Starting phenix.real_space_refine on Thu Feb 15 16:59:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osi_13052/02_2024/7osi_13052.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osi_13052/02_2024/7osi_13052.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/7osi_13052/02_2024/7osi_13052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osi_13052/02_2024/7osi_13052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osi_13052/02_2024/7osi_13052.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osi_13052/02_2024/7osi_13052.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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 Cu 1 5.60 5 Mg 1 5.21 5 S 45 5.16 5 C 8200 2.51 5 N 2249 2.21 5 O 2329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 40": "OD1" <-> "OD2" 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 ASP 218": "OD1" <-> "OD2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "B 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 252": "OE1" <-> "OE2" Residue "B ASP 279": "OD1" <-> "OD2" 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 ASP 234": "OD1" <-> "OD2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 292": "NH1" <-> "NH2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D ASP 190": "OD1" <-> "OD2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H ARG 152": "NH1" <-> "NH2" Residue "H GLU 157": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12826 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3077 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2375 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain: "C" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2015 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain breaks: 1 Chain: "E" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1896 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 2 Chain: "H" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1092 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11839 SG CYS H 45 45.497 43.363 48.339 1.00124.97 S ATOM 11862 SG CYS H 48 43.467 44.396 45.986 1.00123.33 S ATOM 12043 SG CYS H 72 46.344 45.442 44.473 1.00127.30 S Time building chain proxies: 7.39, per 1000 atoms: 0.58 Number of scatterers: 12826 At special positions: 0 Unit cell: (81.648, 92.016, 191.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 S 45 16.00 Mg 1 11.99 O 2329 8.00 N 2249 7.00 C 8200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.12 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 45 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 72 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 48 " 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 13 sheets defined 45.9% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 344 through 348 removed outlier: 4.283A pdb=" N GLY A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.702A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.608A pdb=" N MET A 390 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.607A pdb=" N TRP A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.608A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.559A 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 143 removed outlier: 3.774A pdb=" N ALA B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.560A pdb=" N GLN B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 4.234A pdb=" N VAL B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 192' Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 236 through 244 removed outlier: 4.250A pdb=" N TRP B 240 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 removed outlier: 3.954A pdb=" N ARG B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.552A pdb=" N LEU C 50 " --> pdb=" O MET C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.642A pdb=" N ARG C 74 " --> pdb=" O PRO C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 106 through 111 removed outlier: 4.489A pdb=" N ASP C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 106 through 111' Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 160 through 177 removed outlier: 3.719A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.896A pdb=" N ALA C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.864A pdb=" N TRP C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 removed outlier: 3.775A pdb=" N ALA C 243 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 removed outlier: 3.680A pdb=" N LEU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 