Starting phenix.real_space_refine on Sat Apr 6 02:23:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gge_40004/04_2024/8gge_40004_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gge_40004/04_2024/8gge_40004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gge_40004/04_2024/8gge_40004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gge_40004/04_2024/8gge_40004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gge_40004/04_2024/8gge_40004_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gge_40004/04_2024/8gge_40004_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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 32 5.16 5 C 4236 2.51 5 N 1204 2.21 5 O 1233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" 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: 6708 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2526 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 13, 'TRANS': 347} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 476 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 378 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 19, 'PHE:plan': 5, 'GLU:plan': 23, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 304 Chain: "B" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2408 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 8, 'ARG:plan': 9, 'ASN:plan1': 4, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 143 Chain: "G" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 340 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 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: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1387 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 505 Unresolved non-hydrogen angles: 664 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 9, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 252 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: 3.89, per 1000 atoms: 0.58 Number of scatterers: 6708 At special positions: 0 Unit cell: (84.1669, 136.229, 103.256, 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 32 16.00 P 3 15.00 O 1233 8.00 N 1204 7.00 C 4236 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: 2.21 Conformation dependent library (CDL) restraints added in 1.4 seconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1870 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 8 sheets defined 41.4% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 removed outlier: 4.148A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.679A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.600A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.519A pdb=" N TYR A 130 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 132 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 removed outlier: 3.803A pdb=" N GLU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 165 removed outlier: 3.959A pdb=" N ARG A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 183 through 186 No H-bonds generated for 'chain 'A' and resid 183 through 186' Processing helix chain 'A' and resid 233 through 236 removed outlier: 3.995A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 236' 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 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.610A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 388 removed outlier: 5.293A pdb=" N ASN A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE A 383 " --> pdb=" O CYS A 379 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLN A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.906A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) 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 11 through 23 removed outlier: 3.652A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 34 through 53 removed outlier: 4.317A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 77 removed outlier: 3.657A pdb=" N LEU R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 93 Processing helix chain 'R' and resid 103 through 136 removed outlier: 4.384A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP R 113 " --> pdb=" O TRP R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 170 removed outlier: 3.633A pdb=" N MET R 156 " --> pdb=" O VAL R 152 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.870A 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 199 through 207 Processing helix chain 'R' and resid 209 through 229 removed outlier: 3.979A pdb=" N VAL R 216 " --> pdb=" O LEU R 212 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE R 217 " --> pdb=" O VAL R 213 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR R 219 " --> pdb=" O MET R 215 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER R 220 " --> pdb=" O VAL R 216 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL R 222 " --> pdb=" O VAL R 218 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS R 227 " --> pdb=" O PHE R 223 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG R 228 " --> pdb=" O GLN R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 298 removed outlier: 3.641A pdb=" N GLY R 276 " --> pdb=" O LEU R 272 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE R 277 " --> pdb=" O LYS R 273 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.733A pdb=" N ILE R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 313 Processing helix chain 'R' and resid 316 through 325 removed outlier: 3.643A pdb=" N SER R 319 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN R 322 " --> pdb=" O SER R 319 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 4.029A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.033A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.541A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.830A 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: 3.820A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 3.902A 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: 3.934A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 264 removed outlier: 4.030A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.756A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.776A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 741 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: 1.62 Time building geometry restraints manager: 2.46 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: 1797 1.33 - 1.45: 1256 1.45 - 1.57: 3726 1.57 - 1.69: 6 1.69 - 1.81: 44 Bond restraints: 6829 Sorted by residual: bond pdb=" CA GLN A 384 " pdb=" C GLN A 384 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.32e-02 5.74e+03 3.86e+01 bond pdb=" N ARG A 385 " pdb=" CA ARG A 385 " ideal model delta sigma weight residual 1.459 1.408 0.051 1.19e-02 7.06e+03 1.85e+01 bond pdb=" CA PHE A 376 " pdb=" C PHE A 376 " ideal model delta sigma weight residual 1.526 1.474 0.052 1.39e-02 5.18e+03 1.40e+01 bond pdb=" CA LEU A 388 " pdb=" C LEU A 388 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" CA ASP A 381 " pdb=" C ASP A 381 " ideal model delta sigma weight residual 1.527 1.481 0.046 1.30e-02 5.92e+03 1.26e+01 ... (remaining 6824 not shown) Histogram of bond angle deviations from ideal: 98.94 - 105.95: 103 105.95 - 112.96: 3732 112.96 - 119.98: 2157 119.98 - 126.99: 3287 126.99 - 134.00: 78 Bond angle restraints: 9357 Sorted by residual: angle pdb=" N HIS A 387 " pdb=" CA HIS A 387 " pdb=" C HIS A 387 " ideal model delta sigma weight residual 111.14 121.58 -10.44 1.08e+00 8.57e-01 9.34e+01 angle pdb=" N TYR A 391 " pdb=" CA TYR A 391 " pdb=" C TYR A 391 " ideal model delta sigma weight residual 113.43 102.56 10.87 1.26e+00 6.30e-01 7.44e+01 angle pdb=" N ASP A 381 " pdb=" CA ASP A 381 " pdb=" C ASP A 381 " ideal model delta sigma weight residual 111.39 102.62 8.77 1.38e+00 5.25e-01 4.04e+01 angle pdb=" N PHE A 376 " pdb=" CA PHE A 376 " pdb=" C PHE A 376 " ideal model delta sigma weight residual 111.90 103.54 8.36 1.32e+00 5.74e-01 4.01e+01 angle pdb=" N CYS A 379 " pdb=" CA CYS A 379 " pdb=" C CYS A 379 " ideal model delta sigma weight residual 111.52 102.69 8.83 1.40e+00 5.10e-01 3.98e+01 ... (remaining 9352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 3667 17.57 - 35.15: 239 35.15 - 52.72: 41 52.72 - 70.29: 4 70.29 - 87.86: 3 Dihedral angle restraints: 3954 sinusoidal: 1088 harmonic: 2866 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 18.88 85.71 1 2.00e+01 2.50e-03 2.22e+01 dihedral pdb=" CA GLU A 259 " pdb=" C GLU A 259 " pdb=" N ASP A 260 " pdb=" CA ASP A 260 " ideal model delta harmonic sigma weight residual 180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CB LYS B 89 " pdb=" CG LYS B 89 " pdb=" CD LYS B 89 " pdb=" CE LYS B 89 " ideal model delta sinusoidal sigma weight residual -60.00 -109.82 49.82 3 1.50e+01 4.44e-03 8.82e+00 ... (remaining 3951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 916 0.051 - 0.103: 176 0.103 - 0.154: 34 0.154 - 0.205: 2 0.205 - 0.257: 1 Chirality restraints: 1129 Sorted by residual: chirality pdb=" CA HIS A 387 " pdb=" N HIS A 387 " pdb=" C HIS A 387 " pdb=" CB HIS A 387 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA GLU A 392 " pdb=" N GLU A 392 " pdb=" C GLU A 392 " pdb=" CB GLU A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.20e-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 2.56 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 1126 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 375 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C VAL A 375 