Starting phenix.real_space_refine on Mon Mar 11 17:25:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk3_34843/03_2024/8hk3_34843.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk3_34843/03_2024/8hk3_34843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk3_34843/03_2024/8hk3_34843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk3_34843/03_2024/8hk3_34843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk3_34843/03_2024/8hk3_34843.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk3_34843/03_2024/8hk3_34843.pdb" } resolution = 3.2 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= 0.002 sd= 0.033 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 69 5.16 5 C 5585 2.51 5 N 1488 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8746 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1801 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2244 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 15, 'TRANS': 268} Chain breaks: 1 Chain: "G" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 4.91, per 1000 atoms: 0.56 Number of scatterers: 8746 At special positions: 0 Unit cell: (105.04, 115.44, 131.04, 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 69 16.00 O 1604 8.00 N 1488 7.00 C 5585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " 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: 3.01 Conformation dependent library (CDL) restraints added in 1.7 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 39.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 4.111A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 54 removed outlier: 3.976A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.661A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.020A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.855A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.597A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.552A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.876A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 51 removed outlier: 4.223A pdb=" N LEU C 38 " --> pdb=" O PHE C 34 " (cutoff:3.500A) Proline residue: C 39 - end of helix Processing helix chain 'C' and resid 55 through 84 Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 91 through 126 removed outlier: 4.043A pdb=" N CYS C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 96 " --> pdb=" O ARG C 92 " (cutoff:3.500A) Proline residue: C 99 - end of helix removed outlier: 3.772A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 134 removed outlier: 3.602A pdb=" N ASN C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 161 Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 331 through 365 removed outlier: 5.709A pdb=" N LEU C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 372 through 403 removed outlier: 3.855A pdb=" N PHE C 376 " --> pdb=" O GLN C 372 " (cutoff:3.500A) Proline residue: C 392 - end of helix removed outlier: 3.552A pdb=" N LEU C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 402 " --> pdb=" O VAL C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 431 removed outlier: 3.623A pdb=" N LYS C 411 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS C 420 " --> pdb=" O TRP C 416 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 421 " --> pdb=" O ASP C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 439 through 454 removed outlier: 3.516A pdb=" N ARG C 443 " --> pdb=" O GLY C 439 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS C 444 " --> pdb=" O LYS C 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.704A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.510A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 187 