Processing helix chain 'D' and resid 3 through 16 removed outlier: 4.016A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.544A pdb=" N ILE D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.594A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Proline residue: D 67 - end of helix Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.678A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.112A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 168 removed outlier: 4.496A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.813A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.549A 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: 3.505A pdb=" N ASN D 225 " --> pdb=" O TYR D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 244 removed outlier: 3.679A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 272 removed outlier: 3.546A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 7 through 16 removed outlier: 3.678A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.547A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA E 41 " --> pdb=" O TRP E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 4.034A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 78 through 85 Processing helix chain 'E' and resid 85 through 92 removed outlier: 3.575A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR E 92 " --> pdb=" O MET E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.684A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 135 through 143 removed outlier: 3.781A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.619A pdb=" N VAL E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.541A pdb=" N ALA E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 removed outlier: 3.652A pdb=" N LEU E 196 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E 197 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 213 removed outlier: 4.072A pdb=" N TRP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 Processing helix chain 'E' and resid 248 through 272 removed outlier: 4.095A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 55 removed outlier: 3.772A 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 148 removed outlier: 3.647A pdb=" N GLY H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 172 removed outlier: 3.679A pdb=" N GLN H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47 removed outlier: 6.072A pdb=" N TRP A 45 " --> pdb=" O ARG A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.746A pdb=" N GLN A 73 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 58 removed outlier: 5.948A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 333 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS A 311 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.574A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.312A 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: 6.332A pdb=" N LEU A 216 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 25 removed outlier: 5.831A pdb=" N VAL B 9 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN B 23 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN B 7 " --> pdb=" O ASN B 23 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN B 25 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU B 5 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 4.116A 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: 7.475A pdb=" N GLY B 77 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ASP B 153 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 246 through 249 removed outlier: 3.654A pdb=" N GLU B 256 " --> pdb=" O ARG B 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 26 removed outlier: 3.530A pdb=" N GLN C 59 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.591A pdb=" N GLY C 77 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ASP C 153 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU C 79 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU C 150 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N CYS C 184 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU C 152 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE C 35 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA C 198 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL C 209 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE C 200 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 247 through 248 removed outlier: 3.939A pdb=" N ARG C 248 