Starting phenix.real_space_refine on Fri Nov 15 08:08:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk3_34843/11_2024/8hk3_34843.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk3_34843/11_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_34843/11_2024/8hk3_34843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk3_34843/11_2024/8hk3_34843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk3_34843/11_2024/8hk3_34843.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk3_34843/11_2024/8hk3_34843.cif" } 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. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 5.36, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 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: 1.06 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: 2.56 Time building geometry restraints manager: 2.76 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: 0.00 - 2.45: 12061 2.45 - 4.90: 55 4.90 - 7.34: 4 7.34 - 9.79: 0 9.79 - 12.24: 1 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 3.040 nonbonded pdb=" OG1 THR C 55 " pdb=" OG1 THR C 58 " model vdw 2.149 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.181 3.120 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.197 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.710 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 0.998 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: 0.2306 time to fit residues: 87.6114 Evaluate side-chains 229 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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: 0.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7336 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 8935 Z= 0.399 Angle : 0.627 9.906 12121 Z= 0.323 Chirality : 0.046 0.170 1390 Planarity : 0.005 0.044 1528 Dihedral : 4.405 57.750 1218 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.70 % Allowed : 8.73 % Favored : 89.56 % 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 (0.24), residues: 1119 helix: 1.47 (0.26), residues: 402 sheet: -0.54 (0.29), residues: 284 loop : -1.51 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.010 0.002 HIS B 91 PHE 0.032 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 to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.982 Fit side-chains REVERT: A 33 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6684 (mt-10) REVERT: B 14 LEU cc_start: 0.7917 (mm) cc_final: 0.7686 (mt) REVERT: B 155 ASN cc_start: 0.7765 (t0) cc_final: 0.7410 (t0) REVERT: B 170 ASP cc_start: 0.6903 (t70) cc_final: 0.6653 (t0) REVERT: B 220 GLN cc_start: 0.8104 (mt0) cc_final: 0.7866 (mt0) REVERT: B 295 ASN cc_start: 0.8223 (m-40) cc_final: 0.8001 (m-40) REVERT: B 317 CYS cc_start: 0.7176 (p) cc_final: 0.6946 (p) REVERT: B 325 MET cc_start: 0.7399 (tpp) cc_final: 0.7171 (tpp) REVERT: C 391 THR cc_start: 0.8169 (m) cc_final: 0.7926 (m) REVERT: C 399 LEU cc_start: 0.7995 (mp) cc_final: 0.7745 (mt) REVERT: H 80 PHE cc_start: 0.7595 (m-80) cc_final: 0.7392 (m-10) REVERT: H 119 VAL cc_start: 0.7780 (t) cc_final: 0.7448 (p) REVERT: H 161 SER cc_start: 0.8386 (t) cc_final: 0.8171 (p) outliers start: 16 outliers final: 13 residues processed: 225 average time/residue: 0.2079 time to fit residues: 64.4187 Evaluate side-chains 210 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER 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 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: 3.9990 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 B 110 ASN B 156 GLN ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8935 Z= 0.185 Angle : 0.505 6.886 12121 Z= 0.261 Chirality : 0.041 0.158 1390 Planarity : 0.004 0.046 1528 Dihedral : 4.065 57.750 1218 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.60 % Allowed : 11.18 % Favored : 87.22 % 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: 0.27 (0.25), residues: 1119 helix: 1.87 (0.27), residues: 404 sheet: -0.23 (0.29), residues: 287 loop : -1.17 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS B 91 PHE 0.019 0.001 PHE B 199 TYR 0.013 0.001 TYR H 95 ARG 0.005 0.000 ARG B 137 *********************** 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 209 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.975 Fit side-chains REVERT: A 197 LYS cc_start: 0.7773 (mtpt) cc_final: 0.7475 (mtmt) REVERT: A 225 VAL cc_start: 0.8581 (p) cc_final: 0.8288 (m) REVERT: B 61 MET cc_start: 0.7054 (ppp) cc_final: 0.6807 (ppp) REVERT: B 78 LYS cc_start: 0.8221 (mttm) cc_final: 0.7970 (mttp) REVERT: B 155 ASN cc_start: 0.7818 (t0) cc_final: 0.7434 (t0) REVERT: B 170 ASP cc_start: 0.6877 (t70) cc_final: 0.6613 (t0) REVERT: B 290 ASP cc_start: 0.7416 (m-30) cc_final: 0.7203 (m-30) REVERT: B 317 CYS cc_start: 0.7289 (p) cc_final: 0.7038 (p) REVERT: B 325 MET cc_start: 0.7382 (tpp) cc_final: 0.7117 (tpp) REVERT: C 340 ARG cc_start: 0.7296 (ttp-170) cc_final: 0.6861 (ttp-170) REVERT: C 391 THR cc_start: 0.8143 (m) cc_final: 0.7897 (m) REVERT: C 399 LEU cc_start: 0.8059 (mp) cc_final: 0.7787 (mt) REVERT: C 414 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6530 (mpp) REVERT: G 27 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.7970 (mtt-85) REVERT: H 67 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7796 (ttp80) REVERT: H 103 TYR cc_start: 0.7983 (t80) cc_final: 0.7774 (t80) REVERT: H 119 VAL cc_start: 0.7819 (t) cc_final: 0.7438 (p) outliers start: 15 outliers final: 7 residues processed: 202 average time/residue: 0.2439 time to fit residues: 65.3285 Evaluate side-chains 200 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 192 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9980 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.0470 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 0.0050 chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.5292 ------------------------------------------------------------------------------- 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 ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8935 Z= 0.158 Angle : 0.476 7.150 12121 Z= 0.247 Chirality : 0.040 0.162 1390 Planarity : 0.004 0.045 1528 Dihedral : 3.978 57.922 1218 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.70 % Allowed : 13.42 % Favored : 84.88 % 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: 0.53 (0.25), residues: 1119 helix: 2.05 (0.26), residues: 408 sheet: -0.12 (0.29), residues: 293 loop : -0.98 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS B 91 PHE 0.018 0.001 PHE B 199 TYR 0.009 0.001 TYR A 320 ARG 0.005 0.000 ARG B 137 *********************** 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 216 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7769 (mtpt) cc_final: 0.7455 (mtmt) REVERT: A 225 VAL cc_start: 0.8584 (p) cc_final: 0.8304 (m) REVERT: B 61 MET cc_start: 0.7055 (ppp) cc_final: 0.6653 (ppp) REVERT: B 155 ASN cc_start: 0.7871 (t0) cc_final: 0.7446 (t0) REVERT: B 170 ASP cc_start: 0.6888 (t70) cc_final: 0.6604 (t0) REVERT: B 271 CYS cc_start: 0.7444 (p) cc_final: 0.7189 (p) REVERT: C 340 ARG cc_start: 0.7271 (ttp-170) cc_final: 0.6840 (ttp-170) REVERT: C 387 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7556 (mt) REVERT: C 391 THR cc_start: 0.8160 (m) cc_final: 0.7912 (m) REVERT: C 414 MET cc_start: 0.6864 (mtp) cc_final: 0.6526 (mpp) REVERT: G 27 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.7895 (mtt-85) REVERT: H 119 VAL cc_start: 0.7813 (t) cc_final: 0.7414 (p) outliers start: 16 outliers final: 12 residues processed: 207 average time/residue: 0.2403 time to fit residues: 66.6967 Evaluate side-chains 205 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 13 GLN 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 C residue 25 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 341 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.0050 chunk 21 optimal weight: 2.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- 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 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3912 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= 0.211 Angle : 0.495 7.328 12121 Z= 0.256 Chirality : 0.041 0.156 1390 Planarity : 0.004 0.047 1528 Dihedral : 4.084 59.108 1218 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.81 % Allowed : 13.63 % Favored : 84.56 % 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: 0.60 (0.25), residues: 1119 helix: 2.03 (0.26), residues: 412 sheet: -0.05 (0.29), residues: 292 loop : -0.90 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS B 91 PHE 0.020 0.001 PHE B 199 TYR 0.018 0.001 TYR H 95 ARG 0.006 0.000 ARG B 137 *********************** 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 to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7783 (mtpt) cc_final: 0.7464 (mtmt) REVERT: A 225 VAL cc_start: 0.8618 (p) cc_final: 0.8306 (m) REVERT: B 155 ASN cc_start: 0.7908 (t0) cc_final: 0.7477 (t0) REVERT: B 170 ASP cc_start: 0.6993 (t70) cc_final: 0.6662 (t0) REVERT: C 340 ARG cc_start: 0.7259 (ttp-170) cc_final: 0.6829 (ttp-170) REVERT: C 391 THR cc_start: 0.8230 (m) cc_final: 0.7989 (m) REVERT: C 414 MET cc_start: 0.6884 (mtp) cc_final: 0.6552 (mpp) REVERT: G 27 ARG cc_start: 0.8361 (ttm-80) cc_final: 0.8086 (mtt-85) REVERT: H 67 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7745 (ttp80) REVERT: H 119 VAL cc_start: 0.7893 (t) cc_final: 0.7492 (p) outliers start: 17 outliers final: 15 residues processed: 203 average time/residue: 0.2439 time to fit residues: 65.5977 Evaluate side-chains 208 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 13 GLN 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 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 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 428 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 0.0170 chunk 12 optimal weight: 0.4980 chunk 61 optimal weight: 0.0470 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3951 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= 0.136 Angle : 0.466 7.268 12121 Z= 0.239 Chirality : 0.040 0.143 1390 Planarity : 0.004 0.046 1528 Dihedral : 3.893 57.758 1218 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.70 % Allowed : 13.95 % Favored : 84.35 % 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: 0.79 (0.25), residues: 1119 helix: 2.13 (0.26), residues: 416 sheet: 0.03 (0.29), residues: 292 loop : -0.73 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS A 188 PHE 0.016 0.001 PHE B 199 TYR 0.009 0.001 TYR H 228 ARG 0.004 0.000 ARG B 137 *********************** 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 225 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8598 (p) cc_final: 0.8294 (m) REVERT: A 341 ASP cc_start: 0.7059 (t70) cc_final: 0.6548 (t0) REVERT: B 61 MET cc_start: 0.6770 (ppp) cc_final: 0.6391 (ppp) REVERT: B 155 ASN cc_start: 0.7937 (t0) cc_final: 0.7580 (t0) REVERT: B 170 ASP cc_start: 0.6958 (t70) cc_final: 0.6688 (t0) REVERT: B 230 ASN cc_start: 0.7757 (m110) cc_final: 0.7549 (m110) REVERT: B 246 ASP cc_start: 0.7409 (m-30) cc_final: 0.7076 (m-30) REVERT: B 290 ASP cc_start: 0.7324 (m-30) cc_final: 0.7095 (m-30) REVERT: C 340 ARG cc_start: 0.7229 (ttp-170) cc_final: 0.6782 (ttp-170) REVERT: C 391 THR cc_start: 0.8140 (m) cc_final: 0.7893 (m) REVERT: C 414 MET cc_start: 0.6866 (mtp) cc_final: 0.6523 (mpp) REVERT: C 437 LEU cc_start: 0.8429 (mp) cc_final: 0.8194 (mt) REVERT: G 27 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.8014 (mtt-85) REVERT: H 67 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7739 (ttm170) REVERT: H 95 TYR cc_start: 0.8000 (m-80) cc_final: 0.7508 (m-80) REVERT: H 119 VAL cc_start: 0.7892 (t) cc_final: 0.7472 (p) REVERT: H 166 LEU cc_start: 0.8472 (tp) cc_final: 0.8261 (tt) outliers start: 16 outliers final: 14 residues processed: 214 average time/residue: 0.2428 time to fit residues: 69.2771 Evaluate side-chains 217 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain B residue 13 GLN 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 C residue 25 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 341 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 83 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: 0.0570 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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: 0.7312 moved from start: 0.4028 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 : 0.475 7.714 12121 Z= 0.244 Chirality : 0.040 0.137 1390 Planarity : 0.004 0.048 1528 Dihedral : 3.929 58.344 1218 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.60 % Allowed : 14.27 % Favored : 84.13 % 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: 0.87 (0.26), residues: 1119 helix: 2.18 (0.26), residues: 416 sheet: 0.12 (0.30), residues: 290 loop : -0.73 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS C 169 PHE 0.018 0.001 PHE B 199 TYR 0.009 0.001 TYR H 190 ARG 0.004 0.000 ARG B 137 *********************** 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 217 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8605 (p) cc_final: 0.8305 (m) REVERT: A 240 MET cc_start: 0.3843 (mmm) cc_final: 