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 375 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 376 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 393 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C LEU A 393 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A 393 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 394 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO G 49 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.023 5.00e-02 4.00e+02 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1254 2.77 - 3.30: 6289 3.30 - 3.83: 10180 3.83 - 4.37: 10588 4.37 - 4.90: 19592 Nonbonded interactions: 47903 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.232 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.259 2.440 nonbonded pdb=" NZ LYS A 53 " pdb=" O1G GTP A 401 " model vdw 2.265 2.520 nonbonded pdb=" O VAL A 375 " pdb=" N ASP A 378 " model vdw 2.286 2.520 nonbonded pdb=" O MET R 171 " pdb=" ND1 HIS R 172 " model vdw 2.287 2.520 ... (remaining 47898 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 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: 7.690 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 20.480 Find NCS groups from input model: 0.210 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 0.082 6829 Z= 0.234 Angle : 0.593 10.867 9357 Z= 0.358 Chirality : 0.042 0.257 1129 Planarity : 0.003 0.041 1203 Dihedral : 12.439 87.864 2084 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.02 (0.28), residues: 954 helix: 1.70 (0.28), residues: 377 sheet: -1.02 (0.40), residues: 184 loop : -1.17 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 286 HIS 0.006 0.001 HIS A 387 PHE 0.021 0.001 PHE R 289 TYR 0.009 0.001 TYR R 174 ARG 0.007 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.782 Fit side-chains REVERT: A 331 ASP cc_start: 0.8236 (t0) cc_final: 0.7971 (t70) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1480 time to fit residues: 19.5404 Evaluate side-chains 73 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 3.9990 chunk 73 optimal weight: 0.0020 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 0.0040 chunk 29 optimal weight: 0.0270 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6829 Z= 0.217 Angle : 0.491 6.221 9357 Z= 0.269 Chirality : 0.042 0.146 1129 Planarity : 0.004 0.045 1203 Dihedral : 5.093 85.957 1059 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.18 % Allowed : 11.00 % Favored : 87.82 % 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: -0.30 (0.27), residues: 954 helix: 1.26 (0.26), residues: 399 sheet: -0.93 (0.40), residues: 184 loop : -1.40 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 99 HIS 0.006 0.001 HIS A 387 PHE 0.021 0.002 PHE R 282 TYR 0.018 0.001 TYR R 174 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.756 Fit side-chains REVERT: A 154 TRP cc_start: 0.7962 (t-100) cc_final: 0.7232 (t-100) outliers start: 6 outliers final: 4 residues processed: 85 average time/residue: 0.1300 time to fit residues: 16.5351 Evaluate side-chains 78 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6829 Z= 0.161 Angle : 0.444 6.218 9357 Z= 0.242 Chirality : 0.041 0.155 1129 Planarity : 0.003 0.042 1203 Dihedral : 4.875 84.451 1059 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.36 % Allowed : 15.72 % Favored : 81.93 % 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: -0.07 (0.28), residues: 954 helix: 1.45 (0.27), residues: 403 sheet: -0.65 (0.41), residues: 179 loop : -1.40 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 99 HIS 0.005 0.001 HIS A 387 PHE 0.023 0.001 PHE R 282 TYR 0.010 0.001 TYR R 174 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.749 Fit side-chains REVERT: A 154 TRP cc_start: 0.7963 (t-100) cc_final: 0.7361 (t-100) REVERT: A 211 LYS cc_start: 0.8810 (mmtm) cc_final: 0.8587 (mmtm) REVERT: A 368 ASP cc_start: 0.7826 (t0) cc_final: 0.7626 (t0) outliers start: 12 outliers final: 6 residues processed: 94 average time/residue: 0.1419 time to fit residues: 19.9310 Evaluate side-chains 84 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 45 optimal weight: 0.0060 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6829 Z= 0.135 Angle : 0.434 6.305 9357 Z= 0.234 Chirality : 0.040 0.149 1129 Planarity : 0.003 0.040 1203 Dihedral : 4.729 83.145 1059 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.57 % Allowed : 19.06 % Favored : 79.37 % 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: -0.01 (0.28), residues: 954 helix: 1.50 (0.27), residues: 407 sheet: -0.48 (0.41), residues: 173 loop : -1.47 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 99 HIS 0.003 0.001 HIS A 387 PHE 0.024 0.001 PHE R 282 TYR 0.012 0.001 TYR R 308 ARG 0.006 