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.192A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.672A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.856A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.849A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.554A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.470A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.548A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 162 through 165 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.643A pdb=" N VAL H 5 " --> pdb=" O SER H 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.107A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.587A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN H 194 " --> pdb=" O TYR H 190 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1194 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: 2.58 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1408 1.31 - 1.43: 2456 1.43 - 1.56: 4973 1.56 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 8935 Sorted by residual: bond pdb=" C LEU C 32 " pdb=" O LEU C 32 " ideal model delta sigma weight residual 1.236 1.183 0.054 1.26e-02 6.30e+03 1.82e+01 bond pdb=" C PHE C 345 " pdb=" O PHE C 345 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.36e-02 5.41e+03 1.46e+01 bond pdb=" C LEU C 38 " pdb=" O LEU C 38 " ideal model delta sigma weight residual 1.241 1.206 0.036 9.80e-03 1.04e+04 1.33e+01 bond pdb=" CA GLN C 372 " pdb=" C GLN C 372 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.30e-02 5.92e+03 5.32e+00 bond pdb=" C THR C 33 " pdb=" O THR C 33 " ideal model delta sigma weight residual 1.237 1.211 0.025 1.16e-02 7.43e+03 4.76e+00 ... (remaining 8930 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.46: 284 107.46 - 114.09: 5115 114.09 - 120.72: 3654 120.72 - 127.36: 2965 127.36 - 133.99: 103 Bond angle restraints: 12121 Sorted by residual: angle pdb=" N GLY C 91 " pdb=" CA GLY C 91 " pdb=" C GLY C 91 " ideal model delta sigma weight residual 112.83 119.62 -6.79 1.70e+00 3.46e-01 1.60e+01 angle pdb=" CA LEU C 35 " pdb=" CB LEU C 35 " pdb=" CG LEU C 35 " ideal model delta sigma weight residual 116.30 128.54 -12.24 3.50e+00 8.16e-02 1.22e+01 angle pdb=" CA GLN C 372 " pdb=" CB GLN C 372 " pdb=" CG GLN C 372 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N ARG C 92 " pdb=" CA ARG C 92 " pdb=" C ARG C 92 " ideal model delta sigma weight residual 111.69 115.66 -3.97 1.23e+00 6.61e-01 1.04e+01 angle pdb=" C LEU C 38 " pdb=" N PRO C 39 " pdb=" CA PRO C 39 " ideal model delta sigma weight residual 118.97 115.99 2.98 1.04e+00 9.25e-01 8.22e+00 ... (remaining 12116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 5192 15.97 - 31.94: 67 31.94 - 47.92: 15 47.92 - 63.89: 2 63.89 - 79.86: 2 Dihedral angle restraints: 5278 sinusoidal: 1996 harmonic: 3282 Sorted by residual: dihedral pdb=" N GLN C 372 " pdb=" C GLN C 372 " pdb=" CA GLN C 372 " pdb=" CB GLN C 372 " ideal model delta harmonic sigma weight residual 122.80 131.22 -8.42 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" N LEU C 38 " pdb=" C LEU C 38 " pdb=" CA LEU C 38 " pdb=" CB LEU C 38 " ideal model delta harmonic sigma weight residual 122.80 130.89 -8.09 0 2.50e+00 1.60e-01 1.05e+01 dihedral pdb=" C GLN C 372 " pdb=" N GLN C 372 " pdb=" CA GLN C 372 " pdb=" CB GLN C 372 " ideal model delta harmonic sigma weight residual -122.60 -130.23 7.63 0 2.50e+00 1.60e-01 9.32e+00 ... (remaining 5275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1278 0.073 - 0.147: 107 0.147 - 0.220: 0 0.220 - 0.293: 2 0.293 - 0.367: 3 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA LEU C 38 " pdb=" N LEU C 38 " pdb=" C LEU C 38 " pdb=" CB LEU C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA GLN C 372 " pdb=" N GLN C 372 " pdb=" C GLN C 372 " pdb=" CB GLN C 372 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CG LEU C 38 " pdb=" CB LEU C 38 " pdb=" CD1 LEU C 38 " pdb=" CD2 LEU C 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 1387 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 90 