Starting phenix.real_space_refine on Wed Feb 14 21:05:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btw_30189/02_2024/7btw_30189.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btw_30189/02_2024/7btw_30189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btw_30189/02_2024/7btw_30189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btw_30189/02_2024/7btw_30189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btw_30189/02_2024/7btw_30189.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btw_30189/02_2024/7btw_30189.pdb" } resolution = 2.9 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= 0.020 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 6552 2.51 5 N 1747 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ASP 326": "OD1" <-> "OD2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ASP 377": "OD1" <-> "OD2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "C ASP 12": "OD1" <-> "OD2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 240": "NH1" <-> "NH2" Residue "C ASP 244": "OD1" <-> "OD2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D GLU 161": "OE1" <-> "OE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "D ARG 211": "NH1" <-> "NH2" Residue "D ARG 215": "NH1" <-> "NH2" Residue "D PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D ASP 272": "OD1" <-> "OD2" Residue "D ASP 285": "OD1" <-> "OD2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D ASP 326": "OD1" <-> "OD2" Residue "D ASP 327": "OD1" <-> "OD2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 364": "OD1" <-> "OD2" Residue "D ARG 366": "NH1" <-> "NH2" Residue "D ASP 377": "OD1" <-> "OD2" Residue "D TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10246 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2775 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2410 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain breaks: 2 Chain: "C" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2286 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 6, 'TRANS': 277} Chain breaks: 2 Chain: "D" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2775 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.69, per 1000 atoms: 0.56 Number of scatterers: 10246 At special positions: 0 Unit cell: (104.58, 103.335, 103.335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1902 8.00 N 1747 7.00 C 6552 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: 3.95 Conformation dependent library (CDL) restraints added in 1.8 seconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 31.3% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 263 through 270 removed outlier: 3.639A pdb=" N SER A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.537A pdb=" N GLN A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 37 removed outlier: 3.580A pdb=" N GLU B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 157 through 181 removed outlier: 3.716A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 193 removed outlier: 3.537A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.658A pdb=" N GLN B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.615A pdb=" N LEU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 234 through 243 removed outlier: 3.794A pdb=" N GLY B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 273 removed outlier: 3.632A pdb=" N SER B 251 " --> pdb=" O ASN B 247 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 252 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 297 removed outlier: 3.588A pdb=" N TYR B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 312 Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 324 through 327 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.611A pdb=" N SER C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.729A pdb=" N LEU C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 121 through 132 removed outlier: 3.914A pdb=" N LEU C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.545A pdb=" N TYR C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.506A pdb=" N LEU C 149 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 154 removed outlier: 3.787A pdb=" N TRP C 154 " --> pdb=" O PHE C 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 155 through 169 removed outlier: 3.630A pdb=" N GLN C 160 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 161 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 244 removed outlier: 3.584A pdb=" N GLU C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 263 removed outlier: 3.599A pdb=" N LEU C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 