Starting phenix.real_space_refine on Fri Feb 16 02:32:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bnz_16137/02_2024/8bnz_16137.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bnz_16137/02_2024/8bnz_16137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bnz_16137/02_2024/8bnz_16137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bnz_16137/02_2024/8bnz_16137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bnz_16137/02_2024/8bnz_16137.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bnz_16137/02_2024/8bnz_16137.pdb" } resolution = 3.5 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= 0.031 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 41 5.16 5 C 8855 2.51 5 N 2409 2.21 5 O 2768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "P TYR 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 1072": "OE1" <-> "OE2" Residue "P TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 1150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 1154": "OE1" <-> "OE2" Residue "P PHE 1300": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14073 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6209 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 29, 'TRANS': 755} Chain: "B" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2750 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 355} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 414 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 6, 'TRANS': 50} Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "P" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2333 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Time building chain proxies: 7.73, per 1000 atoms: 0.55 Number of scatterers: 14073 At special positions: 0 Unit cell: (127.41, 131.13, 139.5, 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 41 16.00 O 2768 8.00 N 2409 7.00 C 8855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS P1293 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 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: 5.77 Conformation dependent library (CDL) restraints added in 2.4 seconds 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3286 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 19 sheets defined 21.1% alpha, 47.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.641A pdb=" N LEU A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 4.371A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'A' and resid 128 through 144 removed outlier: 3.618A pdb=" N ASP A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.873A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 233 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.624A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.715A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.880A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 452 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.626A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 731 removed outlier: 4.102A pdb=" N ASN A 731 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.955A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 58 " --> pdb=" O GLN D 54 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 120 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.739A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 228 through 241 Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'P' and resid 1000 through 1036 removed outlier: 4.289A pdb=" N ASP P1014 " --> pdb=" O LEU P1010 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR P1015 " --> pdb=" O PHE P1011 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS P1027 " --> pdb=" O ASN P1023 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG P1028 " --> pdb=" O ASN P1024 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET P1029 " --> pdb=" O LEU P1025 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 98 removed outlier: 5.736A pdb=" N VAL A 163 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 96 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 167 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 4.573A pdb=" N ILE A 177 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 256 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN A 179 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL A 258 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN A 181 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE A 260 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL A 183 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 4.236A pdb=" N LEU A 268 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N LEU A 337 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY A 270 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL A 339 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA A 343 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN A 276 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 