0.3564 (mmm) REVERT: A 341 ASP cc_start: 0.7083 (t70) cc_final: 0.6553 (t0) REVERT: B 61 MET cc_start: 0.6669 (ppp) cc_final: 0.6346 (ppp) REVERT: B 136 SER cc_start: 0.8157 (t) cc_final: 0.7917 (p) REVERT: B 155 ASN cc_start: 0.7954 (t0) cc_final: 0.7597 (t0) REVERT: B 170 ASP cc_start: 0.7009 (t70) cc_final: 0.6724 (t0) REVERT: B 246 ASP cc_start: 0.7398 (m-30) cc_final: 0.7159 (m-30) REVERT: C 340 ARG cc_start: 0.7228 (ttp-170) cc_final: 0.6783 (ttp-170) REVERT: C 391 THR cc_start: 0.8138 (m) cc_final: 0.7894 (m) REVERT: C 414 MET cc_start: 0.6853 (mtp) cc_final: 0.6504 (mpp) REVERT: C 437 LEU cc_start: 0.8410 (mp) cc_final: 0.8175 (mt) REVERT: G 27 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.8027 (mtt-85) REVERT: H 95 TYR cc_start: 0.7964 (m-80) cc_final: 0.7418 (m-80) REVERT: H 119 VAL cc_start: 0.7898 (t) cc_final: 0.7482 (p) REVERT: H 166 LEU cc_start: 0.8509 (tp) cc_final: 0.8302 (tt) outliers start: 15 outliers final: 13 residues processed: 207 average time/residue: 0.2532 time to fit residues: 69.7862 Evaluate side-chains 213 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 341 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 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: 2.9990 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 9 optimal weight: 0.0670 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 93 optimal weight: 0.0000 chunk 99 optimal weight: 0.8980 overall best weight: 0.3522 ------------------------------------------------------------------------------- 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: 0.7297 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8935 Z= 0.131 Angle : 0.464 7.760 12121 Z= 0.238 Chirality : 0.040 0.137 1390 Planarity : 0.004 0.046 1528 Dihedral : 3.833 57.084 1218 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.02 % Allowed : 13.74 % Favored : 84.24 % 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: 416 sheet: 0.22 (0.30), residues: 284 loop : -0.73 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.015 0.001 PHE B 199 TYR 0.008 0.001 TYR H 190 ARG 0.004 0.000 ARG C 443 *********************** 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 223 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7914 (mt) REVERT: A 225 VAL cc_start: 0.8593 (p) cc_final: 0.8281 (m) REVERT: A 240 MET cc_start: 0.3956 (mmm) cc_final: 0.3627 (mmm) REVERT: A 341 ASP cc_start: 0.7095 (t70) cc_final: 0.6574 (t0) REVERT: B 61 MET cc_start: 0.6581 (ppp) cc_final: 0.6282 (ppp) REVERT: B 136 SER cc_start: 0.8130 (t) cc_final: 0.7880 (p) REVERT: B 155 ASN cc_start: 0.7950 (t0) cc_final: 0.7586 (t0) REVERT: B 170 ASP cc_start: 0.7018 (t70) cc_final: 0.6740 (t0) REVERT: B 246 ASP cc_start: 0.7522 (m-30) cc_final: 0.7170 (m-30) REVERT: B 259 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7427 (pt0) REVERT: B 290 ASP cc_start: 0.7364 (m-30) cc_final: 0.7148 (m-30) REVERT: C 340 ARG cc_start: 0.7229 (ttp-170) cc_final: 0.6770 (ttp-170) REVERT: C 347 LEU cc_start: 0.7882 (tp) cc_final: 0.7582 (mt) REVERT: C 391 THR cc_start: 0.8116 (m) cc_final: 0.7876 (m) REVERT: C 414 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6490 (mpp) REVERT: C 437 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8173 (mt) REVERT: G 27 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.8046 (mtt-85) REVERT: H 95 TYR cc_start: 0.7928 (m-80) cc_final: 0.7305 (m-80) REVERT: H 119 VAL cc_start: 0.7914 (t) cc_final: 0.7490 (p) REVERT: H 166 LEU cc_start: 0.8529 (tp) cc_final: 0.8319 (tt) outliers start: 19 outliers final: 14 residues processed: 208 average time/residue: 0.2373 time to fit residues: 65.9557 Evaluate side-chains 220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 341 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 C residue 437 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8935 Z= 0.181 Angle : 0.487 8.015 12121 Z= 0.250 Chirality : 0.040 0.168 1390 Planarity : 0.004 0.048 1528 Dihedral : 3.931 56.978 1218 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.02 % Allowed : 14.16 % 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: 1.05 (0.26), residues: 1119 helix: 2.38 (0.26), residues: 410 sheet: 0.28 (0.30), residues: 284 loop : -0.68 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.019 0.001 PHE B 199 TYR 0.009 0.001 TYR H 190 ARG 0.004 0.000 ARG C 443 *********************** 