.9042 (mmp) REVERT: C 47 LYS cc_start: 0.9621 (mttt) cc_final: 0.9333 (mmmm) REVERT: C 133 MET cc_start: 0.8878 (mtp) cc_final: 0.8401 (mtt) REVERT: D 66 MET cc_start: 0.9200 (mmm) cc_final: 0.8742 (mmm) REVERT: E 76 ASP cc_start: 0.8552 (p0) cc_final: 0.8283 (p0) REVERT: E 81 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8218 (mt-10) REVERT: E 135 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8610 (tm-30) REVERT: E 138 MET cc_start: 0.7401 (tpt) cc_final: 0.6982 (tmm) REVERT: H 40 HIS cc_start: 0.8502 (m-70) cc_final: 0.8157 (m90) REVERT: H 98 MET cc_start: 0.8460 (tpp) cc_final: 0.8121 (mmt) REVERT: H 161 GLN cc_start: 0.8411 (mt0) cc_final: 0.8019 (mt0) outliers start: 22 outliers final: 9 residues processed: 122 average time/residue: 0.2730 time to fit residues: 48.3138 Evaluate side-chains 90 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain E residue 188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 417 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 HIS E 205 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 13094 Z= 0.480 Angle : 0.766 9.999 17767 Z= 0.384 Chirality : 0.045 0.180 2038 Planarity : 0.004 0.044 2282 Dihedral : 5.244 27.470 1814 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.46 % Allowed : 16.26 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.20), residues: 1653 helix: -0.33 (0.19), residues: 718 sheet: -2.34 (0.32), residues: 222 loop : -2.47 (0.21), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 253 HIS 0.013 0.002 HIS B 194 PHE 0.022 0.002 PHE H 71 TYR 0.015 0.002 TYR B 86 ARG 0.006 0.001 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 80 time to evaluate : 1.755 Fit side-chains revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9513 (mt) cc_final: 0.9168 (pt) REVERT: A 217 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8799 (mm) REVERT: A 305 LYS cc_start: 0.8747 (mmtt) cc_final: 0.8419 (mmmt) REVERT: B 162 ILE cc_start: 0.9061 (mt) cc_final: 0.8830 (mm) REVERT: C 43 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9011 (t) REVERT: C 47 LYS cc_start: 0.9661 (mttt) cc_final: 0.9352 (mmmm) REVERT: C 292 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8340 (ttm-80) REVERT: D 66 MET cc_start: 0.9285 (mmm) cc_final: 0.9052 (mmm) REVERT: E 11 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8427 (mm-30) REVERT: E 81 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8043 (mt-10) outliers start: 33 outliers final: 19 residues processed: 108 average time/residue: 0.2356 time to fit residues: 38.7600 Evaluate side-chains 98 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 165 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS B 11 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN H 149 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13094 Z= 0.197 Angle : 0.564 8.991 17767 Z= 0.283 Chirality : 0.042 0.146 2038 Planarity : 0.003 0.035 2282 Dihedral : 4.761 25.785 1814 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.54 % Allowed : 16.63 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.21), residues: 1653 helix: 0.55 (0.21), residues: 713 sheet: -2.21 (0.32), residues: 233 loop : -2.19 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 253 HIS 0.011 0.001 HIS B 194 PHE 0.012 0.001 PHE D 157 TYR 0.012 0.001 TYR B 86 ARG 0.004 0.000 ARG B 302 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 84 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9496 (mt) cc_final: 0.9128 (pt) REVERT: A 305 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8382 (mmmt) REVERT: B 2 ASN cc_start: 0.8927 (m110) cc_final: 0.8565 (m-40) REVERT: C 24 LEU cc_start: 0.9575 (tp) cc_final: 0.9342 (tt) REVERT: C 47 LYS cc_start: 0.9718 (mttt) cc_final: 0.9415 (mmmm) REVERT: D 66 MET cc_start: 0.9210 (mmm) cc_final: 0.8988 (mmm) REVERT: D 169 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8548 (p0) REVERT: D 264 LEU cc_start: 0.9185 (tp) cc_final: 0.8778 (tt) REVERT: E 11 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8187 (mm-30) REVERT: E 64 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8780 (m-80) REVERT: H 92 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8567 (mmtt) REVERT: H 98 MET cc_start: 0.8764 (tpp) cc_final: 0.8101 (mmt) outliers start: 34 outliers final: 17 residues processed: 112 average time/residue: 0.2259 time to fit residues: 39.1781 Evaluate side-chains 98 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 10.0000 chunk 89 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 80 optimal weight: 0.2980 chunk 142 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13094 Z= 0.289 Angle : 0.610 9.793 17767 Z= 0.303 Chirality : 0.042 0.143 2038 Planarity : 0.003 0.031 2282 Dihedral : 4.747 27.154 1813 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.83 % Allowed : 18.42 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1653 helix: 0.96 (0.21), residues: 713 sheet: -2.20 (0.32), residues: 233 loop : -2.04 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 253 HIS 0.005 0.001 HIS A 417 PHE 0.015 0.001 PHE D 157 TYR 0.012 0.001 TYR B 86 ARG 0.003 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 78 time to evaluate : 1.562 Fit side-chains revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9492 (mt) cc_final: 0.9134 (pt) REVERT: A 305 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8405 (mmmt) REVERT: B 2 ASN cc_start: 0.8962 (m110) cc_final: 0.8497 (t0) REVERT: C 24 LEU cc_start: 0.9576 (tp) cc_final: 0.9335 (tt) REVERT: C 47 LYS cc_start: 0.9678 (mttt) cc_final: 0.9373 (mmmm) REVERT: D 66 MET cc_start: 0.9176 (mmm) cc_final: 0.8948 (mmm) REVERT: D 264 LEU cc_start: 0.9211 (tp) cc_final: 0.8801 (tt) REVERT: E 11 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8023 (mm-30) REVERT: E 64 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8718 (m-80) REVERT: H 92 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8580 (mmtt) outliers start: 38 outliers final: 24 residues processed: 113 average time/residue: 0.2243 time to fit residues: 39.1835 Evaluate side-chains 101 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 93 optimal weight: 40.0000 chunk 39 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13094 Z= 0.288 Angle : 0.608 10.272 17767 Z= 0.302 Chirality : 0.043 0.141 2038 Planarity : 0.003 0.038 2282 Dihedral : 4.688 26.737 1812 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.76 % Allowed : 19.02 % Favored : 78.23 % 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: -0.91 (0.22), residues: 1653 helix: 1.19 (0.21), residues: 715 sheet: -2.10 (0.32), residues: 244 loop : -1.98 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 253 HIS 0.003 0.001 HIS B 194 PHE 0.015 0.001 PHE D 157 TYR 0.010 0.001 TYR B 293 ARG 0.002 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 76 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9496 (mt) cc_final: 0.9137 (pt) REVERT: A 305 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8393 (mmmt) REVERT: B 2 ASN cc_start: 0.8962 (m110) cc_final: 0.8503 (t0) REVERT: B 86 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.8609 (m-80) REVERT: C 16 MET cc_start: 0.8435 (ttp) cc_final: 0.8213 (ttp) REVERT: D 66 MET cc_start: 0.9177 (mmm) cc_final: 0.8949 (mmm) REVERT: D 169 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8584 (p0) REVERT: D 264 LEU cc_start: 0.9200 (tp) cc_final: 0.8805 (tt) REVERT: E 11 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8046 (mm-30) REVERT: E 64 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8739 (m-80) REVERT: H 92 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8542 (mmtt) REVERT: H 98 MET cc_start: 0.8823 (tpp) cc_final: 0.8263 (mmt) outliers start: 37 outliers final: 26 residues processed: 110 average time/residue: 0.2259 time to fit residues: 39.1625 Evaluate side-chains 102 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 73 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13094 Z= 0.221 Angle : 0.574 9.874 17767 Z= 0.283 Chirality : 0.042 0.142 2038 Planarity : 0.003 0.041 2282 Dihedral : 4.525 25.982 1812 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.76 % Allowed : 19.31 % Favored : 77.93 % 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: -0.67 (0.22), residues: 1653 helix: 1.43 (0.21), residues: 716 sheet: -1.98 (0.33), residues: 241 loop : -1.92 