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 225 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER C 228 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 3.512A 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 121 removed outlier: 3.553A pdb=" N VAL H 121 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG H 152 " --> pdb=" O VAL H 121 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1449 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: 3.67 Time building geometry restraints manager: 5.52 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: 4104 1.34 - 1.45: 2233 1.45 - 1.57: 6650 1.57 - 1.69: 3 1.69 - 1.81: 77 Bond restraints: 13067 Sorted by residual: bond pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 1.525 1.590 -0.065 2.10e-02 2.27e+03 9.44e+00 bond pdb=" CG1 ILE A 186 " pdb=" CD1 ILE A 186 " ideal model delta sigma weight residual 1.513 1.417 0.096 3.90e-02 6.57e+02 6.12e+00 bond pdb=" CG LEU A 173 " pdb=" CD1 LEU A 173 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.76e+00 bond pdb=" CB VAL A 336 " pdb=" CG1 VAL A 336 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.58e+00 bond pdb=" CB TYR A 291 " pdb=" CG TYR A 291 " ideal model delta sigma weight residual 1.512 1.464 0.048 2.20e-02 2.07e+03 4.70e+00 ... (remaining 13062 not shown) Histogram of bond angle deviations from ideal: 97.10 - 104.81: 209 104.81 - 112.51: 6563 112.51 - 120.22: 5852 120.22 - 127.93: 4955 127.93 - 135.63: 147 Bond angle restraints: 17726 Sorted by residual: angle pdb=" C SER C 231 " pdb=" N GLU C 232 " pdb=" CA GLU C 232 " ideal model delta sigma weight residual 121.54 133.37 -11.83 1.91e+00 2.74e-01 3.84e+01 angle pdb=" C LYS C 47 " pdb=" N LEU C 48 " pdb=" CA LEU C 48 " ideal model delta sigma weight residual 120.38 128.38 -8.00 1.37e+00 5.33e-01 3.41e+01 angle pdb=" CA THR A 226 " pdb=" CB THR A 226 " pdb=" CG2 THR A 226 " ideal model delta sigma weight residual 110.50 119.20 -8.70 1.70e+00 3.46e-01 2.62e+01 angle pdb=" N THR A 226 " pdb=" CA THR A 226 " pdb=" CB THR A 226 " ideal model delta sigma weight residual 110.57 118.99 -8.42 1.69e+00 3.50e-01 2.48e+01 angle pdb=" N GLY C 229 " pdb=" CA GLY C 229 " pdb=" C GLY C 229 " ideal model delta sigma weight residual 113.18 101.63 11.55 2.37e+00 1.78e-01 2.38e+01 ... (remaining 17721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.82: 7131 20.82 - 41.64: 526 41.64 - 62.47: 64 62.47 - 83.29: 12 83.29 - 104.11: 3 Dihedral angle restraints: 7736 sinusoidal: 3041 harmonic: 4695 Sorted by residual: dihedral pdb=" CA GLY C 229 " pdb=" C GLY C 229 " pdb=" N ILE C 230 " pdb=" CA ILE C 230 " ideal model delta harmonic sigma weight residual -180.00 -75.89 -104.11 0 5.00e+00 4.00e-02 4.34e+02 dihedral pdb=" CA GLU C 232 " pdb=" C GLU C 232 " pdb=" N ARG C 233 " pdb=" CA ARG C 233 " ideal model delta harmonic sigma weight residual -180.00 -109.11 -70.89 0 5.00e+00 4.00e-02 2.01e+02 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 180.00 149.59 30.41 0 5.00e+00 4.00e-02 3.70e+01 ... (remaining 7733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1744 0.090 - 0.179: 245 0.179 - 0.269: 35 0.269 - 0.359: 5 0.359 - 0.449: 1 Chirality restraints: 2030 Sorted by residual: chirality pdb=" CB VAL A 413 " pdb=" CA VAL A 413 " pdb=" CG1 VAL A 413 " pdb=" CG2 VAL A 413 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" CB VAL B 260 " pdb=" CA VAL B 260 " pdb=" CG1 VAL B 260 " pdb=" CG2 VAL B 260 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA ASP A 182 " pdb=" N ASP A 182 " pdb=" C ASP A 182 " pdb=" CB ASP A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 2027 not shown) Planarity restraints: 2276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 209 " -0.065 5.00e-02 4.00e+02 9.66e-02 1.49e+01 pdb=" N PRO E 210 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 282 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C ILE B 282 " -0.066 2.00e-02 2.50e+03 pdb=" O ILE B 282 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS B 283 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 298 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ALA B 298 " 0.060 2.00e-02 2.50e+03 pdb=" O ALA B 298 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY B 299 " -0.020 2.00e-02 2.50e+03 ... (remaining 2273 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 115 2.54 - 3.13: 8963 3.13 - 3.72: 20094 3.72 - 4.31: 28466 4.31 - 4.90: 46811 Nonbonded interactions: 104449 Sorted by