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C TYR C 90 " -0.059 2.00e-02 2.50e+03 pdb=" O TYR C 90 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY C 91 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 31 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C SER C 31 " 0.045 2.00e-02 2.50e+03 pdb=" O SER C 31 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU C 32 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 345 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C PHE C 345 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE C 345 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU C 346 " -0.010 2.00e-02 2.50e+03 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 82 2.63 - 3.20: 8136 3.20 - 3.77: 12881 3.77 - 4.33: 18184 4.33 - 4.90: 30718 Nonbonded interactions: 70001 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.069 2.440 nonbonded pdb=" OG1 THR C 55 " pdb=" OG1 THR C 58 " model vdw 2.149 2.440 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.160 2.440 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.181 2.520 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.197 2.440 ... (remaining 69996 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 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: 0.440 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: 0.000 Extract box with map and model: 2.100 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.260 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 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 : 0.002 0.054 8935 Z= 0.150 Angle : 0.421 12.240 12121 Z= 0.233 Chirality : 0.042 0.367 1390 Planarity : 0.002 0.034 1528 Dihedral : 6.311 79.860 3155 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.11 % Allowed : 1.81 % Favored : 98.08 % 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: -1.02 (0.24), residues: 1119 helix: 0.65 (0.26), residues: 397 sheet: -1.05 (0.28), residues: 287 loop : -1.56 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 99 HIS 0.001 0.000 HIS C 394 PHE 0.008 0.001 PHE C 34 TYR 0.003 0.000 TYR H 190 ARG 0.002 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 280 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7685 (mt) cc_final: 0.7460 (mp) REVERT: A 191 PHE cc_start: 0.8168 (t80) cc_final: 0.7968 (t80) REVERT: A 197 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7081 (mtpp) REVERT: B 61 MET cc_start: 0.6755 (ppp) cc_final: 0.6376 (ppp) REVERT: B 102 THR cc_start: 0.7984 (t) cc_final: 0.7769 (t) REVERT: B 170 ASP cc_start: 0.6201 (t70) cc_final: 0.5998 (t0) REVERT: B 246 ASP cc_start: 0.7459 (m-30) cc_final: 0.7216 (m-30) REVERT: B 277 SER cc_start: 0.8547 (t) cc_final: 0.8103 (m) REVERT: C 138 MET cc_start: 0.6859 (ttp) cc_final: 0.6429 (ttp) REVERT: C 141 SER cc_start: 0.7926 (t) cc_final: 0.7724 (p) REVERT: C 156 PRO cc_start: 0.7669 (Cg_exo) cc_final: 0.7437 (Cg_endo) REVERT: C 399 LEU cc_start: 0.7811 (mp) cc_final: 0.7580 (mt) REVERT: H 161 SER cc_start: 0.8318 (t) cc_final: 0.8117 (p) outliers start: 1 outliers final: 1 residues processed: 281 average time/residue: 0.2109 time to fit residues: 79.5437 Evaluate side-chains 229 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 75 GLN B 125 ASN B 220 GLN B 268 ASN B 295 ASN ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 HIS H 179 GLN H 194 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 8935 Z= 0.431 Angle : 0.644 10.510 12121 Z= 0.332 Chirality : 0.047 0.172 1390 Planarity : 0.005 0.044 1528 Dihedral : 4.507 58.480 1218 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.24 % Allowed : 8.41 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.24), residues: 1119 helix: 1.35 (0.26), residues: 408 sheet: -0.49 (0.29), residues: 284 loop : -1.51 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 47 HIS 0.012 0.002 HIS B 91 PHE 0.035 0.003 PHE B 199 TYR 0.025 