296 removed outlier: 4.039A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N SER C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N GLU C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 291 " --> pdb=" O MET C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 removed outlier: 4.439A pdb=" N ASN C 321 " --> pdb=" O MET C 317 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 270 removed outlier: 3.639A pdb=" N SER D 268 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 270 " --> pdb=" O MET D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 434 removed outlier: 3.536A pdb=" N GLN D 433 " --> pdb=" O ASN D 429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.692A pdb=" N GLY A 128 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER A 171 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 168 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN A 196 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 416 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR A 440 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 442 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.692A pdb=" N GLY A 128 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER A 171 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 168 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN A 196 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 416 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR A 440 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 442 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 21 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.733A pdb=" N ILE B 130 " --> pdb=" O GLY B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA5, first strand: chain 'C' and resid 44 through 47 removed outlier: 7.038A pdb=" N GLY C 4 " --> pdb=" O GLN C 45 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL C 47 " --> pdb=" O GLY C 4 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL C 6 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 126 through 127 removed outlier: 4.069A pdb=" N SER D 171 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE D 168 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN D 196 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 416 " --> pdb=" O TYR D 390 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR D 440 " --> pdb=" O ILE D 463 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 442 " --> pdb=" O LEU D 461 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1863 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: 3.37 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 9 1.18 - 1.34: 3201 1.34 - 1.50: 2926 1.50 - 1.65: 4261 1.65 - 1.81: 67 Bond restraints: 10464 Sorted by residual: bond pdb=" C ARG D 164 " pdb=" O ARG D 164 " ideal model delta sigma weight residual 1.234 1.023 0.211 1.28e-02 6.10e+03 2.72e+02 bond pdb=" CA ASN A 135 " pdb=" C ASN A 135 " ideal model delta sigma weight residual 1.522 1.309 0.212 1.33e-02 5.65e+03 2.55e+02 bond pdb=" C ARG A 164 " pdb=" O ARG A 164 " ideal model delta sigma weight residual 1.234 1.106 0.128 1.11e-02 8.12e+03 1.33e+02 bond pdb=" C ASN A 135 " pdb=" O ASN A 135 " ideal model delta sigma weight residual 1.238 1.032 0.206 1.83e-02 2.99e+03 1.27e+02 bond pdb=" C ASN A 133 " pdb=" O ASN A 133 " ideal model delta sigma weight residual 1.236 1.148 0.089 1.16e-02 7.43e+03 5.88e+01 ... (remaining 10459 not shown) Histogram of bond angle deviations from ideal: 95.85 - 103.96: 105 103.96 - 112.06: 4942 112.06 - 120.16: 4590 120.16 - 128.26: 4401 128.26 - 136.37: 92 Bond angle restraints: 14130 Sorted by residual: angle pdb=" N ASN A 135 " pdb=" CA ASN A 135 " pdb=" C ASN A 135 " ideal model delta sigma weight residual 113.56 95.85 17.71 1.39e+00 5.18e-01 1.62e+02 angle pdb=" O LEU D 163 " pdb=" C LEU D 163 " pdb=" N ARG D 164 " ideal model delta sigma weight residual 123.29 110.02 13.27 1.18e+00 7.18e-01 1.27e+02 angle pdb=" CA LEU D 163 " pdb=" C LEU D 163 " pdb=" N ARG D 164 " ideal model delta sigma weight residual 116.28 127.17 -10.89 1.26e+00 6.30e-01 7.47e+01 angle pdb=" C ALA D 139 " pdb=" N TYR D 140 " pdb=" CA TYR D 140 " ideal model delta sigma weight residual 122.81 108.60 14.21 1.68e+00 3.54e-01 7.15e+01 angle pdb=" C ARG D 164 " pdb=" N GLY D 165 " pdb=" CA GLY D 165 " ideal model delta sigma weight residual 120.84 136.37 -15.53 1.91e+00 2.74e-01 6.61e+01 ... (remaining 14125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 5301 17.14 - 34.29: 638 34.29 - 51.43: 200 51.43 - 68.57: 81 68.57 - 85.72: 14 Dihedral angle