4.255A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355 removed outlier: 4.255A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 802 through 806 removed outlier: 6.438A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL P1292 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL P1272 " --> pdb=" O ILE P1268 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU P1227 " --> pdb=" O VAL P1208 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU P1202 " --> pdb=" O LEU P1233 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA P1165 " --> pdb=" O VAL P1161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 802 through 806 removed outlier: 6.438A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL P1292 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL P1272 " --> pdb=" O ILE P1268 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU P1227 " --> pdb=" O VAL P1208 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU P1202 " --> pdb=" O LEU P1233 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA P1117 " --> pdb=" O PHE P1113 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER P1097 " --> pdb=" O THR P1133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.152A pdb=" N ALA A 672 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.154A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER B 389 " --> pdb=" O TRP B 48 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.548A pdb=" N TRP B 143 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.501A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.693A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.543A pdb=" N ARG B 295 " --> pdb=" O ASP B 292 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 308 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333 removed outlier: 5.473A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.985A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.697A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 1181 through 1184 removed outlier: 4.688A pdb=" N LYS P1181 " --> pdb=" O ASP P1196 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP P1196 " --> pdb=" O LYS P1181 " (cutoff:3.500A) 905 hydrogen bonds defined for protein. 2553 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: 6.38 Time building geometry restraints manager: 6.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 2115 1.25 - 1.40: 3237 1.40 - 1.54: 7250 1.54 - 1.69: 1696 1.69 - 1.83: 80 Bond restraints: 14378 Sorted by residual: bond pdb=" CA VAL A 173 " pdb=" CB VAL A 173 " ideal model delta sigma weight residual 1.548 1.399 0.150 1.49e-02 4.50e+03 1.01e+02 bond pdb=" CA GLU B 26 " pdb=" CB GLU B 26 " ideal model delta sigma weight residual 1.530 1.706 -0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" CA LYS A 103 " pdb=" C LYS A 103 " ideal model delta sigma weight residual 1.524 1.395 0.129 1.57e-02 4.06e+03 6.79e+01 bond pdb=" C LYS A 103 " pdb=" O LYS A 103 " ideal model delta sigma weight residual 1.235 1.110 0.125 1.62e-02 3.81e+03 5.97e+01 bond pdb=" CB LYS A 103 " pdb=" CG LYS A 103 " ideal model delta sigma weight residual 1.520 1.750 -0.230 3.00e-02 1.11e+03 5.88e+01 ... (remaining 14373 not shown) Histogram of bond angle deviations from ideal: 90.57 - 100.98: 40 100.98 - 111.40: 4939 111.40 - 121.81: 11946 121.81 - 132.23: 2556 132.23 - 142.64: 35 Bond angle restraints: 19516 Sorted by residual: angle pdb=" O GLU B 27 " pdb=" C GLU B 27 " pdb=" N ASP B 28 " ideal model delta sigma weight residual 123.27 103.23 20.04 1.22e+00 6.72e-01 2.70e+02 angle pdb=" CB LYS A 103 " pdb=" CG LYS A 103 " pdb=" CD LYS A 103 " ideal model delta sigma weight residual 111.30 142.64 -31.34 2.30e+00 1.89e-01 1.86e+02 angle pdb=" CA LYS A 103 " pdb=" C LYS A 103 " pdb=" O LYS A 103 " ideal model delta sigma weight residual 120.32 105.83 14.49 1.18e+00 7.18e-01 1.51e+02 angle pdb=" C GLU B 26 " pdb=" CA GLU B 26 " pdb=" CB GLU B 26 " ideal model delta sigma weight residual 110.10 132.96 -22.86 1.90e+00 2.77e-01 1.45e+02 angle pdb=" C GLU B 26 " pdb=" N GLU B 27 " pdb=" CA GLU B 27 " ideal model delta sigma weight residual 122.73 142.21 -19.48 1.62e+00 3.81e-01 1.45e+02 ... (remaining 19511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7813 17.87 - 35.74: 498 35.74 - 53.60: 79 53.60 - 71.47: 49 71.47 - 89.34: 30 Dihedral angle restraints: 8469 sinusoidal: 3290 harmonic: 5179 Sorted by residual: dihedral pdb=" C SER A 104 " pdb=" N SER A 104 " pdb=" CA SER A 104 " pdb=" CB SER A 104 " ideal model delta harmonic sigma weight residual -122.60 -159.60 37.00 0 2.50e+00 1.60e-01 2.19e+02 dihedral pdb=" N SER A 104 " pdb=" C SER A 104 " pdb=" CA SER A 104 " pdb=" CB SER A 104 " ideal model delta harmonic sigma weight residual 122.80 158.82 -36.02 0 2.50e+00 1.60e-01 2.08e+02 dihedral pdb=" N GLU B 26 " pdb=" C GLU B 26 " pdb=" CA GLU B 26 " pdb=" CB GLU B 26 " ideal model delta harmonic sigma weight residual 122.80 104.54 18.26 0 2.50e+00 1.60e-01 