0.003 TYR H 102 ARG 0.005 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 214 time to evaluate : 0.988 Fit side-chains REVERT: B 155 ASN cc_start: 0.7841 (t0) cc_final: 0.7478 (t0) REVERT: B 170 ASP cc_start: 0.6960 (t70) cc_final: 0.6660 (t0) REVERT: B 220 GLN cc_start: 0.8155 (mt0) cc_final: 0.7927 (mt0) REVERT: B 317 CYS cc_start: 0.7114 (p) cc_final: 0.6886 (p) REVERT: B 325 MET cc_start: 0.7411 (tpp) cc_final: 0.7165 (tpp) REVERT: C 153 MET cc_start: 0.7224 (tpp) cc_final: 0.6754 (mmm) REVERT: C 380 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.8055 (t) REVERT: C 391 THR cc_start: 0.8251 (m) cc_final: 0.7979 (m) REVERT: C 399 LEU cc_start: 0.7857 (mp) cc_final: 0.7611 (mt) REVERT: H 119 VAL cc_start: 0.7748 (t) cc_final: 0.7452 (p) REVERT: H 161 SER cc_start: 0.8379 (t) cc_final: 0.8167 (p) outliers start: 21 outliers final: 16 residues processed: 224 average time/residue: 0.2048 time to fit residues: 63.4533 Evaluate side-chains 210 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 0.0050 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN B 75 GLN ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8935 Z= 0.169 Angle : 0.490 6.894 12121 Z= 0.252 Chirality : 0.040 0.149 1390 Planarity : 0.004 0.045 1528 Dihedral : 4.030 58.456 1218 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.92 % Allowed : 11.29 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1119 helix: 1.80 (0.27), residues: 412 sheet: -0.25 (0.29), residues: 290 loop : -1.14 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.003 0.001 HIS B 91 PHE 0.019 0.001 PHE B 199 TYR 0.015 0.001 TYR H 95 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 1.023 Fit side-chains REVERT: A 197 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7566 (mtmt) REVERT: B 14 LEU cc_start: 0.7861 (mm) cc_final: 0.7576 (mt) REVERT: B 61 MET cc_start: 0.7065 (ppp) cc_final: 0.6851 (ppp) REVERT: B 78 LYS cc_start: 0.8230 (mttm) cc_final: 0.7963 (mttp) REVERT: B 155 ASN cc_start: 0.7889 (t0) cc_final: 0.7526 (t0) REVERT: B 170 ASP cc_start: 0.6702 (t70) cc_final: 0.6448 (t0) REVERT: B 184 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8124 (p) REVERT: B 317 CYS cc_start: 0.7286 (p) cc_final: 0.7025 (p) REVERT: C 340 ARG cc_start: 0.7255 (ttp-170) cc_final: 0.6826 (ttp-170) REVERT: C 387 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7541 (mt) REVERT: C 391 THR cc_start: 0.8239 (m) cc_final: 0.7993 (m) REVERT: C 414 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6568 (mpp) REVERT: G 27 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.8006 (mtt-85) REVERT: H 67 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7283 (ttp80) REVERT: H 80 PHE cc_start: 0.7809 (m-80) cc_final: 0.7604 (m-10) REVERT: H 119 VAL cc_start: 0.7746 (t) cc_final: 0.7406 (p) outliers start: 18 outliers final: 11 residues processed: 203 average time/residue: 0.2409 time to fit residues: 64.6882 Evaluate side-chains 207 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.0000 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 89 optimal weight: 0.0270 chunk 60 optimal weight: 0.8980 overall best weight: 0.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8935 Z= 0.134 Angle : 0.451 6.694 12121 Z= 0.233 Chirality : 0.039 0.155 1390 Planarity : 0.003 0.042 1528 Dihedral : 3.831 58.088 1218 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.70 % Allowed : 12.46 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1119 helix: 2.16 (0.27), residues: 407 sheet: -0.09 (0.29), residues: 296 loop : -0.96 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.002 0.001 HIS B 91 PHE 0.018 0.001 PHE B 199 TYR 0.008 0.001 TYR H 102 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 196 time to evaluate : 1.009 Fit side-chains REVERT: A 197 LYS cc_start: 0.7754 (mtpt) cc_final: 0.7445 (mtmt) REVERT: B 61 MET cc_start: 0.7033 (ppp) cc_final: 