Starting phenix.real_space_refine on Sat Apr 6 02:43:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg1_29991/04_2024/8gg1_29991_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg1_29991/04_2024/8gg1_29991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg1_29991/04_2024/8gg1_29991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg1_29991/04_2024/8gg1_29991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg1_29991/04_2024/8gg1_29991_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg1_29991/04_2024/8gg1_29991_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 46 5.16 5 C 4317 2.51 5 N 1161 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 344": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6755 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1750 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain breaks: 3 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 126 Chain: "B" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2443 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 79 Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 347 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2163 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 20 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 5} Link IDs: {None: 5} Time building chain proxies: 4.27, per 1000 atoms: 0.63 Number of scatterers: 6755 At special positions: 0 Unit cell: (83.2992, 134.493, 98.0501, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 3 15.00 O 1228 8.00 N 1161 7.00 C 4317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 2.41 Conformation dependent library (CDL) restraints added in 1.3 seconds 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 8 sheets defined 43.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.673A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 233 through 237 removed outlier: 4.016A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.656A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 7 through 23 removed outlier: 3.619A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 12 through 23 Processing helix chain 'G' and resid 30 through 44 removed outlier: 3.664A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'R' and resid 33 through 60 removed outlier: 3.636A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 85 removed outlier: 3.715A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 96 Processing helix chain 'R' and resid 102 through 136 removed outlier: 3.894A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 170 removed outlier: 3.890A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 197 through 208 Processing helix chain 'R' and resid 210 through 237 removed outlier: 3.550A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 298 removed outlier: 3.757A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.000A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 320 removed outlier: 3.851A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 326 Processing helix chain 'R' and resid 330 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.080A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.583A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.100A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.843A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.819A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.618A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.601A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.671A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 951 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: 1.87 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1702 1.33 - 1.45: 1398 1.45 - 1.58: 3725 1.58 - 1.70: 5 1.70 - 1.82: 64 Bond restraints: 6894 Sorted by residual: bond pdb=" CA GLN R 299 " pdb=" C GLN R 299 " ideal model delta sigma weight residual 1.521 1.487 0.034 1.17e-02 7.31e+03 8.57e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.29e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 5.93e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.568 -0.045 2.00e-02 2.50e+03 4.98e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.562 -0.042 2.00e-02 2.50e+03 4.41e+00 ... (remaining 6889 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.64: 146 106.64 - 113.48: 3832 113.48 - 120.32: 2430 120.32 - 127.16: 2921 127.16 - 134.00: 77 Bond angle restraints: 9406 Sorted by residual: angle pdb=" N SER R 207 " pdb=" CA SER R 207 " pdb=" C SER R 207 " ideal model delta sigma weight residual 111.36 118.66 -7.30 1.09e+00 8.42e-01 4.49e+01 angle pdb=" N PHE R 208 " pdb=" CA PHE R 208 " pdb=" C PHE R 208 " ideal model delta sigma weight residual 114.39 123.06 -8.67 1.45e+00 4.76e-01 3.57e+01 angle pdb=" N ILE R 205 " pdb=" CA ILE R 205 " pdb=" C ILE R 205 " ideal model delta