5.33e+01 ... (remaining 8466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.303: 2070 0.303 - 0.606: 41 0.606 - 0.908: 0 0.908 - 1.211: 0 1.211 - 1.514: 1 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CA SER A 104 " pdb=" N SER A 104 " pdb=" C SER A 104 " pdb=" CB SER A 104 " both_signs ideal model delta sigma weight residual False 2.51 1.00 1.51 2.00e-01 2.50e+01 5.73e+01 chirality pdb=" CB VAL A 173 " pdb=" CA VAL A 173 " pdb=" CG1 VAL A 173 " pdb=" CG2 VAL A 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.03 -0.60 2.00e-01 2.50e+01 8.97e+00 chirality pdb=" CA THR B 239 " pdb=" N THR B 239 " pdb=" C THR B 239 " pdb=" CB THR B 239 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.54 2.00e-01 2.50e+01 7.17e+00 ... (remaining 2109 not shown) Planarity restraints: 2571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 184 " 0.167 2.00e-02 2.50e+03 9.35e-02 1.75e+02 pdb=" CG TYR D 184 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR D 184 " -0.071 2.00e-02 2.50e+03 pdb=" CD2 TYR D 184 " -0.069 2.00e-02 2.50e+03 pdb=" CE1 TYR D 184 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR D 184 " -0.055 2.00e-02 2.50e+03 pdb=" CZ TYR D 184 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR D 184 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 229 " -0.078 2.00e-02 2.50e+03 8.10e-02 1.31e+02 pdb=" CG TYR A 229 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 229 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 229 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 229 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TYR A 229 " 0.079 2.00e-02 2.50e+03 pdb=" CZ TYR A 229 " 0.071 2.00e-02 2.50e+03 pdb=" OH TYR A 229 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 93 " 0.035 2.00e-02 2.50e+03 6.06e-02 9.19e+01 pdb=" CG TRP B 93 " -0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP B 93 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 93 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP B 93 " 0.103 2.00e-02 2.50e+03 pdb=" CE2 TRP B 93 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP B 93 " 0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 93 " -0.066 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 93 " 0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP B 93 " -0.027 2.00e-02 2.50e+03 ... (remaining 2568 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 774 2.72 - 3.27: 12872 3.27 - 3.81: 22518 3.81 - 4.36: 29491 4.36 - 4.90: 49812 Nonbonded interactions: 115467 Sorted by model distance: nonbonded pdb=" O LYS A 103 " pdb=" CB LYS A 103 " model vdw 2.180 2.752 nonbonded pdb=" O GLU B 27 " pdb=" CA ASP B 28 " model vdw 2.292 2.776 nonbonded pdb=" O LYS A 103 " pdb=" CA GLU B 26 " model vdw 2.335 3.470 nonbonded pdb=" CB LYS A 103 " pdb=" O GLU B 27 " model vdw 2.346 3.440 nonbonded pdb=" N VAL A 105 " pdb=" OE2 GLU B 26 " model vdw 2.353 2.520 ... (remaining 115462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.870 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: 4.420 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 42.450 Find NCS groups from input model: 0.350 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5602 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 : 0.018 0.230 14378 Z= 1.141 Angle : 2.270 31.343 19516 Z= 1.605 Chirality : 0.122 1.514 2112 Planarity : 0.017 0.149 2571 Dihedral : 14.407 89.338 5177 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.93 % Rotamer: Outliers : 0.67 % Allowed : 6.10 % Favored : 93.23 % Cbeta Deviations : 0.91 % 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 (0.19), residues: 1795 helix: 1.93 (0.27), residues: 352 sheet: 0.37 (0.21), residues: 602 loop : -1.81 (0.18), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.123 0.018 TRP B 93 HIS 0.018 0.005 HIS A 677 PHE 0.068 0.012 PHE B 356 TYR 0.167 0.022 TYR D 184 ARG 0.032 0.004 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 450 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 TYR cc_start: 0.5421 (m-80) cc_final: 0.5161 (m-10) REVERT: C 58 LEU cc_start: 0.8255 (mt) cc_final: 0.8052 (mp) REVERT: E 32 ILE cc_start: 0.8533 (mm) cc_final: 0.8268 (mt) REVERT: P 1285 LYS cc_start: 0.3243 (tttp) cc_final: 0.2608 (tmtt) outliers start: 10 outliers final: 3 residues processed: 460 average time/residue: 0.2777 time to fit residues: 180.8660 Evaluate side-chains 266 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 263 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain P residue 1053 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 215 GLN A 280 HIS A 448 ASN A 561 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN A 731 ASN A 748 ASN B 121 HIS B 170 GLN B 172 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 359 GLN D 70 GLN D 82 ASN D 104 ASN D 138 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1026 ASN P1036 ASN P1064 GLN P1170 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14378 Z= 0.280 