restraints: 6234 sinusoidal: 2526 harmonic: 3708 Sorted by residual: dihedral pdb=" CA LEU C 60 " pdb=" C LEU C 60 " pdb=" N PRO C 61 " pdb=" CA PRO C 61 " ideal model delta harmonic sigma weight residual 180.00 129.36 50.64 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" N ASN A 133 " pdb=" C ASN A 133 " pdb=" CA ASN A 133 " pdb=" CB ASN A 133 " ideal model delta harmonic sigma weight residual 122.80 142.10 -19.30 0 2.50e+00 1.60e-01 5.96e+01 dihedral pdb=" CA THR D 199 " pdb=" C THR D 199 " pdb=" N ASN D 200 " pdb=" CA ASN D 200 " ideal model delta harmonic sigma weight residual 180.00 142.03 37.97 0 5.00e+00 4.00e-02 5.77e+01 ... (remaining 6231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 1542 0.149 - 0.298: 27 0.298 - 0.447: 3 0.447 - 0.596: 0 0.596 - 0.745: 2 Chirality restraints: 1574 Sorted by residual: chirality pdb=" CA THR C 87 " pdb=" N THR C 87 " pdb=" C THR C 87 " pdb=" CB THR C 87 " both_signs ideal model delta sigma weight residual False 2.53 1.78 0.74 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CA ASN A 133 " pdb=" N ASN A 133 " pdb=" C ASN A 133 " pdb=" CB ASN A 133 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA LEU B 128 " pdb=" N LEU B 128 " pdb=" C LEU B 128 " pdb=" CB LEU B 128 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 1571 not shown) Planarity restraints: 1790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 135 " 0.029 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C ASN A 135 " -0.095 2.00e-02 2.50e+03 pdb=" O ASN A 135 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP A 136 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 163 " 0.026 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" C LEU D 163 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU D 163 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG D 164 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 60 " -0.074 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO C 61 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.059 5.00e-02 4.00e+02 ... (remaining 1787 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.22: 1 2.22 - 2.89: 3711 2.89 - 3.56: 13062 3.56 - 4.23: 24478 4.23 - 4.90: 42307 Nonbonded interactions: 83559 Sorted by model distance: nonbonded pdb=" O THR D 129 " pdb=" O ALA D 137 " model vdw 1.556 3.040 nonbonded pdb=" ND2 ASN D 130 " pdb=" O GLU D 138 " model vdw 2.231 2.520 nonbonded pdb=" N ASN A 135 " pdb=" N ASP A 136 " model vdw 2.232 2.560 nonbonded pdb=" OG SER B 184 " pdb=" OE2 GLU B 301 " model vdw 2.278 2.440 nonbonded pdb=" OG SER A 344 " pdb=" O SER A 348 " model vdw 2.279 2.440 ... (remaining 83554 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 'A' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.800 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.300 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.212 10464 Z= 0.531 Angle : 1.122 17.707 14130 Z= 0.625 Chirality : 0.063 0.745 1574 Planarity : 0.008 0.111 1790 Dihedral : 18.114 85.718 3840 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.02 % Favored : 91.59 % Rotamer: Outliers : 9.60 % Allowed : 7.59 % Favored : 82.81 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.49 % 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: -5.22 (0.18), residues: 1260 helix: -4.29 (0.11), residues: 360 sheet: -2.41 (0.24), residues: 384 loop : -3.49 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 301 HIS 0.008 0.002 HIS A 310 PHE 0.064 0.003 PHE A 331 TYR 0.024 0.003 TYR C 137 ARG 0.005 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 186 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.4619 (OUTLIER) cc_final: 0.4411 (mmmt) REVERT: A 170 SER cc_start: 0.8131 (p) cc_final: 0.7906 (t) REVERT: A 291 MET cc_start: 0.5037 (ttp) cc_final: 0.3673 (tmm) REVERT: A 405 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.5806 (pptt) REVERT: A 409 ARG cc_start: 0.7815 (mmt90) cc_final: 0.7512 (mmm-85) REVERT: A 457 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7122 (tm) REVERT: B 151 ARG cc_start: 0.8090 (ttm110) cc_final: 0.7890 (ttp-170) REVERT: B 162 MET cc_start: 0.8046 (mmp) cc_final: 0.7174 (mmp) REVERT: B 168 ASP cc_start: 0.8259 (m-30) cc_final: 0.8052 (m-30) REVERT: B 185 ASP cc_start: 0.7820 (m-30) cc_final: 0.7488 (m-30) REVERT: B 189 MET cc_start: 0.8433 (mmm) cc_final: 0.8106 (mmm) REVERT: C 21 ASP cc_start: 0.7056 (m-30) cc_final: 0.6768 (m-30) REVERT: D 154 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5312 (pp) REVERT: D 164 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5487 (mtm-85) REVERT: D 193 GLN cc_start: 0.7427 (pt0) cc_final: 0.7226 (pt0) REVERT: D 442 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7788 (t) outliers start: 110 outliers final: 13 residues processed: 276 average time/residue: 1.1196 time to fit residues: 333.0358 Evaluate side-chains 138 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 254 GLN Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 442 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.0060 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 422 HIS A 458 ASN A 476 GLN B 72 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN C 7 HIS C 82 HIS C 138 ASN C 222 ASN C 269 ASN D 175 ASN D 200 ASN D 254 GLN D 280 HIS D 303 ASN D 346 GLN D 422 HIS D 429 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10464 Z= 0.246 Angle : 0.703 9.767 14130 Z= 0.377 Chirality : 0.045 0.244 1574 Planarity : 0.006 0.089 1790 Dihedral : 8.417 59.389 1405 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.62 % Favored : 92.22 % Rotamer: Outliers : 4.36 % Allowed : 17.28 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.32 % 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: -3.65 (0.20), residues: 1260 helix: -1.77 (0.22), residues: 369 sheet: -1.79 (0.25), residues: 358 loop : -3.30 (0.21), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 323 HIS 0.006 0.001 HIS B 234 PHE 0.019 0.002 PHE B 18 TYR 0.018 0.002 TYR C 137 ARG 0.006 0.001 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 130 time to evaluate : 1.052 Fit side-chains REVERT: A 291 MET cc_start: 0.5469 (ttp) cc_final: 0.4384 (tmt) REVERT: A 452 MET cc_start: 0.5922 (OUTLIER) cc_final: 0.5708 (mmm) REVERT: B 151 ARG cc_start: 0.8172 (ttm110) cc_final: 0.7928 (ttp-110) REVERT: C 14 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: C 21 ASP cc_start: 0.7131 (m-30) cc_final: 0.6920 (m-30) REVERT: D 136 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7320 (m-30) REVERT: D 442 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7972 (t) outliers start: 50 outliers final: 20 residues processed: 165 average time/residue: 1.1013 time to fit residues: 197.5258 Evaluate side-chains 117 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 442 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN B 72 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 253 ASN C 84 ASN C 129 GLN D 346 GLN ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 10464 Z= 0.423 Angle : 0.768 10.719 14130 Z= 0.409 Chirality : 0.049 0.282 1574 Planarity : 0.006 0.097 1790 Dihedral : 7.350 58.336 1375 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.25 % Favored : 91.59 % Rotamer: Outliers : 5.67 % Allowed : 18.67 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.24 % 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: -3.01 (0.21), residues: 1260 helix: -0.75 (0.25), residues: 372 sheet: -1.48 (0.25), residues: 356 loop : -3.29 (0.22), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 323 HIS 0.007 0.002 HIS B 234 PHE 0.021 0.003 PHE D 331 TYR 0.022 0.002 TYR C 137 ARG 0.004 0.001 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 119 time to evaluate : 1.147 Fit side-chains REVERT: A 198 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7312 (m-40) REVERT: A 437 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6480 (mt-10) REVERT: B 73 THR cc_start: 0.8551 (t) cc_final: 0.8286 (p) REVERT: B 263 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7073 (mm-30) REVERT: B 312 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6892 (mt-10) REVERT: C 14 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6165 (mp0) REVERT: D 454 ARG cc_start: 0.7981 (ttt180) cc_final: 0.7751 (ttp-170) REVERT: D 456 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6748 (mt-10) outliers start: 65 outliers final: 33 residues processed: 172 average time/residue: 1.1522 time to fit residues: 214.6702 Evaluate side-chains 133 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 96 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS A 347 GLN A 476 GLN B 72 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN D 346 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10464 Z= 0.262 Angle : 0.656 9.633 14130 Z= 0.352 Chirality : 0.044 0.227 1574 Planarity : 0.006 0.090 1790 Dihedral : 6.840 55.817 1374 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.94 % Favored : 91.98 % Rotamer: Outliers : 4.89 % Allowed : 21.29 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.16 % 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: -2.49 (0.22), residues: 1260 helix: 0.01 (0.27), residues: 