Starting phenix.real_space_refine on Sat Apr 6 04:48:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg9_29999/04_2024/8gg9_29999_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg9_29999/04_2024/8gg9_29999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg9_29999/04_2024/8gg9_29999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg9_29999/04_2024/8gg9_29999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg9_29999/04_2024/8gg9_29999_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg9_29999/04_2024/8gg9_29999_updated.pdb" } resolution = 3.4 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= 0.022 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 42 5.16 5 C 4461 2.51 5 N 1226 2.21 5 O 1291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7023 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2173 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 6, 'TRANS': 293} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 316 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 201 Chain: "B" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2467 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 101 Chain: "G" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 355 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 1981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 1981 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 155 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.47, per 1000 atoms: 0.64 Number of scatterers: 7023 At special positions: 0 Unit cell: (83.2992, 136.229, 98.9178, 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 42 16.00 P 3 15.00 O 1291 8.00 N 1226 7.00 C 4461 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.3 seconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1850 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 8 sheets defined 44.3% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 4.051A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.510A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 111 removed outlier: 3.668A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 173 through 179 removed outlier: 4.241A pdb=" N GLN A 176 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR A 177 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE A 178 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 179 " --> pdb=" O GLN A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 179' Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.624A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) 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 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.649A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 392 removed outlier: 3.582A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 383 " --> pdb=" O CYS A 379 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 23 removed outlier: 3.882A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'G' and resid 10 through 23 removed outlier: 3.573A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 44 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 32 through 60 removed outlier: 3.760A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL R 52 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 85 Processing helix chain 'R' and resid 87 through 96 Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.586A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 removed outlier: 3.915A pdb=" N GLN R 142 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 170 removed outlier: 3.670A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.905A 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 207 Processing helix chain 'R' and resid 209 through 237 removed outlier: 3.621A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 298 removed outlier: 3.582A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.780A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 325 removed outlier: 3.958A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix 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: 7.225A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.942A 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: 3.715A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.819A 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 103 removed outlier: 7.024A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.710A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.731A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.751A 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: 7.032A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.775A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.818A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 936 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: 1.92 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1242 1.32 - 1.45: 1903 1.45 - 1.57: 3958 1.57 - 1.69: 4 1.69 - 1.81: 57 Bond restraints: 7164 Sorted by residual: bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.24e-02 6.50e+03 8.67e+00 bond pdb=" N ASP A 223 " pdb=" CA ASP A 223 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.21e-02 6.83e+03 8.37e+00 bond pdb=" N VAL A 202 " pdb=" CA VAL A 202 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.33e+00 bond pdb=" C2 GTP A 401 " pdb=" N3 GTP A 401 " ideal model delta sigma weight residual 1.380 1.324 0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" N LEU A 203 " pdb=" CA LEU A 203 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.34e-02 5.57e+03 6.87e+00 ... (remaining 7159 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.40: 91 105.40 - 112.68: 3870 112.68 - 119.96: 2388 119.96 - 127.24: 3371 127.24 - 134.52: 78 Bond angle restraints: 9798 Sorted by residual: angle pdb=" N GLY B 53 " pdb=" CA GLY B 53 " pdb=" C GLY B 53 " ideal model delta sigma weight residual 115.64 125.19 -9.55 1.46e+00 4.69e-01 4.27e+01 angle pdb=" N GLN A 227 " pdb=" CA GLN A 227 " pdb=" C GLN A 227 " ideal model delta sigma weight residual 111.07 105.47 5.60 1.07e+00 8.73e-01 2.74e+01 angle pdb=" CA GLY A 226 " pdb=" C GLY A 226 " pdb=" O GLY A 226 " ideal model delta sigma weight residual 121.57 117.35 4.22 8.70e-01 1.32e+00 2.35e+01 angle pdb=" N LYS A 233 " pdb=" CA LYS A 233 " pdb=" C LYS A 233 " ideal model delta sigma weight residual 113.17 107.78 5.39 1.26e+00 6.30e-01 1.83e+01 angle pdb=" CA GLY A 226 " pdb=" C GLY A 226 " pdb=" N GLN A 227 " ideal model delta sigma weight residual 114.98 119.67 -4.69 1.14e+00 7.69e-01 1.69e+01 ... (remaining 9793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.97: 4091 33.97 - 67.95: 68 67.95 - 101.92: 5 101.92 - 135.89: 1 135.89 - 169.86: 4 Dihedral angle restraints: 4169 sinusoidal: 1326 harmonic: 2843 Sorted by residual: 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 -65.27 169.86 1 2.00e+01 2.50e-03 4.76e+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 -96.66 165.93 1 2.00e+01 2.50e-03 4.73e+01 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 303.79 157.34 146.45 1 2.00e+01 2.50e-03 4.40e+01 ... (remaining 4166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 869 0.045 - 0.090: 221 0.090 - 0.135: 65 0.135 - 0.180: 7 0.180 - 0.226: 4 Chirality restraints: 1166 Sorted by residual: chirality pdb=" C2' GTP A 401 " pdb=" C1' GTP A 401 " pdb=" C3' GTP A 401 " pdb=" O2' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA GLN A 227 " pdb=" N GLN A 227 " pdb=" C GLN A 227 " pdb=" CB GLN A 227 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ARG A 231 " pdb=" N ARG A 231 " pdb=" C ARG A 231 " pdb=" CB ARG A 231 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 ... (remaining 1163 not shown) Planarity restraints: 1248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 201 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.89e+00 pdb=" C ARG A 201 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG A 201 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 202 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 222 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C PHE A 222 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE A 222 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 223 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 52 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C ARG B 52 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG B 52 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY B 53 " 0.010 2.00e-02 2.50e+03 ... (remaining 1245 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 563 2.74 - 3.28: 6777 3.28 - 3.82: 10915 3.82 - 4.36: 11944 4.36 - 4.90: 22158 Nonbonded interactions: 52357 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.198 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.262 2.440 nonbonded pdb=" NE2 HIS B 142 " pdb=" OG SER B 161 " model vdw 2.280 2.520 nonbonded pdb=" NE2 GLN A 213 " pdb=" OD1 ASN A 218 " model vdw 2.315 2.520 nonbonded pdb=" O LYS B 57 " pdb=" OG SER B 74 " model vdw 2.320 2.440 ... (remaining 52352 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: 1.820 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: 7.620 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.050 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 : 0.004 0.056 7164 Z= 0.304 Angle : 0.681 11.867 9798 Z= 0.377 Chirality : 0.045 0.226 1166 Planarity : 0.003 0.034 1248 Dihedral : 14.830 169.863 2319 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.44 (0.27), residues: 955 helix: 1.59 (0.26), residues: 411 sheet: -0.33 (0.44), residues: 150 loop : -0.83 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 234 HIS 0.007 0.001 HIS B 54 PHE 0.013 0.001 PHE B 235 TYR 0.011 0.001 TYR R 308 ARG 0.003 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.8861 (tptt) cc_final: 0.8657 (tttp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1693 time to fit residues: 20.7798 Evaluate side-chains 72 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN R 229 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7164 Z= 0.189 Angle : 0.479 6.798 9798 Z= 0.259 Chirality : 0.041 0.139 1166 Planarity : 0.003 0.035 1248 Dihedral : 10.777 169.413 1061 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.79 % Allowed : 8.11 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.28), residues: 955 helix: 1.89 (0.26), residues: 432 sheet: -0.41 (0.42), residues: 166 loop : -0.82 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.003 0.001 HIS B 54 PHE 0.010 0.001 PHE B 235 TYR 0.009 0.001 TYR R 308 ARG 0.003 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.897 Fit side-chains REVERT: A 50 