model distance: nonbonded pdb=" OE1 GLU H 76 " pdb="ZN ZN H 201 " model vdw 1.948 2.230 nonbonded pdb=" NE2 HIS A 207 " pdb="CU CU A 502 " model vdw 1.978 2.320 nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 2.135 2.170 nonbonded pdb=" O LEU A 365 " pdb="MG MG A 501 " model vdw 2.152 2.170 nonbonded pdb=" SD MET A 231 " pdb="CU CU A 502 " model vdw 2.186 2.600 ... (remaining 104444 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: 0.500 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: 0.020 Extract box with map and model: 2.520 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 38.680 Find NCS groups from input model: 0.640 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.010 0.096 13067 Z= 0.622 Angle : 1.211 16.346 17726 Z= 0.647 Chirality : 0.068 0.449 2030 Planarity : 0.008 0.097 2276 Dihedral : 14.632 104.111 4740 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.26 % Favored : 93.68 % Rotamer: Outliers : 1.12 % Allowed : 9.38 % Favored : 89.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -5.48 (0.15), residues: 1645 helix: -4.33 (0.09), residues: 695 sheet: -3.13 (0.30), residues: 200 loop : -2.93 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP C 236 HIS 0.020 0.003 HIS C 37 PHE 0.031 0.003 PHE B 35 TYR 0.028 0.003 TYR A 204 ARG 0.007 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.8955 (p) REVERT: A 235 LYS cc_start: 0.9215 (tptt) cc_final: 0.8898 (mmmm) REVERT: A 420 MET cc_start: 0.9114 (mmm) cc_final: 0.8503 (mmt) REVERT: B 200 ILE cc_start: 0.9626 (mt) cc_final: 0.9360 (tt) REVERT: B 242 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.6346 (p0) REVERT: B 248 ARG cc_start: 0.8089 (ttt180) cc_final: 0.7876 (ttm-80) REVERT: C 133 MET cc_start: 0.8753 (mtm) cc_final: 0.8535 (mtm) REVERT: D 10 LYS cc_start: 0.8766 (tmtt) cc_final: 0.8547 (ttpp) REVERT: D 219 ASP cc_start: 0.8742 (m-30) cc_final: 0.8158 (m-30) REVERT: E 88 MET cc_start: 0.8400 (mmt) cc_final: 0.8156 (tpp) REVERT: H 52 ILE cc_start: 0.9522 (mt) cc_final: 0.9306 (mm) REVERT: H 64 GLU cc_start: 0.7641 (tt0) cc_final: 0.7275 (tm-30) REVERT: H 87 ARG cc_start: 0.9088 (mmm160) cc_final: 0.8401 (mmm160) outliers start: 15 outliers final: 6 residues processed: 150 average time/residue: 0.3504 time to fit residues: 69.8440 Evaluate side-chains 85 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 213 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 141 GLN A 145 ASN A 174 HIS A 175 ASN A 179 ASN A 212 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 324 ASN A 417 HIS B 20 HIS B 37 HIS B 176 GLN C 194 HIS D 225 ASN E 225 ASN H 40 HIS ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13067 Z= 0.170 Angle : 0.621 9.344 17726 Z= 0.317 Chirality : 0.041 0.147 2030 Planarity : 0.005 0.060 2276 Dihedral : 5.602 54.446 1815 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.49 % Allowed : 13.25 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.17), residues: 1645 helix: -1.93 (0.15), residues: 725 sheet: -2.85 (0.29), residues: 223 loop : -2.49 (0.21), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 236 HIS 0.005 0.001 HIS H 40 PHE 0.013 0.001 PHE E 157 TYR 0.017 0.001 TYR B 86 ARG 0.007 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8477 (mpp) cc_final: 0.7320 (mpp) REVERT: A 235 LYS cc_start: 0.9170 (tptt) cc_final: 0.8899 (mmmm) REVERT: A 334 LYS cc_start: 0.9103 (tttt) cc_final: 0.8783 (tttp) REVERT: A 420 MET cc_start: 0.9012 (mmm) cc_final: 0.8752 (mmt) REVERT: C 13 TYR cc_start: 0.8130 (p90) cc_final: 0.7710 (p90) REVERT: C 133 MET cc_start: 0.8574 (mtm) cc_final: 0.8347 (mtm) REVERT: C 268 LEU cc_start: 0.9355 (mt) cc_final: 0.9071 (tt) REVERT: D 169 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7926 (p0) REVERT: D 219 ASP cc_start: 0.8749 (m-30) cc_final: 0.8429 (m-30) REVERT: E 187 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9076 (pp) REVERT: H 87 ARG cc_start: 0.9025 (mmm160) cc_final: 0.8338 (mmm160) REVERT: H 98 MET cc_start: 0.9263 (mmm) cc_final: 0.8930 (mmm) REVERT: H 141 ASP cc_start: 0.8751 (p0) cc_final: 0.8159 (p0) REVERT: H 148 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8141 (tmm) outliers start: 20 outliers final: 7 residues processed: 103 average time/residue: 0.2869 time to fit residues: 42.5898 Evaluate side-chains 78 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 148 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 132 optimal weight: 0.0050 chunk 147 