Angle : 0.667 14.839 19516 Z= 0.360 Chirality : 0.046 0.285 2112 Planarity : 0.005 0.073 2571 Dihedral : 5.728 67.603 1985 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.55 % Allowed : 11.86 % Favored : 84.58 % 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: 0.11 (0.19), residues: 1795 helix: 2.57 (0.27), residues: 360 sheet: 0.42 (0.21), residues: 608 loop : -1.40 (0.19), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 48 HIS 0.007 0.001 HIS A 280 PHE 0.017 0.002 PHE A 804 TYR 0.026 0.002 TYR D 184 ARG 0.005 0.001 ARG P1257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 263 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 ARG cc_start: 0.7641 (mtm180) cc_final: 0.7383 (mtt-85) REVERT: B 80 LEU cc_start: 0.6208 (tt) cc_final: 0.5657 (tp) REVERT: B 359 GLN cc_start: 0.5525 (OUTLIER) cc_final: 0.5095 (tt0) REVERT: B 368 GLN cc_start: 0.6701 (pp30) cc_final: 0.6447 (pp30) REVERT: C 58 LEU cc_start: 0.8475 (mt) cc_final: 0.8190 (mp) outliers start: 53 outliers final: 30 residues processed: 294 average time/residue: 0.2617 time to fit residues: 112.2843 Evaluate side-chains 256 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 225 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1092 SER Chi-restraints excluded: chain P residue 1270 ASP Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 495 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1064 GLN P1170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14378 Z= 0.324 Angle : 0.652 12.192 19516 Z= 0.348 Chirality : 0.045 0.167 2112 Planarity : 0.005 0.055 2571 Dihedral : 5.576 64.683 1981 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.35 % Allowed : 14.54 % Favored : 82.10 % 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: -0.05 (0.19), residues: 1795 helix: 2.19 (0.27), residues: 350 sheet: 0.21 (0.20), residues: 643 loop : -1.25 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 48 HIS 0.013 0.001 HIS A 677 PHE 0.023 0.002 PHE A 804 TYR 0.024 0.002 TYR D 184 ARG 0.006 0.001 ARG D 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 241 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 VAL cc_start: 0.4138 (OUTLIER) cc_final: 0.3771 (m) REVERT: A 661 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7257 (mtt180) REVERT: C 58 LEU cc_start: 0.8618 (mt) cc_final: 0.8242 (mp) outliers start: 50 outliers final: 33 residues processed: 277 average time/residue: 0.2565 time to fit residues: 105.6165 Evaluate side-chains 243 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 209 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1270 ASP Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 chunk 172 optimal weight: 30.0000 chunk 154 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 143 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 448 ASN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN ** P1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1062 HIS P1160 HIS P1170 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 14378 Z= 0.536 Angle : 0.755 10.533 19516 Z= 0.405 Chirality : 0.049 0.350 2112 Planarity : 0.005 0.063 2571 Dihedral : 6.016 66.489 1981 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.69 % Allowed : 15.08 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.19), residues: 1795 helix: 1.26 (0.26), residues: 360 sheet: -0.10 (0.20), residues: 629 loop : -1.38 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 48 HIS 0.011 0.002 HIS A 677 PHE 0.023 0.003 PHE A 804 TYR 0.028 0.003 TYR B 132 ARG 0.005 0.001 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 209 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 VAL cc_start: 0.3943 (OUTLIER) cc_final: 0.3618 (m) REVERT: A 521 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6314 (mm-30) REVERT: A 777 MET cc_start: 0.5411 (mmm) cc_final: 0.5059 (mmt) REVERT: B 132 TYR cc_start: 0.7928 (m-80) cc_final: 0.7677 (m-80) REVERT: B 368 GLN cc_start: 0.6858 (pp30) cc_final: 0.6609 (pp30) REVERT: C 58 LEU cc_start: 0.8755 (mt) cc_final: 0.8347 (mp) outliers start: 70 outliers final: 47 residues processed: 262 average time/residue: 0.2376 time to fit residues: 94.8490 Evaluate side-chains 239 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 191 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain P residue 1025 LEU Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1210 VAL Chi-restraints excluded: chain P residue 1270 ASP Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 40.0000 chunk 128 optimal weight: 0.0870 chunk 70 optimal weight: 0.0970 chunk 146 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 87 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN A 563 ASN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN D 230 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1023 ASN P1024 ASN ** P1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1128 HIS P1170 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6015 