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 226 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7926 (mt) REVERT: A 225 VAL cc_start: 0.8625 (p) cc_final: 0.8307 (m) REVERT: A 341 ASP cc_start: 0.7097 (t70) cc_final: 0.6557 (t0) REVERT: B 136 SER cc_start: 0.8158 (t) cc_final: 0.7917 (p) REVERT: B 155 ASN cc_start: 0.7967 (t0) cc_final: 0.7636 (t0) REVERT: B 170 ASP cc_start: 0.7065 (t70) cc_final: 0.6763 (t0) REVERT: B 220 GLN cc_start: 0.8140 (mt0) cc_final: 0.7927 (mt0) REVERT: B 246 ASP cc_start: 0.7523 (m-30) cc_final: 0.7260 (m-30) REVERT: B 290 ASP cc_start: 0.7327 (m-30) cc_final: 0.7097 (m-30) REVERT: B 325 MET cc_start: 0.7412 (tpp) cc_final: 0.7102 (tpp) REVERT: C 340 ARG cc_start: 0.7254 (ttp-170) cc_final: 0.6798 (ttp-170) REVERT: C 391 THR cc_start: 0.8140 (m) cc_final: 0.7899 (m) REVERT: C 414 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6517 (mpp) REVERT: C 437 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8125 (mt) REVERT: G 27 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.8037 (mtt-85) REVERT: H 95 TYR cc_start: 0.7909 (m-80) cc_final: 0.7254 (m-80) outliers start: 19 outliers final: 16 residues processed: 214 average time/residue: 0.2315 time to fit residues: 66.1507 Evaluate side-chains 220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 13 GLN 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 259 GLN 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 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 437 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 170 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4226 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= 0.192 Angle : 0.498 8.062 12121 Z= 0.255 Chirality : 0.041 0.154 1390 Planarity : 0.004 0.047 1528 Dihedral : 4.004 57.094 1218 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.92 % Allowed : 14.70 % Favored : 83.39 % 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: 1.05 (0.26), residues: 1119 helix: 2.39 (0.26), residues: 410 sheet: 0.24 (0.30), residues: 288 loop : -0.66 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.019 0.001 PHE B 199 TYR 0.010 0.001 TYR A 320 ARG 0.005 0.000 ARG C 443 ********************** 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 222 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8629 (p) cc_final: 0.8320 (m) REVERT: A 245 GLU cc_start: 0.6835 (tp30) cc_final: 0.6161 (tp30) REVERT: A 341 ASP cc_start: 0.7090 (t70) cc_final: 0.6550 (t0) REVERT: B 155 ASN cc_start: 0.7982 (t0) cc_final: 0.7637 (t0) REVERT: B 170 ASP cc_start: 0.7099 (t70) cc_final: 0.6773 (t0) REVERT: B 246 ASP cc_start: 0.7521 (m-30) cc_final: 0.7166 (m-30) REVERT: B 259 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: C 340 ARG cc_start: 0.7247 (ttp-170) cc_final: 0.6797 (ttp-170) REVERT: C 357 SER cc_start: 0.7945 (m) cc_final: 0.7708 (m) REVERT: C 391 THR cc_start: 0.8152 (m) cc_final: 0.7904 (m) REVERT: C 414 MET cc_start: 0.6875 (mtp) cc_final: 0.6529 (mpp) REVERT: C 437 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8218 (mt) REVERT: G 27 ARG cc_start: 0.8308 (ttm-80) cc_final: 0.8070 (mtt-85) outliers start: 18 outliers final: 15 residues processed: 210 average time/residue: 0.2398 time to fit residues: 68.0888 Evaluate side-chains 220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 259 GLN 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 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 437 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.129323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111419 restraints weight = 12053.470| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.94 r_work: 0.3239 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8935 Z= 0.201 Angle : 0.514 7.945 12121 Z= 0.262 Chirality : 0.041 0.149 1390 Planarity : 0.004 0.047 1528 Dihedral : 4.044 57.426 1218 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.02 % Allowed : 14.80 % 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: 1.06 (0.26), residues: 1119 helix: 2.39 (0.26), residues: 410 sheet: 0.26 (0.30), residues: 288 loop : -0.65 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.019 0.001 PHE B 199 TYR 0.012 0.001 TYR H 190 ARG 0.005 0.000 ARG C 443 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2445.33 seconds wall clock time: 45 minutes 9.13 seconds (2709.13 seconds total)