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN E 225 ASN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13067 Z= 0.233 Angle : 0.597 8.669 17726 Z= 0.304 Chirality : 0.041 0.187 2030 Planarity : 0.004 0.053 2276 Dihedral : 4.907 34.540 1805 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.79 % Allowed : 14.37 % Favored : 83.84 % 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: -2.11 (0.20), residues: 1645 helix: -0.23 (0.19), residues: 724 sheet: -2.61 (0.29), residues: 248 loop : -2.14 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 211 HIS 0.009 0.001 HIS H 40 PHE 0.014 0.001 PHE D 157 TYR 0.015 0.001 TYR B 86 ARG 0.004 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 71 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.9017 (mtm) cc_final: 0.8551 (mpp) REVERT: A 125 MET cc_start: 0.8745 (mpp) cc_final: 0.7542 (mpp) REVERT: A 235 LYS cc_start: 0.9139 (tptt) cc_final: 0.8867 (mmmm) REVERT: A 253 MET cc_start: 0.8496 (ptp) cc_final: 0.8285 (ptp) REVERT: A 334 LYS cc_start: 0.9106 (tttt) cc_final: 0.8811 (tttp) REVERT: C 133 MET cc_start: 0.8576 (mtm) cc_final: 0.8315 (mtm) REVERT: D 169 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7622 (p0) REVERT: D 219 ASP cc_start: 0.8812 (m-30) cc_final: 0.8456 (m-30) REVERT: E 93 TYR cc_start: 0.8671 (m-80) cc_final: 0.8461 (m-80) REVERT: H 87 ARG cc_start: 0.9043 (mmm160) cc_final: 0.8640 (mmm160) REVERT: H 129 MET cc_start: 0.8592 (tpp) cc_final: 0.8086 (tpp) REVERT: H 141 ASP cc_start: 0.8744 (p0) cc_final: 0.8116 (p0) REVERT: H 148 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8224 (tmm) outliers start: 24 outliers final: 12 residues processed: 93 average time/residue: 0.2964 time to fit residues: 40.3186 Evaluate side-chains 76 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 148 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 5.9990 chunk 111 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 176 GLN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 HIS H 96 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13067 Z= 0.289 Angle : 0.616 8.429 17726 Z= 0.310 Chirality : 0.042 0.163 2030 Planarity : 0.004 0.050 2276 Dihedral : 4.813 37.042 1805 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.31 % Allowed : 15.41 % Favored : 82.28 % 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: -1.40 (0.21), residues: 1645 helix: 0.58 (0.20), residues: 721 sheet: -2.41 (0.30), residues: 237 loop : -1.99 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 211 HIS 0.003 0.001 HIS B 194 PHE 0.016 0.001 PHE D 157 TYR 0.012 0.001 TYR B 293 ARG 0.003 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 67 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8990 (mtm) cc_final: 0.8455 (mpp) REVERT: A 125 MET cc_start: 0.8824 (mpp) cc_final: 0.7506 (mpp) REVERT: A 235 LYS cc_start: 0.9149 (tptt) cc_final: 0.8883 (mmmm) REVERT: A 420 MET cc_start: 0.8628 (mmt) cc_final: 0.8351 (mmt) REVERT: C 13 TYR cc_start: 0.8155 (p90) cc_final: 0.7732 (p90) REVERT: C 37 HIS cc_start: 0.7054 (t70) cc_final: 0.6781 (t70) REVERT: C 133 MET cc_start: 0.8554 (mtm) cc_final: 0.8257 (mtm) REVERT: C 295 MET cc_start: 0.9232 (mmm) cc_final: 0.8865 (mmm) REVERT: D 88 MET cc_start: 0.8185 (tpp) cc_final: 0.7924 (tpp) REVERT: D 147 MET cc_start: 0.8820 (mmm) cc_final: 0.8434 (mmt) REVERT: D 169 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7827 (p0) REVERT: D 219 ASP cc_start: 0.8827 (m-30) cc_final: 0.8413 (m-30) REVERT: E 187 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9103 (pp) REVERT: H 87 ARG cc_start: 0.9041 (mmm160) cc_final: 0.8652 (mmm160) REVERT: H 98 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.9030 (mmm) REVERT: H 129 MET cc_start: 0.8489 (tpp) cc_final: 0.8192 (tpp) REVERT: H 140 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8088 (mp10) REVERT: H 141 ASP cc_start: 0.8738 (p0) cc_final: 0.8088 (p0) REVERT: H 148 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8225 (tmm) outliers start: 31 outliers final: 17 residues processed: 94 average time/residue: 0.2728 time to fit residues: 38.1268 Evaluate side-chains 80 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 148 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 9.9990 chunk 89 optimal weight: 0.0770 chunk 2 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 HIS H 40 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13067 Z= 0.200 Angle : 0.559 8.301 17726 Z= 0.280 Chirality : 0.041 0.143 2030 Planarity : 