376 sheet: -1.24 (0.26), residues: 338 loop : -3.17 (0.21), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 323 HIS 0.006 0.001 HIS D 352 PHE 0.018 0.002 PHE D 331 TYR 0.018 0.002 TYR C 137 ARG 0.004 0.001 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 115 time to evaluate : 1.425 Fit side-chains revert: symmetry clash REVERT: A 198 ASN cc_start: 0.7614 (OUTLIER) cc_final: 0.7254 (m-40) REVERT: A 295 LYS cc_start: 0.7985 (tptt) cc_final: 0.7587 (ttpt) REVERT: A 321 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8230 (ttpt) REVERT: C 14 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6203 (mp0) REVERT: D 146 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6687 (tt) REVERT: D 215 ARG cc_start: 0.7383 (ttt180) cc_final: 0.7182 (ttm-80) REVERT: D 261 MET cc_start: 0.1948 (mtt) cc_final: 0.1317 (mtp) REVERT: D 321 LYS cc_start: 0.6962 (mtpt) cc_final: 0.6564 (mmtt) outliers start: 56 outliers final: 25 residues processed: 158 average time/residue: 1.0326 time to fit residues: 177.9662 Evaluate side-chains 131 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 0.0670 chunk 50 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 109 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 overall best weight: 1.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN D 346 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10464 Z= 0.303 Angle : 0.676 9.879 14130 Z= 0.360 Chirality : 0.045 0.243 1574 Planarity : 0.006 0.093 1790 Dihedral : 6.622 55.953 1370 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.73 % Favored : 91.11 % Rotamer: Outliers : 6.11 % Allowed : 21.03 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.16 % 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: -2.25 (0.22), residues: 1260 helix: 0.32 (0.27), residues: 373 sheet: -1.27 (0.26), residues: 358 loop : -3.02 (0.23), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 301 HIS 0.006 0.001 HIS B 234 PHE 0.017 0.002 PHE D 331 TYR 0.017 0.002 TYR C 137 ARG 0.003 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 103 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 295 LYS cc_start: 0.7950 (tptt) cc_final: 0.7607 (ttpt) REVERT: A 321 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8324 (ttpt) REVERT: B 312 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: C 14 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6215 (mp0) REVERT: D 250 LYS cc_start: 0.6372 (OUTLIER) cc_final: 0.5914 (mptt) REVERT: D 261 MET cc_start: 0.1969 (mtt) cc_final: 0.1490 (mtp) outliers start: 70 outliers final: 38 residues processed: 157 average time/residue: 1.1095 time to fit residues: 188.7914 Evaluate side-chains 145 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 103 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 431 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 0.0770 chunk 117 optimal weight: 0.7980 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10464 Z= 0.317 Angle : 0.683 9.839 14130 Z= 0.362 Chirality : 0.045 0.246 1574 Planarity : 0.006 0.092 1790 Dihedral : 6.603 56.675 1370 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.49 % Favored : 91.35 % Rotamer: Outliers : 6.11 % Allowed : 21.64 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.22), residues: 1260 helix: 0.38 (0.27), residues: 377 sheet: -1.19 (0.26), residues: 346 loop : -2.95 (0.23), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 197 HIS 0.006 0.001 HIS A 310 PHE 0.015 0.002 PHE A 237 TYR 0.019 0.002 TYR C 137 ARG 0.004 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 103 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 295 LYS cc_start: 0.7956 (tptt) cc_final: 0.7631 (ttpt) REVERT: A 321 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8357 (ttpt) REVERT: A 325 ASN cc_start: 0.6274 (OUTLIER) cc_final: 0.6041 (m-40) REVERT: A 376 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.6480 (mpt-90) REVERT: B 312 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: C 14 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6221 (mp0) REVERT: D 193 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6212 (pm20) REVERT: D 250 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6299 (mptt) REVERT: D 261 MET cc_start: 0.2254 (mtt) cc_final: 0.1476 (mtp) REVERT: D 459 PHE cc_start: 0.7952 (t80) cc_final: 0.7501 (t80) outliers start: 70 outliers final: 39 residues processed: 159 average time/residue: 1.2200 time to fit residues: 209.2433 Evaluate side-chains 155 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 109 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN C 300 ASN D 130 ASN D 346 GLN D 450 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10464 Z= 0.198 Angle : 0.611 10.270 14130 Z= 0.326 Chirality : 0.043 0.210 1574 Planarity : 0.005 0.085 1790 Dihedral : 6.220 54.451 1370 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.94 % Favored : 91.98 % Rotamer: Outliers : 4.71 % Allowed : 23.30 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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: -1.82 (0.23), residues: 1260 helix: 0.80 (0.28), residues: 378 sheet: -1.08 (0.26), residues: 342 loop : -2.82 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 197 HIS 0.004 0.001 HIS B 234 PHE 0.018 0.001 PHE A 237 TYR 0.017 0.001 TYR C 137 ARG 0.005 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 114 time to evaluate : 1.132 Fit side-chains REVERT: A 295 LYS cc_start: 0.7815 (tptt) cc_final: 0.7456 (ttpt) REVERT: A 437 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6451 (mt-10) REVERT: B 173 ASP cc_start: 0.8394 (m-30) cc_final: 0.8001 (m-30) REVERT: B 326 ASN cc_start: 0.7554 (m110) cc_final: 0.7187 (m110) REVERT: C 14 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6268 (mp0) REVERT: C 111 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6547 (tm-30) REVERT: D 193 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6096 (pm20) REVERT: D 250 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.6099 (mptt) REVERT: D 261 MET cc_start: 0.1640 (mtt) cc_final: 0.1016 (mtp) REVERT: D 321 LYS cc_start: 0.6969 (mtpt) cc_final: 0.6612 (tptt) REVERT: D 459 PHE cc_start: 0.7882 (t80) cc_final: 0.7426 (t80) outliers start: 54 outliers final: 24 residues processed: 155 average time/residue: 1.1065 time to fit residues: 186.2730 Evaluate side-chains 135 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN B 178 GLN B 264 ASN D 130 ASN D 346 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 10464 Z= 0.622 Angle : 0.873 11.268 14130 Z= 0.458 Chirality : 0.054 0.322 1574 Planarity : 0.007 0.100 1790 Dihedral : 7.213 58.867 1370 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.37 % Favored : 90.40 % Rotamer: Outliers : 6.02 % Allowed : 22.60 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.32 % 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: -2.36 (0.22), residues: 1260 helix: 0.01 (0.26), residues: 375 sheet: -1.16 (0.25), residues: 359 loop : -3.06 (0.23), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 412 HIS 0.013 0.002 HIS D 466 PHE 0.024 0.003 PHE A 194 TYR 0.022 0.003 TYR C 137 ARG 0.005 0.001 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 120 time to evaluate : 1.372 Fit side-chains REVERT: A 273 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: A 295 LYS cc_start: 0.8059 (tptt) cc_final: 0.7704 (ttpt) REVERT: A 321 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8200 (ttpt) REVERT: A 376 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.6491 (mpt-90) REVERT: A 437 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: B 173 ASP cc_start: 0.8518 (m-30) cc_final: 0.8082 (m-30) REVERT: B 229 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7804 (mtmt) REVERT: C 14 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6234 (mp0) REVERT: C 111 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6860 (tm-30) REVERT: D 193 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6468 (pm20) REVERT: D 250 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6332 (mptt) REVERT: D 449 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7039 (mtt-85) outliers start: 69 outliers final: 40 residues processed: 176 average time/residue: 1.0939 time to fit residues: 209.0521 Evaluate side-chains 162 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 113 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 449 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 68 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN A 303 ASN ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN B 178 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10464 Z= 0.228 Angle : 0.653 9.884 14130 Z= 0.345 Chirality : 0.044 0.225 1574 Planarity : 0.005 0.086 1790 Dihedral : 6.537 56.420 1370 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.62 % Favored : 92.30 % Rotamer: Outliers : 3.84 % Allowed : 25.74 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.16 % 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: -1.91 (0.22), residues: 1260 helix: 0.71 (0.27), residues: 374 sheet: -1.16 (0.25), residues: 351 loop : -2.84 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 301 HIS 0.005 