sigma weight residual 110.62 116.39 -5.77 1.02e+00 9.61e-01 3.20e+01 angle pdb=" C PRO R 211 " pdb=" N LEU R 212 " pdb=" CA LEU R 212 " ideal model delta sigma weight residual 120.44 126.57 -6.13 1.36e+00 5.41e-01 2.03e+01 angle pdb=" N VAL R 295 " pdb=" CA VAL R 295 " pdb=" C VAL R 295 " ideal model delta sigma weight residual 110.62 115.06 -4.44 1.02e+00 9.61e-01 1.89e+01 ... (remaining 9401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 3780 21.12 - 42.25: 208 42.25 - 63.37: 23 63.37 - 84.50: 6 84.50 - 105.62: 2 Dihedral angle restraints: 4019 sinusoidal: 1406 harmonic: 2613 Sorted by residual: dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual -56.21 -161.83 105.62 1 2.00e+01 2.50e-03 3.05e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 0.07 104.53 1 2.00e+01 2.50e-03 3.00e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 147.70 -78.43 1 2.00e+01 2.50e-03 1.92e+01 ... (remaining 4016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 854 0.046 - 0.092: 204 0.092 - 0.138: 46 0.138 - 0.184: 4 0.184 - 0.230: 1 Chirality restraints: 1109 Sorted by residual: chirality pdb=" CA PHE R 208 " pdb=" N PHE R 208 " pdb=" C PHE R 208 " pdb=" CB PHE R 208 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA TYR R 209 " pdb=" N TYR R 209 " pdb=" C TYR R 209 " pdb=" CB TYR R 209 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 1106 not shown) Planarity restraints: 1179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 203 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C SER R 203 " 0.038 2.00e-02 2.50e+03 pdb=" O SER R 203 " -0.014 2.00e-02 2.50e+03 pdb=" N SER R 204 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO R 211 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 208 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C PHE R 208 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE R 208 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR R 209 " 0.011 2.00e-02 2.50e+03 ... (remaining 1176 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 399 2.74 - 3.28: 6360 3.28 - 3.82: 10648 3.82 - 4.36: 12321 4.36 - 4.90: 22904 Nonbonded interactions: 52632 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.195 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.204 2.440 nonbonded pdb=" OG1 THR A 55 " pdb=" O1A GTP A 401 " model vdw 2.287 2.440 nonbonded pdb=" O SER R 137 " pdb=" OG SER R 137 " model vdw 2.298 2.440 nonbonded pdb=" O TYR R 132 " pdb=" OG1 THR R 136 " model vdw 2.300 2.440 ... (remaining 52627 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: 1.940 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: 7.700 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.970 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 : 0.003 0.050 6894 Z= 0.212 Angle : 0.544 8.669 9406 Z= 0.320 Chirality : 0.041 0.230 1109 Planarity : 0.003 0.049 1179 Dihedral : 13.129 105.622 2318 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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 (0.28), residues: 878 helix: 1.35 (0.26), residues: 399 sheet: 0.41 (0.40), residues: 171 loop : -0.76 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.005 0.001 HIS R 296 PHE 0.011 0.001 PHE R 208 TYR 0.012 0.001 TYR A 339 ARG 0.009 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.798 Fit side-chains REVERT: A 29 GLN cc_start: 0.8375 (tp-100) cc_final: 0.8090 (mm-40) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 1.2132 time to fit residues: 130.3805 Evaluate side-chains 79 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 17 GLN B 32 GLN B 75 GLN B 237 ASN R 51 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6894 Z= 0.189 Angle : 0.490 6.524 9406 Z= 0.263 Chirality : 0.041 0.139 1109 Planarity : 0.003 0.031 1179 Dihedral : 6.739 107.474 985 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.51 % Allowed : 7.24 % Favored : 91.25 % 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: 1.10 (0.28), residues: 878 helix: 1.92 (0.26), residues: 398 sheet: 0.57 (0.40), residues: 170 loop : -0.73 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.006 0.001 HIS R 296 PHE 0.012 0.001 PHE B 292 TYR 0.014 0.001 TYR A 339 ARG 0.002 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.813 Fit side-chains REVERT: A 29 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8159 (mm-40) REVERT: B 36 ASN cc_start: 0.7955 (m-40) cc_final: 0.7168 (p0) REVERT: B 219 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.6887 (mtt90) REVERT: B 314 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.6719 (ttm170) outliers start: 10 outliers final: 5 residues processed: 94 average time/residue: 1.0413 time to fit residues: 103.6160 Evaluate side-chains 89 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 55 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 75 GLN R 51 ASN