0.003 0.049 2276 Dihedral : 4.589 34.577 1805 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.53 % Allowed : 16.75 % Favored : 80.71 % 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: -1.02 (0.21), residues: 1645 helix: 0.99 (0.20), residues: 724 sheet: -2.24 (0.30), residues: 245 loop : -1.91 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 211 HIS 0.009 0.001 HIS H 40 PHE 0.013 0.001 PHE D 157 TYR 0.012 0.001 TYR B 86 ARG 0.007 0.000 ARG D 272 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 69 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8924 (mtm) cc_final: 0.8393 (mpp) REVERT: A 125 MET cc_start: 0.8946 (mpp) cc_final: 0.7505 (mpp) REVERT: A 197 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8558 (p0) REVERT: A 235 LYS cc_start: 0.9142 (tptt) cc_final: 0.8942 (mmmm) REVERT: A 334 LYS cc_start: 0.9117 (tttt) cc_final: 0.8834 (tttp) REVERT: B 102 LYS cc_start: 0.9460 (mtpp) cc_final: 0.9234 (mttp) REVERT: B 183 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8459 (mm) REVERT: C 13 TYR cc_start: 0.8237 (p90) cc_final: 0.7902 (p90) REVERT: C 133 MET cc_start: 0.8609 (mtm) cc_final: 0.8276 (mtm) REVERT: D 88 MET cc_start: 0.8220 (tpp) cc_final: 0.7951 (tpp) REVERT: D 147 MET cc_start: 0.8642 (mmm) cc_final: 0.8292 (mmt) REVERT: D 219 ASP cc_start: 0.8831 (m-30) cc_final: 0.8464 (m-30) REVERT: E 187 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9053 (pp) REVERT: E 190 ASP cc_start: 0.9071 (OUTLIER) cc_final: 0.8613 (m-30) REVERT: H 98 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.9051 (mmm) REVERT: H 129 MET cc_start: 0.8298 (tpp) cc_final: 0.7641 (tpp) REVERT: H 140 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: H 141 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8179 (p0) REVERT: H 148 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8319 (tmm) outliers start: 34 outliers final: 15 residues processed: 97 average time/residue: 0.2668 time to fit residues: 38.2504 Evaluate side-chains 83 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 60 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 148 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 157 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 82 ASN C 97 HIS ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13067 Z= 0.141 Angle : 0.533 8.662 17726 Z= 0.262 Chirality : 0.040 0.137 2030 Planarity : 0.003 0.048 2276 Dihedral : 4.291 31.384 1805 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.46 % Allowed : 17.05 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1645 helix: 1.37 (0.21), residues: 729 sheet: -2.16 (0.30), residues: 260 loop : -1.77 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 236 HIS 0.002 0.001 HIS B 20 PHE 0.012 0.001 PHE D 157 TYR 0.009 0.001 TYR C 293 ARG 0.007 0.000 ARG D 272 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 72 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8927 (mtm) cc_final: 0.8416 (mpp) REVERT: A 125 MET cc_start: 0.8914 (mpp) cc_final: 0.7496 (mpp) REVERT: A 197 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8396 (p0) REVERT: A 334 LYS cc_start: 0.9149 (tttt) cc_final: 0.8843 (tttp) REVERT: B 183 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8327 (mm) REVERT: C 13 TYR cc_start: 0.8234 (p90) cc_final: 0.7950 (p90) REVERT: C 133 MET cc_start: 0.8540 (mtm) cc_final: 0.8180 (mtm) REVERT: C 295 MET cc_start: 0.9122 (mmm) cc_final: 0.8887 (mmm) REVERT: D 169 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7661 (p0) REVERT: D 219 ASP cc_start: 0.8803 (m-30) cc_final: 0.8428 (m-30) REVERT: E 187 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8925 (pp) REVERT: H 65 LYS cc_start: 0.9306 (ptmm) cc_final: 0.8836 (ttmt) REVERT: H 129 MET cc_start: 0.7814 (tpp) cc_final: 0.7122 (tpp) REVERT: H 140 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: H 141 ASP cc_start: 0.8645 (p0) cc_final: 0.8127 (p0) REVERT: H 148 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8329 (tmm) outliers start: 33 outliers final: 19 residues processed: 103 average time/residue: 0.2832 time to fit residues: 42.2038 Evaluate side-chains 88 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 236 TRP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 148 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 115 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13067 Z= 0.168 Angle : 0.540 9.169 17726 Z= 0.266 Chirality : 0.040 0.155 2030 Planarity : 0.003 0.046 2276 