0.6672 (ppp) REVERT: B 78 LYS cc_start: 0.8216 (mttm) cc_final: 0.7964 (mttp) REVERT: B 155 ASN cc_start: 0.7890 (t0) cc_final: 0.7479 (t0) REVERT: B 170 ASP cc_start: 0.6773 (t70) cc_final: 0.6499 (t0) REVERT: B 290 ASP cc_start: 0.7182 (m-30) cc_final: 0.6823 (m-30) REVERT: B 317 CYS cc_start: 0.7221 (p) cc_final: 0.7008 (p) REVERT: C 340 ARG cc_start: 0.7197 (ttp-170) cc_final: 0.6850 (ttp-170) REVERT: C 391 THR cc_start: 0.8196 (m) cc_final: 0.7938 (m) REVERT: C 414 MET cc_start: 0.6862 (mtp) cc_final: 0.6538 (mpp) REVERT: G 27 ARG cc_start: 0.8334 (ttm-80) cc_final: 0.8052 (mtt-85) REVERT: H 80 PHE cc_start: 0.7786 (m-80) cc_final: 0.7462 (m-10) REVERT: H 119 VAL cc_start: 0.7753 (t) cc_final: 0.7394 (p) outliers start: 16 outliers final: 12 residues processed: 207 average time/residue: 0.2397 time to fit residues: 66.1240 Evaluate side-chains 207 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 195 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN B 259 GLN C 63 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8935 Z= 0.284 Angle : 0.526 8.449 12121 Z= 0.273 Chirality : 0.042 0.162 1390 Planarity : 0.004 0.047 1528 Dihedral : 4.258 59.237 1218 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.56 % Allowed : 12.78 % Favored : 84.66 % 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: 0.63 (0.25), residues: 1119 helix: 2.06 (0.26), residues: 406 sheet: -0.00 (0.29), residues: 289 loop : -0.86 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.005 0.002 HIS B 91 PHE 0.024 0.002 PHE B 199 TYR 0.015 0.002 TYR H 102 ARG 0.005 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7534 (mtmt) REVERT: A 225 VAL cc_start: 0.8658 (p) cc_final: 0.8326 (m) REVERT: B 14 LEU cc_start: 0.7915 (mm) cc_final: 0.7620 (mt) REVERT: B 155 ASN cc_start: 0.7967 (t0) cc_final: 0.7475 (t0) REVERT: B 170 ASP cc_start: 0.7003 (t70) cc_final: 0.6717 (t0) REVERT: B 317 CYS cc_start: 0.7299 (p) cc_final: 0.7007 (p) REVERT: C 340 ARG cc_start: 0.7268 (ttp-170) cc_final: 0.6822 (ttp-170) REVERT: C 391 THR cc_start: 0.8236 (m) cc_final: 0.7994 (m) REVERT: C 414 MET cc_start: 0.6933 (mtp) cc_final: 0.6583 (mpp) REVERT: G 27 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.7906 (mtt-85) REVERT: H 64 VAL cc_start: 0.8431 (t) cc_final: 0.8050 (p) REVERT: H 95 TYR cc_start: 0.8025 (m-80) cc_final: 0.7817 (m-80) REVERT: H 119 VAL cc_start: 0.7886 (t) cc_final: 0.7525 (p) REVERT: H 189 ILE cc_start: 0.8689 (mt) cc_final: 0.8444 (mp) outliers start: 24 outliers final: 19 residues processed: 204 average time/residue: 0.2388 time to fit residues: 64.7173 Evaluate side-chains 207 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 188 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8935 Z= 0.264 Angle : 0.506 8.251 12121 Z= 0.263 Chirality : 0.041 0.170 1390 Planarity : 0.004 0.044 1528 Dihedral : 4.256 59.996 1218 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.77 % Allowed : 13.42 % Favored : 83.81 % 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: 0.72 (0.25), residues: 1119 helix: 2.10 (0.26), residues: 405 sheet: 0.05 (0.29), residues: 290 loop : -0.78 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.023 0.002 PHE H 68 TYR 0.013 0.002 TYR H 102 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 191 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8649 (p) cc_final: 0.8347 (m) REVERT: A 240 MET cc_start: 0.4025 (mmm) cc_final: 0.3754 (mmm) REVERT: B 14 LEU cc_start: 0.7896 (mm) cc_final: 0.7610 (mt) REVERT: B 155 ASN cc_start: 0.7963 (t0) cc_final: 0.7647 (t0) REVERT: B 170 ASP cc_start: 0.7005 (t70) cc_final: 0.6678 (t0) REVERT: B 246 ASP cc_start: 0.7455 (m-30) cc_final: 0.7141 (m-30) REVERT: B 317 CYS cc_start: 0.7275 (p) cc_final: 0.7038 (p) REVERT: C 340 ARG cc_start: 0.7267 (ttp-170) cc_final: 0.6823 (ttp-170) REVERT: C 391 THR cc_start: 0.8204 (m) cc_final: 0.7980 (m) REVERT: G 27 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8012 (mtt-85) REVERT: H 119 VAL cc_start: 0.7911 (t) cc_final: 0.7544 (p) outliers start: 26 outliers final: 20 residues processed: 202 average time/residue: 0.2352 time to fit residues: 63.0367 Evaluate side-chains 204 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 0.0040 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8935 Z= 0.167 Angle : 0.468 7.101 12121 Z= 0.244 Chirality : 0.040 0.147 1390 Planarity : 0.003 0.047 1528 Dihedral : 4.036 58.390 1218 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.66 % Allowed : 13.63 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1119 helix: 2.24 (0.26), residues: 405 sheet: 0.11 (0.29), residues: 289 loop : -0.66 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 PHE 0.017 0.001 PHE B 199 TYR 0.010 0.001 TYR H 190 ARG 0.003 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 201 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8644 (p) cc_final: 0.8356 (m) REVERT: B 14 LEU cc_start: 0.7835 (mm) cc_final: 0.7555 (mt) REVERT: B 61 MET cc_start: 0.7077 (ppp) cc_final: 0.6716 (ppp) REVERT: B 155 ASN cc_start: 0.8004 (t0) cc_final: 0.7688 (t0) REVERT: B 170 ASP cc_start: 0.6948 (t70) cc_final: 0.6659 (t0) REVERT: B 184 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.8045 (p) REVERT: B 246 ASP cc_start: 0.7446 (m-30) cc_final: 0.7112 (m-30) REVERT: B 317 CYS cc_start: 0.7274 (p) cc_final: 0.7031 (p) REVERT: C 340 ARG cc_start: 0.7212 (ttp-170) cc_final: 0.6757 (ttp-170) REVERT: C 391 THR cc_start: 0.8176 (m) cc_final: 0.7961 (m) REVERT: G 27 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.7958 (mtt-85) outliers start: 25 outliers final: 21 residues processed: 209 average time/residue: 0.2436 time to fit residues: 67.4120 Evaluate side-chains 217 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 93 optimal weight: 0.2980 chunk 99 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN C 131 GLN C 170 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8935 Z= 0.161 Angle : 0.468 7.441 12121 Z= 0.243 Chirality : 0.040 0.145 1390 Planarity : 0.004 0.049 1528 Dihedral : 3.973 58.101 1218 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.34 % Allowed : 14.59 % Favored : 83.07 % 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: 0.95 (0.26), residues: 1119 helix: 2.28 (0.26), residues: 406 sheet: 0.15 (0.29), residues: 289 loop : -0.62 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS H 35 PHE 0.035 0.001 PHE H 68 TYR 0.009 0.001 TYR H 190 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 206 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8648 (p) cc_final: 0.8367 (m) REVERT: A 245 GLU cc_start: 0.6930 (tp30) cc_final: 0.6302 (tp30) REVERT: B 14 LEU cc_start: 0.7825 (mm) cc_final: 0.7543 (mt) REVERT: B 61 MET cc_start: 0.7087 (ppp) cc_final: 0.6726 (ppp) REVERT: B 155 ASN cc_start: 0.7999 (t0) cc_final: 0.7672 (t0) REVERT: B 170 ASP cc_start: 0.6921 (t70) cc_final: 0.6635 (t0) REVERT: B 184 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.8040 (p) REVERT: B 246 ASP cc_start: 0.7434 (m-30) cc_final: 0.7197 (m-30) REVERT: C 340 ARG cc_start: 0.7216 (ttp-170) cc_final: 0.6768 (ttp-170) REVERT: C 391 THR cc_start: 0.8164 (m) cc_final: 0.7937 (m) REVERT: C 414 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6553 (mpp) REVERT: G 27 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.7931 (mtt-85) outliers start: 22 outliers final: 18 residues processed: 216 average time/residue: 0.2376 time to fit residues: 68.0787 Evaluate side-chains 222 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 202 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.0670 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 0.0980 chunk 64 optimal weight: 0.5980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN C 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8935 