R 65 GLN R 296 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6894 Z= 0.149 Angle : 0.456 6.471 9406 Z= 0.244 Chirality : 0.040 0.137 1109 Planarity : 0.003 0.029 1179 Dihedral : 6.527 108.148 985 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.11 % Allowed : 10.71 % Favored : 87.18 % 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: 1.32 (0.29), residues: 878 helix: 2.13 (0.26), residues: 400 sheet: 0.62 (0.40), residues: 170 loop : -0.65 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.005 0.001 HIS R 296 PHE 0.011 0.001 PHE B 241 TYR 0.011 0.001 TYR A 339 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.703 Fit side-chains REVERT: B 36 ASN cc_start: 0.7983 (m-40) cc_final: 0.7159 (p0) REVERT: B 219 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7472 (mpt90) REVERT: B 314 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.6760 (ttm170) outliers start: 14 outliers final: 6 residues processed: 94 average time/residue: 1.2083 time to fit residues: 119.7410 Evaluate side-chains 88 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 71 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 75 GLN B 237 ASN B 340 ASN R 51 ASN R 65 GLN R 296 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6894 Z= 0.171 Angle : 0.464 6.532 9406 Z= 0.248 Chirality : 0.040 0.149 1109 Planarity : 0.003 0.027 1179 Dihedral : 6.432 108.439 985 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.81 % Allowed : 13.12 % Favored : 85.07 % 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: 1.44 (0.29), residues: 878 helix: 2.37 (0.27), residues: 392 sheet: 0.58 (0.39), residues: 170 loop : -0.65 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.013 0.001 TYR A 339 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.736 Fit side-chains REVERT: B 219 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7413 (mpt90) REVERT: B 314 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.6782 (ttm170) outliers start: 12 outliers final: 6 residues processed: 90 average time/residue: 1.2170 time to fit residues: 115.7474 Evaluate side-chains 87 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 51 ASN R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6894 Z= 0.168 Angle : 0.465 6.558 9406 Z= 0.248 Chirality : 0.040 0.154 1109 Planarity : 0.003 0.026 1179 Dihedral : 6.392 108.972 985 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.96 % Allowed : 14.18 % Favored : 83.86 % 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: 1.47 (0.29), residues: 878 helix: 2.40 (0.26), residues: 392 sheet: 0.60 (0.39), residues: 170 loop : -0.65 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.001 PHE B 241 TYR 0.012 0.001 TYR A 339 ARG 0.003 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.984 Fit side-chains REVERT: B 219 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7591 (mpt90) REVERT: B 314 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.6800 (ttm170) outliers start: 13 outliers final: 8 residues processed: 91 average time/residue: 1.2463 time to fit residues: 119.6617 Evaluate side-chains 87 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.0170 chunk 7 optimal weight: 0.0770 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 75 GLN B 237 ASN B 340 ASN R 51 ASN R 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6894 Z= 0.138 Angle : 0.443 6.586 9406 Z= 0.238 Chirality : 0.040 0.161 1109 Planarity : 0.003 0.028 1179 Dihedral : 6.277 109.164 985 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.41 % Allowed : 14.18 % Favored : 83.41 % 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: 1.57 (0.29), residues: 878 helix: 2.53 (0.26), residues: 391 sheet: 0.63 (0.39), residues: 170 loop : -0.65 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.007 0.001 HIS A 220 PHE 0.012 0.001 PHE B 241 TYR 0.011 0.001 TYR A 339 ARG 0.003 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.764 Fit side-chains REVERT: B 219 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7526 (mpt90) REVERT: B 314 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.6777 (ttm170) outliers start: 16 outliers final: 10 residues processed: 98 average time/residue: 1.1342 time to fit residues: 117.7582 Evaluate side-chains 98 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 53 optimal weight: 0.0030 chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 75 GLN B 183 HIS R 51 ASN R 65 GLN R 296 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6894 Z= 0.176 Angle : 0.472 6.589 9406 Z= 0.253 Chirality : 0.041 0.171 1109 Planarity : 0.003 0.026 1179 Dihedral : 6.313 109.135 985 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.71 % Allowed : 14.63 % Favored : 82.65 % 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: 1.58 (0.29), residues: 878 helix: 2.52 (0.27), residues: 391 sheet: 0.64 (0.39), residues: 170 loop : -0.63 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.012 0.001 TYR A 339 ARG 0.004 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.768 Fit side-chains REVERT: B 219 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7576 (mpt90) REVERT: B 314 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.6774 (ttm170) outliers start: 18 outliers final: 12 residues processed: 96 average time/residue: 1.1414 time to fit residues: 116.2881 Evaluate side-chains 93 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 0.0670 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 0.0270 chunk 67 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 357 HIS B 75 GLN R 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6894 Z= 0.131 Angle : 0.450 6.592 9406 Z= 0.241 Chirality : 0.040 0.170 1109 Planarity : 0.003 0.027 1179 Dihedral : 6.222 108.826 985 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.56 % Allowed : 15.23 % Favored : 82.20 % 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: 1.64 (0.29), residues: 878 helix: 2.59 (0.27), residues: 391 sheet: 0.70 (0.39), residues: 170 loop : -0.64 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.010 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.011 0.001 TYR A 339 ARG 0.004 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.783 Fit side-chains REVERT: B 219 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7582 (mtt90) REVERT: R 231 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7411 (tt0) REVERT: R 297 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7941 (p) outliers start: 17 outliers final: 10 residues processed: 94 average time/residue: 1.1606 time to fit residues: 115.5836 Evaluate side-chains 91 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 84 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6894 Z= 0.159 Angle : 0.466 6.569 9406 Z= 0.249 Chirality : 0.040 0.178 1109 Planarity : 0.003 0.026 1179 Dihedral : 6.217 108.035 985 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.96 % Allowed : 16.29 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.29), residues: 878 helix: 2.56 (0.26), residues: 391 sheet: 0.69 (0.39), residues: 170 loop : -0.65 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.011 0.001 TYR A 339 ARG 0.004 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.781 Fit side-chains REVERT: A 34 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8371 (tttt) REVERT: B 219 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7532 (mpt90) REVERT: R 297 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7979 (p) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 1.1361 time to fit residues: 111.0506 Evaluate side-chains 94 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN R 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6894 Z= 0.218 Angle : 0.511 8.037 9406 Z= 0.274 Chirality : 0.042 0.180 1109 Planarity : 0.003 0.026 1179 Dihedral : 6.363 108.618 985 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.11 % Allowed : 16.74 % Favored : 81.15 % 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: 1.49 (0.29), residues: 878 helix: 2.44 (0.26), residues: 390 sheet: 0.57 (0.39), residues: 172 loop : -0.64 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.015 0.001 TYR A 339 ARG 0.004 0.000 ARG R 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.717 Fit side-chains REVERT: A 211 LYS cc_start: 0.8357 (mptp) cc_final: 0.8152 (mmtt) REVERT: B 219 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7442 (mpt90) REVERT: R 231 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7434 (tt0) outliers start: 14 outliers final: 11 residues processed: 89 average time/residue: 1.1028 time to fit residues: 103.9695 Evaluate side-chains 89 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 0.0050 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 overall best weight: 0.3752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.102225 restraints weight = 8361.567| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.83 r_work: 0.3028 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 6894 Z= 0.264 Angle : 0.945 59.175 9406 Z= 0.555 Chirality : 0.041 0.243 1109 Planarity : 0.003 0.027 1179 Dihedral : 6.384 108.651 985 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.81 % Allowed : 16.89 % Favored : 81.30 % Cbeta Deviations : 0.12 % 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: 1.46 (0.29), residues: 878 helix: 2.40 (0.27), residues: 390 sheet: 0.56 (0.39), residues: 172 loop : -0.64 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.006 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR A 339 ARG 0.004 0.000 ARG R 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2709.29 seconds wall clock time: 49 minutes 18.34 seconds (2958.34 seconds total)