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14378 Z= 0.164 Angle : 0.584 9.853 19516 Z= 0.308 Chirality : 0.043 0.183 2112 Planarity : 0.004 0.051 2571 Dihedral : 5.291 58.676 1981 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.48 % Allowed : 18.03 % Favored : 79.49 % 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: -0.28 (0.19), residues: 1795 helix: 1.86 (0.27), residues: 360 sheet: 0.02 (0.20), residues: 628 loop : -1.30 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 48 HIS 0.011 0.001 HIS D 102 PHE 0.024 0.001 PHE A 804 TYR 0.024 0.001 TYR D 184 ARG 0.006 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 216 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 VAL cc_start: 0.4027 (OUTLIER) cc_final: 0.3709 (m) REVERT: A 521 GLU cc_start: 0.6373 (mm-30) cc_final: 0.5717 (mm-30) REVERT: A 777 MET cc_start: 0.5354 (mmm) cc_final: 0.5053 (mmt) REVERT: P 1028 ARG cc_start: 0.6433 (tpp-160) cc_final: 0.6133 (tpp-160) REVERT: P 1124 LYS cc_start: 0.4108 (OUTLIER) cc_final: 0.2711 (tptp) outliers start: 37 outliers final: 24 residues processed: 241 average time/residue: 0.2451 time to fit residues: 88.4597 Evaluate side-chains 220 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 194 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1124 LYS Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 30.0000 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 42 optimal weight: 0.2980 chunk 172 optimal weight: 40.0000 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN B 359 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1128 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 14378 Z= 0.482 Angle : 0.700 9.095 19516 Z= 0.377 Chirality : 0.047 0.253 2112 Planarity : 0.005 0.054 2571 Dihedral : 5.694 63.317 1981 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.02 % Allowed : 18.43 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 1795 helix: 1.41 (0.27), residues: 353 sheet: -0.29 (0.20), residues: 632 loop : -1.35 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P1219 HIS 0.016 0.002 HIS P1128 PHE 0.022 0.002 PHE A 347 TYR 0.028 0.002 TYR B 132 ARG 0.005 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 205 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 521 GLU cc_start: 0.6598 (mm-30) cc_final: 0.6358 (mp0) REVERT: D 102 HIS cc_start: 0.5657 (t70) cc_final: 0.5369 (t-170) outliers start: 60 outliers final: 44 residues processed: 248 average time/residue: 0.2343 time to fit residues: 88.1802 Evaluate side-chains 240 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 196 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain P residue 1025 LEU Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1124 LYS Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1161 VAL Chi-restraints excluded: chain P residue 1210 VAL Chi-restraints excluded: chain P residue 1214 PHE Chi-restraints excluded: chain P residue 1270 ASP Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 0.1980 chunk 106 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1128 HIS ** P1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14378 Z= 0.200 Angle : 0.597 8.493 19516 Z= 0.319 Chirality : 0.044 0.361 2112 Planarity : 0.004 0.051 2571 Dihedral : 5.272 58.901 1981 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.95 % Allowed : 19.91 % Favored : 77.14 % 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: -0.43 (0.20), residues: 1795 helix: 1.68 (0.27), residues: 353 sheet: -0.15 (0.21), residues: 617 loop : -1.25 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 317 HIS 0.014 0.001 HIS P1128 PHE 0.026 0.001 PHE A 804 TYR 0.023 0.001 TYR D 184 ARG 0.005 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.7274 (mt-10) cc_final: 0.7028 (mt-10) REVERT: A 777 MET cc_start: 0.5341 (mmm) cc_final: 0.4708 (mmt) REVERT: B 359 GLN cc_start: 0.5131 (OUTLIER) cc_final: 0.4633 (tm-30) REVERT: C 80 LEU cc_start: 0.5664 (tp) cc_final: 0.5458 (tp) REVERT: P 1028 ARG cc_start: 0.6491 (tpp-160) cc_final: 0.6187 (tpp-160) outliers start: 44 outliers final: 33 residues processed: 230 average time/residue: 0.2437 time to fit residues: 84.4599 Evaluate side-chains 226 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain P residue 1025 LEU Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1214 PHE Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 0.0060 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 156 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN A 448 ASN ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1128 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14378 Z= 0.297 Angle : 0.622 8.175 19516 Z= 0.334 Chirality : 0.045 0.262 2112 Planarity : 0.004 0.054 2571 Dihedral : 5.289 59.560 1981 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.35 % Allowed : 19.77 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1795 helix: 1.58 (0.27), residues: 353 sheet: -0.25 (0.21), residues: 617 loop : -1.29 