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.803 Fit side-chains REVERT: A 154 TRP cc_start: 0.7937 (t-100) cc_final: 0.7399 (t-100) REVERT: A 211 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8634 (mmtm) REVERT: A 368 ASP cc_start: 0.7809 (t0) cc_final: 0.7486 (t0) REVERT: R 215 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6376 (mmm) outliers start: 8 outliers final: 4 residues processed: 86 average time/residue: 0.1482 time to fit residues: 18.3864 Evaluate side-chains 82 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 23 optimal weight: 0.0770 overall best weight: 1.3740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6829 Z= 0.229 Angle : 0.475 6.247 9357 Z= 0.258 Chirality : 0.042 0.145 1129 Planarity : 0.003 0.043 1203 Dihedral : 4.948 84.181 1059 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.55 % Allowed : 20.24 % Favored : 77.21 % 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: -0.02 (0.28), residues: 954 helix: 1.52 (0.27), residues: 408 sheet: -0.50 (0.42), residues: 173 loop : -1.51 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 99 HIS 0.005 0.001 HIS B 142 PHE 0.025 0.002 PHE R 282 TYR 0.008 0.001 TYR A 360 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.668 Fit side-chains REVERT: A 154 TRP cc_start: 0.7980 (t-100) cc_final: 0.7423 (t-100) REVERT: A 211 LYS cc_start: 0.8843 (mmtm) cc_final: 0.8631 (mmtm) REVERT: A 368 ASP cc_start: 0.8014 (t0) cc_final: 0.7664 (t0) REVERT: R 215 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6341 (mmm) outliers start: 13 outliers final: 12 residues processed: 84 average time/residue: 0.1302 time to fit residues: 16.3212 Evaluate side-chains 87 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 283 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6829 Z= 0.309 Angle : 0.519 6.136 9357 Z= 0.284 Chirality : 0.043 0.154 1129 Planarity : 0.004 0.046 1203 Dihedral : 5.257 85.222 1059 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.95 % Allowed : 20.04 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.28), residues: 954 helix: 1.39 (0.27), residues: 409 sheet: -0.74 (0.42), residues: 174 loop : -1.57 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.005 0.001 HIS B 142 PHE 0.023 0.002 PHE R 282 TYR 0.011 0.001 TYR A 360 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.770 Fit side-chains REVERT: A 154 TRP cc_start: 0.8001 (t-100) cc_final: 0.7555 (t-100) REVERT: A 368 ASP cc_start: 0.8224 (t0) cc_final: 0.7910 (t0) REVERT: R 215 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6267 (mmm) outliers start: 15 outliers final: 13 residues processed: 81 average time/residue: 0.1326 time to fit residues: 16.0822 Evaluate side-chains 84 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 283 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 7.9990 chunk 53 optimal weight: 0.0970 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 52 optimal weight: 0.3980 chunk 93 optimal weight: 0.0870 chunk 58 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 6829 Z= 0.119 Angle : 0.434 6.251 9357 Z= 0.236 Chirality : 0.040 0.145 1129 Planarity : 0.003 0.040 1203 Dihedral : 4.801 82.865 1059 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.96 % Allowed : 21.02 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.28), residues: 954 helix: 1.53 (0.27), residues: 410 sheet: -0.52 (0.41), residues: 173 loop : -1.53 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.004 0.001 HIS A 387 PHE 0.022 0.001 PHE R 282 TYR 0.013 0.001 TYR A 391 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.828 Fit side-chains REVERT: A 154 TRP cc_start: 0.7962 (t-100) cc_final: 0.7591 (t-100) REVERT: A 368 ASP cc_start: 0.8043 (t0) cc_final: 0.7657 (t0) REVERT: B 262 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7831 (mpp) REVERT: B 292 PHE cc_start: 0.8854 (m-80) cc_final: 0.8369 (m-80) REVERT: R 215 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6168 (mmm) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 0.1377 time to fit residues: 16.3611 Evaluate side-chains 80 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 283 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.7980 chunk 28 optimal weight: 0.0170 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 0.0270 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 73 optimal weight: 0.0010 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.3082 ------------------------------------------------------------------------------- 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** ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 6829 Z= 0.104 Angle : 0.418 6.395 9357 Z= 0.225 Chirality : 0.040 0.145 1129 Planarity : 0.003 0.041 1203 Dihedral : 4.505 80.564 1059 