Z= 0.135 Angle : 0.464 7.649 12121 Z= 0.240 Chirality : 0.040 0.135 1390 Planarity : 0.004 0.048 1528 Dihedral : 3.891 57.280 1218 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.34 % Allowed : 14.48 % Favored : 83.17 % 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: 0.97 (0.26), residues: 1119 helix: 2.31 (0.26), residues: 406 sheet: 0.08 (0.29), residues: 291 loop : -0.56 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.002 0.001 HIS A 188 PHE 0.027 0.001 PHE H 68 TYR 0.009 0.001 TYR H 190 ARG 0.003 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 206 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8650 (p) cc_final: 0.8366 (m) REVERT: A 245 GLU cc_start: 0.6829 (tp30) cc_final: 0.6235 (tp30) REVERT: B 155 ASN cc_start: 0.7997 (t0) cc_final: 0.7657 (t0) REVERT: B 170 ASP cc_start: 0.6914 (t70) cc_final: 0.6584 (t0) REVERT: B 246 ASP cc_start: 0.7423 (m-30) cc_final: 0.7199 (m-30) REVERT: C 340 ARG cc_start: 0.7178 (ttp-170) cc_final: 0.6733 (ttp-170) REVERT: C 391 THR cc_start: 0.8148 (m) cc_final: 0.7922 (m) REVERT: C 414 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6542 (mpp) REVERT: G 27 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.8071 (mtt-85) outliers start: 22 outliers final: 17 residues processed: 215 average time/residue: 0.2520 time to fit residues: 71.9319 Evaluate side-chains 221 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 203 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN C 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8935 Z= 0.162 Angle : 0.482 7.878 12121 Z= 0.248 Chirality : 0.040 0.143 1390 Planarity : 0.004 0.047 1528 Dihedral : 3.915 57.326 1218 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.13 % Allowed : 14.59 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1119 helix: 2.29 (0.26), residues: 407 sheet: 0.10 (0.29), residues: 291 loop : -0.56 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS H 35 PHE 0.043 0.001 PHE H 68 TYR 0.011 0.001 TYR H 190 ARG 0.003 0.000 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 201 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8657 (p) cc_final: 0.8368 (m) REVERT: A 245 GLU cc_start: 0.6830 (tp30) cc_final: 0.6159 (tp30) REVERT: B 14 LEU cc_start: 0.7747 (mm) cc_final: 0.7529 (mt) REVERT: B 155 ASN cc_start: 0.7969 (t0) cc_final: 0.7650 (t0) REVERT: B 170 ASP cc_start: 0.6917 (t70) cc_final: 0.6651 (t0) REVERT: B 246 ASP cc_start: 0.7421 (m-30) cc_final: 0.7107 (m-30) REVERT: C 340 ARG cc_start: 0.7204 (ttp-170) cc_final: 0.6754 (ttp-170) REVERT: C 391 THR cc_start: 0.8154 (m) cc_final: 0.7927 (m) REVERT: C 414 MET cc_start: 0.6898 (mtp) cc_final: 0.6548 (mpp) REVERT: G 27 ARG cc_start: 0.8276 (ttm-80) cc_final: 0.8046 (mtt-85) outliers start: 20 outliers final: 18 residues processed: 211 average time/residue: 0.2373 time to fit residues: 65.8805 Evaluate side-chains 221 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 203 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.128717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110779 restraints weight = 12100.962| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.92 r_work: 0.3242 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8935 Z= 0.205 Angle : 0.495 7.874 12121 Z= 0.255 Chirality : 0.040 0.155 1390 Planarity : 0.004 0.047 1528 Dihedral : 4.010 57.358 1218 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.34 % Allowed : 14.80 % Favored : 82.85 % 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: 0.97 (0.26), residues: 1119 helix: 2.26 (0.26), residues: 406 sheet: 0.10 (0.30), residues: 291 loop : -0.52 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS H 35 PHE 0.042 0.002 PHE H 68 TYR 0.010 0.001 TYR H 102 ARG 0.003 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2357.30 seconds wall clock time: 43 minutes 26.67 seconds (2606.67 seconds total)