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P1219 HIS 0.009 0.001 HIS D 102 PHE 0.015 0.001 PHE A 804 TYR 0.032 0.002 TYR A 550 ARG 0.005 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 196 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1028 ARG cc_start: 0.6506 (tpp-160) cc_final: 0.6184 (tpp-160) outliers start: 50 outliers final: 45 residues processed: 230 average time/residue: 0.2505 time to fit residues: 87.6328 Evaluate side-chains 237 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 192 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain P residue 1025 LEU Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1214 PHE Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 20.0000 chunk 159 optimal weight: 20.0000 chunk 164 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN A 448 ASN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1128 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14378 Z= 0.183 Angle : 0.591 8.251 19516 Z= 0.315 Chirality : 0.044 0.229 2112 Planarity : 0.004 0.061 2571 Dihedral : 5.094 56.656 1981 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.02 % Allowed : 20.17 % Favored : 76.81 % 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 (0.20), residues: 1795 helix: 1.72 (0.27), residues: 353 sheet: -0.20 (0.20), residues: 632 loop : -1.23 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 317 HIS 0.015 0.001 HIS P1128 PHE 0.018 0.001 PHE A 804 TYR 0.029 0.001 TYR A 550 ARG 0.006 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 197 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 GLU cc_start: 0.6263 (mm-30) cc_final: 0.6047 (mp0) REVERT: A 777 MET cc_start: 0.5008 (mmm) cc_final: 0.4669 (mmt) REVERT: E 51 THR cc_start: 0.6951 (OUTLIER) cc_final: 0.6655 (m) REVERT: P 1028 ARG cc_start: 0.6478 (tpp-160) cc_final: 0.6166 (tpp-160) outliers start: 45 outliers final: 40 residues processed: 228 average time/residue: 0.2408 time to fit residues: 84.6021 Evaluate side-chains 228 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 187 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain P residue 1025 LEU Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1214 PHE Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 163 optimal weight: 30.0000 chunk 141 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 0.1980 chunk 112 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN A 693 GLN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14378 Z= 0.296 Angle : 0.619 8.688 19516 Z= 0.330 Chirality : 0.045 0.221 2112 Planarity : 0.004 0.062 2571 Dihedral : 5.170 57.181 1981 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.02 % Allowed : 19.91 % Favored : 77.08 % 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: -0.53 (0.20), residues: 1795 helix: 1.64 (0.27), residues: 353 sheet: -0.26 (0.21), residues: 613 loop : -1.29 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P1219 HIS 0.012 0.001 HIS P1128 PHE 0.014 0.001 PHE A 347 TYR 0.035 0.002 TYR A 550 ARG 0.005 0.000 ARG B 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 191 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 GLU cc_start: 0.6401 (mm-30) cc_final: 0.6167 (mp0) REVERT: A 777 MET cc_start: 0.5106 (mmm) cc_final: 0.4781 (mmt) REVERT: B 359 GLN cc_start: 0.5197 (OUTLIER) cc_final: 0.4353 (tm-30) outliers start: 45 outliers final: 42 residues processed: 223 average time/residue: 0.2292 time to fit residues: 78.7144 Evaluate side-chains 233 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain P residue 1025 LEU Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1210 VAL Chi-restraints excluded: chain P residue 1214 PHE Chi-restraints excluded: chain P residue 1292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.0040 chunk 124 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 475 ASN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1128 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.227661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.183020 restraints weight = 17185.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.177562 restraints weight = 17718.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.172379 restraints weight = 11632.069| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14378 Z= 0.188 Angle : 0.596 11.185 19516 Z= 0.315 Chirality : 0.044 0.221 2112 Planarity : 0.004 0.064 2571 Dihedral : 5.022 54.687 1981 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.02 % Allowed : 19.97 % Favored : 77.01 % 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 (0.20), residues: 1795 helix: 1.79 (0.27), residues: 353 sheet: -0.19 (0.20), residues: 627 loop : -1.26 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 48 HIS 0.007 0.001 HIS D 102 PHE 0.013 0.001 PHE A 804 TYR 0.024 0.001 TYR B 345 ARG 0.006 0.000 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3106.34 seconds wall clock time: 57 minutes 12.77 seconds (3432.77 seconds total)