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 253 HIS 0.004 0.001 HIS B 37 PHE 0.013 0.001 PHE D 157 TYR 0.010 0.001 TYR B 293 ARG 0.002 0.000 ARG B 302 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 76 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9497 (mt) cc_final: 0.9141 (pt) REVERT: A 231 MET cc_start: 0.7933 (mtp) cc_final: 0.7661 (mtp) REVERT: A 305 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8392 (mmmt) REVERT: B 2 ASN cc_start: 0.8930 (m110) cc_final: 0.8491 (t0) REVERT: B 86 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.8627 (m-80) REVERT: C 16 MET cc_start: 0.8413 (ttp) cc_final: 0.8150 (ttp) REVERT: D 66 MET cc_start: 0.9160 (mmm) cc_final: 0.8946 (mmm) REVERT: D 147 MET cc_start: 0.8794 (mmm) cc_final: 0.8249 (mmt) REVERT: D 169 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8606 (p0) REVERT: D 264 LEU cc_start: 0.9218 (tp) cc_final: 0.8839 (tt) REVERT: E 64 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8701 (m-80) REVERT: H 72 CYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8426 (p) REVERT: H 98 MET cc_start: 0.8771 (tpp) cc_final: 0.8178 (mmt) outliers start: 37 outliers final: 30 residues processed: 109 average time/residue: 0.2205 time to fit residues: 38.0785 Evaluate side-chains 108 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 74 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 72 CYS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN C 59 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13094 Z= 0.247 Angle : 0.588 9.971 17767 Z= 0.289 Chirality : 0.042 0.139 2038 Planarity : 0.003 0.042 2282 Dihedral : 4.516 26.188 1812 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.13 % Allowed : 19.31 % Favored : 77.55 % 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: -0.54 (0.22), residues: 1653 helix: 1.55 (0.21), residues: 718 sheet: -2.00 (0.34), residues: 227 loop : -1.83 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 253 HIS 0.006 0.001 HIS B 37 PHE 0.014 0.001 PHE D 157 TYR 0.010 0.001 TYR B 293 ARG 0.002 0.000 ARG B 302 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 75 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7750 (mpp) cc_final: 0.7526 (mpp) REVERT: A 199 ILE cc_start: 0.9493 (mt) cc_final: 0.9139 (pt) REVERT: A 231 MET cc_start: 0.6771 (mtp) cc_final: 0.6393 (mtp) REVERT: A 305 LYS cc_start: 0.8768 (mmtt) cc_final: 0.8397 (mmmt) REVERT: B 2 ASN cc_start: 0.8914 (m110) cc_final: 0.8464 (t0) REVERT: B 86 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8514 (m-80) REVERT: D 66 MET cc_start: 0.9160 (mmm) cc_final: 0.8945 (mmm) REVERT: D 169 ASN cc_start: 0.9003 (OUTLIER) cc_final: 0.8610 (p0) REVERT: D 264 LEU cc_start: 0.9211 (tp) cc_final: 0.8840 (tt) REVERT: E 64 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8704 (m-80) REVERT: H 50 MET cc_start: 0.8109 (ptt) cc_final: 0.7676 (ptt) REVERT: H 72 CYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8415 (p) REVERT: H 98 MET cc_start: 0.8784 (tpp) cc_final: 0.8181 (mmt) outliers start: 42 outliers final: 34 residues processed: 113 average time/residue: 0.2084 time to fit residues: 37.3605 Evaluate side-chains 113 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 75 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 72 CYS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN C 59 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13094 Z= 0.168 Angle : 0.562 10.620 17767 Z= 0.274 Chirality : 0.041 0.138 2038 Planarity : 0.003 0.039 2282 Dihedral : 4.364 25.695 1812 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.83 % Allowed : 19.76 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.22), residues: 1653 helix: 1.75 (0.21), residues: 716 sheet: -1.82 (0.35), residues: 224 loop : -1.83 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 253 HIS 0.003 0.001 HIS B 20 PHE 0.011 0.001 PHE D 157 TYR 0.010 0.001 TYR B 293 ARG 0.004 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 80 time to evaluate : 1.553 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7786 (mpp) cc_final: 0.7540 (mpp) REVERT: A 199 ILE cc_start: 0.9499 (mt) cc_final: 0.9148 (pt) REVERT: A 305 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8333 (mmmt) REVERT: B 2 ASN cc_start: 0.8894 (m110) cc_final: 0.8469 (t0) REVERT: B 86 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: D 66 MET cc_start: 0.9127 (mmm) cc_final: 0.8914 (mmm) REVERT: D 147 MET cc_start: 0.8759 (mmm) cc_final: 0.8122 (mmt) REVERT: D 264 LEU cc_start: 0.9179 (tp) cc_final: 0.8811 (tt) REVERT: E 64 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8658 (m-80) REVERT: H 50 MET cc_start: 0.8214 (ptt) cc_final: 0.7700 (ptt) REVERT: H 98 MET cc_start: 0.8736 (tpp) cc_final: 0.8126 (mmt) outliers start: 38 outliers final: 28 residues processed: 113 average time/residue: 0.2156 time to fit residues: 38.6066 Evaluate side-chains 108 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 78 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 10.0000 chunk 155 optimal weight: 0.6980 chunk 95 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- 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 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN C 59 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN H 149 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 13094 Z= 0.437 Angle : 0.741 10.446 17767 Z= 0.362 Chirality : 0.045 0.145 2038 Planarity : 0.004 0.041 2282 Dihedral : 4.920 26.832 1812 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.91 % Allowed : 19.84 % Favored : 77.26 % 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: -0.64 (0.22), residues: 1653 helix: 1.47 (0.21), residues: 712 sheet: -1.90 (0.36), residues: 208 loop : -1.95 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 211 HIS 0.008 0.001 HIS B 37 PHE 0.019 0.002 PHE D 157 TYR 0.015 0.002 TYR A 249 ARG 0.005 0.000 ARG D 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 74 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: A 199 ILE cc_start: 0.9501 (mt) cc_final: 0.9160 (pt) REVERT: A 305 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8439 (mmmt) REVERT: B 2 ASN cc_start: 0.8957 (m110) cc_final: 0.8546 (t0) REVERT: B 86 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.8439 (m-80) REVERT: B 304 GLN cc_start: 0.7893 (mp10) cc_final: 0.7615 (mp10) REVERT: C 133 MET cc_start: 0.8976 (mtp) cc_final: 0.8439 (mtt) REVERT: D 66 MET cc_start: 0.9194 (mmm) cc_final: 0.8953 (mmm) REVERT: D 147 MET cc_start: 0.8802 (mmm) cc_final: 0.8600 (mmm) REVERT: D 169 ASN cc_start: 0.9126 (OUTLIER) cc_final: 0.8889 (p0) REVERT: D 264 LEU cc_start: 0.9191 (tp) cc_final: 0.8958 (tp) REVERT: E 64 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8773 (m-80) REVERT: E 135 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8452 (tm-30) outliers start: 39 outliers final: 28 residues processed: 110 average time/residue: 0.2075 time to fit residues: 36.1837 Evaluate side-chains 103 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 72 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 149 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 0.4980 chunk 138 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 133 optimal weight: 0.4980 chunk 16 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 122 ASN A 175 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.060100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.047394 restraints weight = 59526.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.048890 restraints weight = 30805.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.049877 restraints weight = 19935.670| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13094 Z= 0.152 Angle : 0.578 9.235 17767 Z= 0.281 Chirality : 0.041 0.140 2038 Planarity : 0.003 0.037 2282 Dihedral : 4.418 25.270 1812 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.72 % Allowed : 21.10 % Favored : 77.18 % 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: -0.31 (0.22), residues: 1653 helix: 1.82 (0.21), residues: 713 sheet: -1.85 (0.34), residues: 228 loop : -1.81 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 253 HIS 0.014 0.001 HIS H 149 PHE 0.012 0.001 PHE D 157 TYR 0.008 0.001 TYR B 293 ARG 0.003 0.000 ARG H 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2061.32 seconds wall clock time: 39 minutes 7.72 seconds (2347.72 seconds total)