Dihedral : 4.261 32.936 1805 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.38 % Allowed : 17.27 % Favored : 80.34 % 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: -0.49 (0.22), residues: 1645 helix: 1.53 (0.21), residues: 730 sheet: -2.11 (0.30), residues: 258 loop : -1.71 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 236 HIS 0.006 0.001 HIS C 194 PHE 0.012 0.001 PHE D 157 TYR 0.025 0.001 TYR B 86 ARG 0.008 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 70 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8942 (mtm) cc_final: 0.8411 (mpp) REVERT: A 125 MET cc_start: 0.8944 (mpp) cc_final: 0.7544 (mpp) REVERT: A 197 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8422 (p0) REVERT: A 334 LYS cc_start: 0.9154 (tttt) cc_final: 0.8855 (tttp) REVERT: B 183 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8607 (mm) REVERT: C 13 TYR cc_start: 0.8268 (p90) cc_final: 0.8000 (p90) REVERT: C 133 MET cc_start: 0.8561 (mtm) cc_final: 0.8183 (mtm) REVERT: C 295 MET cc_start: 0.9174 (mmm) cc_final: 0.8808 (mmm) REVERT: D 169 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8298 (p0) REVERT: D 219 ASP cc_start: 0.8857 (m-30) cc_final: 0.8480 (m-30) REVERT: E 187 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8962 (pp) REVERT: E 190 ASP cc_start: 0.9109 (OUTLIER) cc_final: 0.8574 (m-30) REVERT: H 50 MET cc_start: 0.8342 (pmm) cc_final: 0.7353 (pmm) REVERT: H 129 MET cc_start: 0.7861 (tpp) cc_final: 0.6992 (tpp) REVERT: H 140 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: H 141 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8147 (p0) REVERT: H 148 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8350 (tmm) outliers start: 32 outliers final: 21 residues processed: 98 average time/residue: 0.2798 time to fit residues: 39.6647 Evaluate side-chains 88 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 59 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 236 TRP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 GLU 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 E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 148 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13067 Z= 0.337 Angle : 0.650 9.380 17726 Z= 0.321 Chirality : 0.043 0.148 2030 Planarity : 0.004 0.044 2276 Dihedral : 4.610 38.833 1805 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.20 % Allowed : 16.75 % Favored : 80.04 % 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: -0.42 (0.22), residues: 1645 helix: 1.57 (0.21), residues: 716 sheet: -2.13 (0.30), residues: 256 loop : -1.56 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 211 HIS 0.009 0.001 HIS C 194 PHE 0.017 0.001 PHE D 157 TYR 0.023 0.002 TYR B 86 ARG 0.008 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 62 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8988 (mtm) cc_final: 0.8461 (mpp) REVERT: A 125 MET cc_start: 0.8956 (mpp) cc_final: 0.7627 (mpp) REVERT: A 197 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8652 (p0) REVERT: B 183 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8561 (mm) REVERT: C 13 TYR cc_start: 0.8394 (p90) cc_final: 0.8120 (p90) REVERT: C 42 LYS cc_start: 0.9340 (tttm) cc_final: 0.9092 (pttm) REVERT: C 133 MET cc_start: 0.8630 (mtm) cc_final: 0.8344 (mtm) REVERT: D 169 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8392 (p0) REVERT: D 219 ASP cc_start: 0.8905 (m-30) cc_final: 0.8478 (m-30) REVERT: E 138 MET cc_start: 0.7115 (ppp) cc_final: 0.6856 (ppp) REVERT: E 190 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8617 (m-30) REVERT: H 50 MET cc_start: 0.8491 (pmm) cc_final: 0.8261 (ptp) REVERT: H 129 MET cc_start: 0.8097 (tpp) cc_final: 0.7347 (tpp) REVERT: H 140 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8045 (mp10) REVERT: H 141 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8238 (p0) REVERT: H 148 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8330 (tmm) outliers start: 43 outliers final: 29 residues processed: 101 average time/residue: 0.2437 time to fit residues: 37.0432 Evaluate side-chains 93 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 57 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 148 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN C 25 ASN C 82 ASN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13067 Z= 0.191 Angle : 0.577 9.617 17726 Z= 0.282 Chirality : 0.041 0.184 2030 Planarity : 0.003 0.045 2276 Dihedral : 4.366 33.815 1805 