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.77 % Allowed : 21.41 % Favored : 76.82 % 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: 0.18 (0.28), residues: 954 helix: 1.69 (0.27), residues: 410 sheet: -0.55 (0.42), residues: 175 loop : -1.35 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.008 0.001 HIS A 220 PHE 0.020 0.001 PHE R 282 TYR 0.013 0.001 TYR A 391 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.754 Fit side-chains REVERT: A 154 TRP cc_start: 0.7968 (t-100) cc_final: 0.7677 (t-100) REVERT: A 368 ASP cc_start: 0.7961 (t0) cc_final: 0.7517 (t0) REVERT: B 292 PHE cc_start: 0.8797 (m-80) cc_final: 0.8297 (m-80) REVERT: R 215 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6296 (mmm) outliers start: 9 outliers final: 7 residues processed: 80 average time/residue: 0.1276 time to fit residues: 15.5317 Evaluate side-chains 79 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 274 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN ** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6829 Z= 0.205 Angle : 0.478 7.203 9357 Z= 0.257 Chirality : 0.042 0.170 1129 Planarity : 0.003 0.042 1203 Dihedral : 4.793 81.895 1059 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.36 % Allowed : 22.20 % Favored : 75.44 % 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: 0.16 (0.28), residues: 954 helix: 1.69 (0.27), residues: 409 sheet: -0.42 (0.43), residues: 168 loop : -1.44 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 63 HIS 0.007 0.001 HIS A 220 PHE 0.023 0.001 PHE R 282 TYR 0.017 0.001 TYR A 391 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.694 Fit side-chains REVERT: A 154 TRP cc_start: 0.7997 (t-100) cc_final: 0.7713 (t-100) REVERT: A 368 ASP cc_start: 0.8145 (t0) cc_final: 0.7774 (t0) REVERT: B 262 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.6944 (mpp) REVERT: B 292 PHE cc_start: 0.8942 (m-80) cc_final: 0.8470 (m-80) REVERT: R 215 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6101 (mmm) outliers start: 12 outliers final: 7 residues processed: 79 average time/residue: 0.1294 time to fit residues: 15.6126 Evaluate side-chains 80 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 283 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 96 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 76 optimal weight: 0.0050 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6829 Z= 0.123 Angle : 0.446 8.711 9357 Z= 0.237 Chirality : 0.040 0.160 1129 Planarity : 0.003 0.040 1203 Dihedral : 4.625 80.913 1059 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.77 % Allowed : 22.59 % Favored : 75.64 % 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: 0.21 (0.28), residues: 954 helix: 1.70 (0.27), residues: 409 sheet: -0.32 (0.43), residues: 168 loop : -1.42 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.004 0.001 HIS A 220 PHE 0.023 0.001 PHE R 282 TYR 0.014 0.001 TYR A 391 ARG 0.005 0.000 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.618 Fit side-chains REVERT: A 154 TRP cc_start: 0.7973 (t-100) cc_final: 0.7706 (t-100) REVERT: A 368 ASP cc_start: 0.8099 (t0) cc_final: 0.7714 (t0) REVERT: B 262 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.6930 (mpp) REVERT: B 292 PHE cc_start: 0.8905 (m-80) cc_final: 0.8408 (m-80) REVERT: R 215 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6051 (mmm) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.1321 time to fit residues: 15.0002 Evaluate side-chains 79 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 274 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 11 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 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 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.140092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103946 restraints weight = 11928.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106740 restraints weight = 6695.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.108650 restraints weight = 4760.966| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6829 Z= 0.146 Angle : 0.448 8.420 9357 Z= 0.238 Chirality : 0.041 0.153 1129 Planarity : 0.003 0.040 1203 Dihedral : 4.636 80.966 1059 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.77 % Allowed : 22.99 % Favored : 75.25 % 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: 0.20 (0.28), residues: 954 helix: 1.72 (0.27), residues: 409 sheet: -0.51 (0.42), residues: 175 loop : -1.37 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.004 0.001 HIS A 220 PHE 0.022 0.001 PHE R 282 TYR 0.015 0.001 TYR R 308 ARG 0.005 0.000 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1597.76 seconds wall clock time: 29 minutes 58.69 seconds (1798.69 seconds total)