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8160 (mm-30) REVERT: B 188 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8262 (mtp) outliers start: 5 outliers final: 3 residues processed: 78 average time/residue: 0.1538 time to fit residues: 17.8415 Evaluate side-chains 74 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 223 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 0.0980 chunk 77 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7164 Z= 0.138 Angle : 0.431 6.514 9798 Z= 0.231 Chirality : 0.040 0.126 1166 Planarity : 0.002 0.033 1248 Dihedral : 10.278 165.751 1061 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.11 % Allowed : 12.24 % Favored : 86.65 % 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: 0.93 (0.28), residues: 955 helix: 2.12 (0.26), residues: 432 sheet: -0.32 (0.42), residues: 165 loop : -0.78 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.002 0.001 HIS R 296 PHE 0.010 0.001 PHE B 241 TYR 0.009 0.001 TYR B 59 ARG 0.003 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.827 Fit side-chains REVERT: A 50 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8229 (mm-30) REVERT: A 255 MET cc_start: 0.8741 (mpp) cc_final: 0.8280 (mtt) REVERT: B 188 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8169 (mtp) outliers start: 7 outliers final: 5 residues processed: 82 average time/residue: 0.1595 time to fit residues: 19.1261 Evaluate side-chains 83 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 232 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7164 Z= 0.228 Angle : 0.474 6.684 9798 Z= 0.253 Chirality : 0.041 0.131 1166 Planarity : 0.003 0.035 1248 Dihedral : 10.088 163.677 1061 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.07 % Allowed : 14.94 % Favored : 82.99 % 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: 0.81 (0.28), residues: 955 helix: 2.10 (0.26), residues: 433 sheet: -0.45 (0.42), residues: 166 loop : -0.92 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 277 HIS 0.004 0.001 HIS B 183 PHE 0.015 0.001 PHE B 241 TYR 0.012 0.001 TYR R 308 ARG 0.002 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.792 Fit side-chains REVERT: B 188 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8150 (mtp) outliers start: 13 outliers final: 9 residues processed: 81 average time/residue: 0.1511 time to fit residues: 17.8593 Evaluate side-chains 82 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 232 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 0.1980 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 229 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7164 Z= 0.158 Angle : 0.434 6.415 9798 Z= 0.232 Chirality : 0.040 0.124 1166 Planarity : 0.002 0.034 1248 Dihedral : 9.816 161.586 1061 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.07 % Allowed : 15.58 % Favored : 82.35 % 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: 0.89 (0.28), residues: 955 helix: 2.17 (0.26), residues: 433 sheet: -0.54 (0.41), residues: 169 loop : -0.82 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 277 HIS 0.002 0.001 HIS R 296 PHE 0.012 0.001 PHE B 241 TYR 0.009 0.001 TYR R 308 ARG 0.003 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.831 Fit side-chains REVERT: A 233 LYS cc_start: 0.8953 (tptt) cc_final: 0.8704 (tttp) REVERT: A 255 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.7903 (mtp) REVERT: B 188 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8024 (mtp) outliers start: 13 outliers final: 9 residues processed: 82 average time/residue: 0.1577 time to fit residues: 18.7698 Evaluate side-chains 84 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 232 LYS Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 48 optimal weight: 0.0040 chunk 89 optimal weight: 10.0000 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 229 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7164 Z= 0.141 Angle : 0.423 6.182 9798 Z= 0.226 Chirality : 0.040 0.125 1166 Planarity : 0.002 0.033 1248 Dihedral : 9.564 159.879 1061 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.54 % Allowed : 15.90 % Favored : 81.56 % 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: 1.02 (0.28), residues: 955 helix: 2.26 (0.26), residues: 433 sheet: -0.36 (0.42), residues: 166 loop : -0.79 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 277 HIS 0.004 0.001 HIS B 142 PHE 0.011 0.001 PHE B 241 TYR 0.008 0.001 TYR R 308 ARG 0.003 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.794 Fit side-chains REVERT: A 233 LYS cc_start: 0.8949 (tptt) cc_final: 0.8667 (tttp) REVERT: A 255 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.7953 (mtp) REVERT: B 188 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8040 (mtp) outliers start: 16 outliers final: 10 residues processed: 85 average time/residue: 0.1491 time to fit residues: 18.3502 Evaluate side-chains 88 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 232 LYS Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7164 Z= 0.186 Angle : 0.447 6.239 9798 Z= 0.238 Chirality : 0.041 0.127 1166 Planarity : 0.003 0.033 1248 Dihedral : 9.497 158.987 1061 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.07 % Allowed : 16.38 % Favored : 81.56 % 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: 0.97 (0.28), residues: 955 helix: 2.26 (0.26), residues: 432 sheet: -0.44 (0.41), residues: 166 loop : -0.82 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 277 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.001 PHE B 241 TYR 0.010 0.001 TYR R 308 ARG 0.003 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.817 Fit side-chains REVERT: A 233 LYS cc_start: 0.8969 (tptt) cc_final: 0.8645 (tttp) REVERT: A 255 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.7922 (mtp) REVERT: B 59 TYR cc_start: 0.8520 (m-80) cc_final: 0.8239 (m-80) REVERT: B 188 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8071 (mtp) outliers start: 13 outliers final: 10 residues processed: 83 average time/residue: 0.1614 time to fit residues: 19.2943 Evaluate side-chains 91 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 232 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.0670 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 229 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7164 Z= 0.130 Angle : 0.419 6.038 9798 Z= 0.223 Chirality : 0.040 0.128 1166 Planarity : 0.002 0.033 1248 Dihedral : 9.336 157.721 1061 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.91 % Allowed : 16.53 % Favored : 81.56 % 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: 1.09 (0.28), residues: 955 helix: 2.32 (0.26), residues: 433 sheet: -0.34 (0.42), residues: 166 loop : -0.76 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 277 HIS 0.003 0.001 HIS B 142 PHE 0.011 0.001 PHE B 241 TYR 0.008 0.001 TYR R 308 ARG 0.003 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.842 Fit side-chains REVERT: A 233 LYS cc_start: 0.8981 (tptt) cc_final: 0.8575 (tttp) REVERT: A 255 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7920 (mtp) REVERT: A 284 THR cc_start: 0.8763 (p) cc_final: 0.8553 (p) REVERT: B 188 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8038 (mtp) outliers start: 12 outliers final: 10 residues processed: 85 average time/residue: 0.1486 time to fit residues: 18.4767 Evaluate side-chains 87 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 229 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7164 Z= 0.140 Angle : 0.421 6.006 9798 Z= 0.224 Chirality : 0.040 0.143 1166 Planarity : 0.002 0.033 1248 Dihedral : 9.226 156.352 1061 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.54 % Allowed : 16.22 % Favored : 81.24 % 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: 1.09 (0.28), residues: 955 helix: 2.35 (0.26), residues: 433 sheet: -0.36 (0.42), residues: 166 loop : -0.77 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 277 HIS 0.003 0.001 HIS B 142 PHE 0.011 0.001 PHE B 241 TYR 0.009 0.001 TYR B 59 ARG 0.002 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.799 Fit side-chains REVERT: A 233 LYS cc_start: 0.8962 (tptt) cc_final: 0.8604 (tttp) REVERT: A 255 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7935 (mtp) REVERT: A 284 THR cc_start: 0.8761 (p) cc_final: 0.8539 (p) REVERT: B 188 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8059 (mtp) outliers start: 16 outliers final: 10 residues processed: 84 average time/residue: 0.1553 time to fit residues: 18.7522 Evaluate side-chains 87 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7164 Z= 0.382 Angle : 0.558 7.237 9798 Z= 0.297 Chirality : 0.044 0.139 1166 Planarity : 0.003 0.034 1248 Dihedral : 9.557 157.469 1061 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.75 % Allowed : 17.49 % Favored : 80.76 % 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: 0.61 (0.28), residues: 955 helix: 2.02 (0.26), residues: 430 sheet: -0.82 (0.40), residues: 169 loop : -0.95 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 277 HIS 0.005 0.001 HIS B 91 PHE 0.017 0.002 PHE B 235 TYR 0.016 0.002 TYR R 308 ARG 0.002 0.000 ARG A 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.738 Fit side-chains REVERT: A 233 LYS cc_start: 0.8988 (tptt) cc_final: 0.8732 (tttp) REVERT: A 255 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8236 (mtt) REVERT: A 380 ARG cc_start: 0.7345 (ptt90) cc_final: 0.6925 (ttm-80) REVERT: B 188 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8182 (mtp) outliers start: 11 outliers final: 6 residues processed: 74 average time/residue: 0.1688 time to fit residues: 17.5616 Evaluate side-chains 78 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 223 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 9 optimal weight: 0.0020 chunk 14 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.152518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123244 restraints weight = 9925.258| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.04 r_work: 0.3302 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7164 Z= 0.173 Angle : 0.456 6.843 9798 Z= 0.242 Chirality : 0.041 0.137 1166 Planarity : 0.003 0.033 1248 Dihedral : 9.338 157.043 1061 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.59 % Allowed : 17.33 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.28), residues: 955 helix: 2.21 (0.26), residues: 433 sheet: -0.73 (0.41), residues: 169 loop : -0.86 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 277 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE B 241 TYR 0.012 0.001 TYR B 59 ARG 0.004 0.000 ARG R 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1742.67 seconds wall clock time: 32 minutes 18.15 seconds (1938.15 seconds total)