0.001 HIS D 466 PHE 0.019 0.002 PHE A 237 TYR 0.020 0.002 TYR C 137 ARG 0.005 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 110 time to evaluate : 1.238 Fit side-chains REVERT: A 295 LYS cc_start: 0.7907 (tptt) cc_final: 0.7512 (ttpt) REVERT: A 321 LYS cc_start: 0.8426 (ttpt) cc_final: 0.8002 (ttpt) REVERT: A 437 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6824 (mt-10) REVERT: B 173 ASP cc_start: 0.8369 (m-30) cc_final: 0.7943 (m-30) REVERT: C 14 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6339 (mp0) REVERT: C 21 ASP cc_start: 0.7168 (m-30) cc_final: 0.6649 (m-30) REVERT: D 154 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6322 (pp) REVERT: D 163 LEU cc_start: 0.8262 (tp) cc_final: 0.7927 (tp) REVERT: D 193 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6213 (pm20) REVERT: D 250 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.6163 (mptt) REVERT: D 452 MET cc_start: 0.7474 (pmt) cc_final: 0.7259 (ptt) REVERT: D 459 PHE cc_start: 0.7835 (t80) cc_final: 0.7432 (t80) REVERT: D 466 HIS cc_start: 0.4825 (OUTLIER) cc_final: 0.4383 (t-90) outliers start: 44 outliers final: 30 residues processed: 148 average time/residue: 1.1035 time to fit residues: 177.2301 Evaluate side-chains 142 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 106 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 466 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 61 optimal weight: 0.0010 chunk 79 optimal weight: 0.3980 chunk 106 optimal weight: 7.9990 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10464 Z= 0.240 Angle : 0.659 9.524 14130 Z= 0.348 Chirality : 0.044 0.219 1574 Planarity : 0.005 0.091 1790 Dihedral : 6.352 54.476 1370 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.94 % Favored : 91.90 % Rotamer: Outliers : 3.32 % Allowed : 26.00 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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: -1.72 (0.23), residues: 1260 helix: 0.92 (0.28), residues: 372 sheet: -1.05 (0.25), residues: 346 loop : -2.74 (0.23), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 301 HIS 0.005 0.001 HIS B 234 PHE 0.017 0.002 PHE A 237 TYR 0.019 0.002 TYR C 137 ARG 0.009 0.000 ARG A 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 108 time to evaluate : 1.152 Fit side-chains REVERT: A 291 MET cc_start: 0.4839 (mtp) cc_final: 0.4516 (mmm) REVERT: A 295 LYS cc_start: 0.7919 (tptt) cc_final: 0.7511 (ttpt) REVERT: A 321 LYS cc_start: 0.8264 (ttpt) cc_final: 0.7877 (ttpt) REVERT: A 437 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: B 173 ASP cc_start: 0.8376 (m-30) cc_final: 0.7948 (m-30) REVERT: C 14 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6310 (mp0) REVERT: D 154 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6436 (pp) REVERT: D 193 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6204 (pm20) REVERT: D 250 LYS cc_start: 0.6796 (OUTLIER) cc_final: 0.6268 (mptt) REVERT: D 266 MET cc_start: 0.7101 (mtt) cc_final: 0.6757 (mtt) REVERT: D 402 LYS cc_start: 0.7769 (mmtt) cc_final: 0.7023 (tmtt) REVERT: D 452 MET cc_start: 0.7390 (pmt) cc_final: 0.7144 (ptt) REVERT: D 459 PHE cc_start: 0.7861 (t80) cc_final: 0.7431 (t80) REVERT: D 466 HIS cc_start: 0.4904 (OUTLIER) cc_final: 0.4488 (t-90) outliers start: 38 outliers final: 30 residues processed: 141 average time/residue: 1.1260 time to fit residues: 172.6632 Evaluate side-chains 142 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 106 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 466 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 12 optimal weight: 0.0070 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.173408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141178 restraints weight = 10403.112| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.01 r_work: 0.3410 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10464 Z= 0.250 Angle : 0.660 9.242 14130 Z= 0.348 Chirality : 0.044 0.226 1574 Planarity : 0.005 0.088 1790 Dihedral : 6.295 52.498 1370 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.86 % Favored : 92.06 % Rotamer: Outliers : 3.84 % Allowed : 25.65 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.23), residues: 1260 helix: 1.01 (0.28), residues: 372 sheet: -1.05 (0.25), residues: 346 loop : -2.71 (0.23), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 301 HIS 0.006 0.001 HIS D 466 PHE 0.017 0.002 PHE A 237 TYR 0.018 0.002 TYR C 137 ARG 0.007 0.000 ARG A 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3783.13 seconds wall clock time: 68 minutes 16.07 seconds (4096.07 seconds total)