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.83 % Allowed : 17.35 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1645 helix: 1.74 (0.21), residues: 720 sheet: -2.07 (0.30), residues: 257 loop : -1.52 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 236 HIS 0.007 0.001 HIS C 194 PHE 0.013 0.001 PHE D 157 TYR 0.023 0.001 TYR B 86 ARG 0.008 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 64 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8926 (mtm) cc_final: 0.8407 (mpp) REVERT: A 125 MET cc_start: 0.8996 (mpp) cc_final: 0.7678 (mpp) REVERT: A 197 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8528 (p0) REVERT: A 334 LYS cc_start: 0.9136 (tttt) cc_final: 0.8853 (tttp) REVERT: B 183 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8340 (mm) REVERT: C 133 MET cc_start: 0.8600 (mtm) cc_final: 0.8295 (mtm) REVERT: D 169 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8170 (p0) REVERT: D 219 ASP cc_start: 0.8857 (m-30) cc_final: 0.8505 (m-30) REVERT: E 190 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8642 (m-30) REVERT: H 129 MET cc_start: 0.7792 (tpp) cc_final: 0.6918 (tpp) REVERT: H 140 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: H 141 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8152 (p0) REVERT: H 148 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8274 (tmm) outliers start: 38 outliers final: 25 residues processed: 98 average time/residue: 0.2583 time to fit residues: 38.3173 Evaluate side-chains 93 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 61 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 148 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 162 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13067 Z= 0.178 Angle : 0.573 9.603 17726 Z= 0.279 Chirality : 0.041 0.170 2030 Planarity : 0.003 0.045 2276 Dihedral : 4.270 33.503 1805 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.76 % Allowed : 17.50 % Favored : 79.75 % 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: -0.13 (0.22), residues: 1645 helix: 1.83 (0.21), residues: 720 sheet: -1.80 (0.30), residues: 268 loop : -1.52 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 236 HIS 0.006 0.001 HIS C 194 PHE 0.013 0.001 PHE D 157 TYR 0.026 0.001 TYR B 86 ARG 0.008 0.000 ARG H 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 65 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8964 (mtm) cc_final: 0.8459 (mpp) REVERT: A 125 MET cc_start: 0.8992 (mpp) cc_final: 0.7678 (mpp) REVERT: A 197 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8527 (p0) REVERT: A 334 LYS cc_start: 0.9161 (tttt) cc_final: 0.8871 (tttp) REVERT: B 183 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8329 (mm) REVERT: C 133 MET cc_start: 0.8590 (mtm) cc_final: 0.8272 (mtm) REVERT: D 169 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8132 (p0) REVERT: D 219 ASP cc_start: 0.8842 (m-30) cc_final: 0.8487 (m-30) REVERT: E 190 ASP cc_start: 0.9116 (OUTLIER) cc_final: 0.8557 (m-30) REVERT: H 129 MET cc_start: 0.7701 (tpp) cc_final: 0.6866 (tpp) REVERT: H 140 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: H 141 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8130 (p0) outliers start: 37 outliers final: 24 residues processed: 98 average time/residue: 0.2622 time to fit residues: 37.9122 Evaluate side-chains 93 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 63 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 54 optimal weight: 0.0970 chunk 132 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.038095 restraints weight = 62116.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.039415 restraints weight = 32267.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.040299 restraints weight = 20972.769| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13067 Z= 0.243 Angle : 0.606 9.509 17726 Z= 0.296 Chirality : 0.042 0.165 2030 Planarity : 0.003 0.044 2276 Dihedral : 4.364 35.755 1805 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.31 % Allowed : 18.09 % Favored : 79.60 % 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: -0.12 (0.22), residues: 1645 helix: 1.79 (0.21), residues: 720 sheet: -1.79 (0.30), residues: 269 loop : -1.45 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 211 HIS 0.006 0.001 HIS C 194 PHE 0.014 0.001 PHE D 157 TYR 0.025 0.001 TYR B 86 ARG 0.010 0.000 ARG H 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2113.21 seconds wall clock time: 39 minutes 52.13 seconds (2392.13 seconds total)